#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
KLHL17	339451	hgsc.bcm.edu	37	1	899359	899359	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:899359G>T	ENST00000338591.3	+	9	1522	c.1415G>T	c.(1414-1416)cGg>cTg	p.R472L	PLEKHN1_ENST00000379410.3_5'Flank|PLEKHN1_ENST00000379407.3_5'Flank|PLEKHN1_ENST00000379409.2_5'Flank	NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	472	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	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;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		ATGAGCACCCGGAGGCGCTAT	0.682																																					p.R472L		Atlas-SNP	.											.	KLHL17	31	.	0			c.G1415T						.						83.0	89.0	87.0					1																	899359		2203	4298	6501	SO:0001583	missense	339451	exon9			GCACCCGGAGGCG	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"""Kelch-like"", ""BTB/POZ domain containing"""	24023	protein-coding gene	gene with protein product	"""actinfilin"""		"""kelch-like 17 (Drosophila)"""			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	ENST00000338591.3:c.1415G>T	chr1.hg19:g.899359G>T	ENSP00000343930:p.Arg472Leu	109.0	0.0		36.0	4.0	NM_198317	Q5SV94	Missense_Mutation	SNP	ENST00000338591.3	hg19	CCDS30550.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.140149	0.77775	.	.	ENSG00000187961	ENST00000338591;ENST00000455747;ENST00000540863	T	0.78816	-1.21	5.5	4.6	0.57074	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	T	0.79986	0.4541	M	0.78801	2.425	0.80722	D	1	P	0.43169	0.8	B	0.42593	0.392	T	0.82633	-0.0361	10	0.66056	D	0.02	.	14.59	0.68356	0.0705:0.0:0.9295:0.0	.	472	Q6TDP4	KLH17_HUMAN	L	472;348;195	ENSP00000343930:R472L	ENSP00000343930:R472L	R	+	2	0	KLHL17	889222	1.000000	0.71417	1.000000	0.80357	0.484000	0.33280	3.778000	0.55371	1.338000	0.45544	-0.369000	0.07265	CGG	.	.		0.682	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317	
TAS1R1	80835	hgsc.bcm.edu	37	1	6630972	6630972	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:6630972T>C	ENST00000333172.6	+	2	388	c.195T>C	c.(193-195)tcT>tcC	p.S65S	TAS1R1_ENST00000351136.3_Silent_p.S65S|TAS1R1_ENST00000328191.4_Silent_p.S65S	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	65					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		TCCACAGGTCTTGTAGCTTCA	0.557																																					p.S65S		Atlas-SNP	.											.	TAS1R1	76	.	0			c.T195C						.						106.0	96.0	99.0					1																	6630972		2203	4300	6503	SO:0001819	synonymous_variant	80835	exon2			CAGGTCTTGTAGC		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14448	protein-coding gene	gene with protein product		606225	"""G protein-coupled receptor 70"""	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.195T>C	chr1.hg19:g.6630972T>C		85.0	0.0		66.0	4.0	NM_177540	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Silent	SNP	ENST00000333172.6	hg19	CCDS81.1																																																																																			.	.		0.557	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1		
THAP3	90326	hgsc.bcm.edu	37	1	6692465	6692465	+	Silent	SNP	G	G	T	rs146637042	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:6692465G>T	ENST00000054650.4	+	5	506	c.348G>T	c.(346-348)gcG>gcT	p.A116A	THAP3_ENST00000377627.3_Silent_p.A123A|THAP3_ENST00000307896.6_Silent_p.A115A|DNAJC11_ENST00000465508.1_5'Flank	NM_001195753.1	NP_001182682.1	Q8WTV1	THAP3_HUMAN	THAP domain containing, apoptosis associated protein 3	116							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|large_intestine(1)|prostate(1)	4	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;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		TCCCTGAGGCGGGGGCCGGAG	0.597																																					p.A123A		Atlas-SNP	.											.	THAP3	43	.	0			c.G369T						.						45.0	44.0	44.0					1																	6692465		2203	4300	6503	SO:0001819	synonymous_variant	90326	exon4			TGAGGCGGGGGCC	BC022081	CCDS86.1, CCDS55572.1, CCDS55573.1	1p36.1	2013-01-25			ENSG00000041988	ENSG00000041988		"""THAP (C2CH-type zinc finger) domain containing"""	20855	protein-coding gene	gene with protein product		612532				12575992	Standard	NM_138350		Approved		uc001aod.3	Q8WTV1	OTTHUMG00000001440	ENST00000054650.4:c.348G>T	chr1.hg19:g.6692465G>T		122.0	0.0		95.0	4.0	NM_138350	Q569K1|Q5TH66|Q5TH67|Q8N8T6|Q9BSC7|Q9Y3H2|Q9Y3H3	Silent	SNP	ENST00000054650.4	hg19	CCDS55572.1																																																																																			.	G|1.000;A|0.000		0.597	THAP3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004203.1	NM_138350	
NMNAT1	64802	hgsc.bcm.edu	37	1	10042608	10042608	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:10042608T>C	ENST00000377205.1	+	5	833	c.689T>C	c.(688-690)cTc>cCc	p.L230P	RP11-807G9.2_ENST00000413148.1_RNA	NM_022787.3	NP_073624.2	Q9HAN9	NMNA1_HUMAN	nicotinamide nucleotide adenylyltransferase 1	230					NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nicotinamide-nucleotide adenylyltransferase activity (GO:0000309)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)			large_intestine(2)|lung(2)|stomach(1)	5		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.31e-08)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(185;0.00028)|BRCA - Breast invasive adenocarcinoma(304;0.00032)|KIRC - Kidney renal clear cell carcinoma(229;0.00101)|STAD - Stomach adenocarcinoma(132;0.00908)|READ - Rectum adenocarcinoma(331;0.0419)		CGGAGAGCCCTCAGAAGGGGC	0.453																																					p.L230P		Atlas-SNP	.											.	NMNAT1	18	.	0			c.T689C						.						73.0	72.0	72.0					1																	10042608		2203	4300	6503	SO:0001583	missense	64802	exon5			GAGCCCTCAGAAG	AF312734	CCDS108.1, CCDS72698.1	1p36.22	2014-01-28	2003-04-30	2003-05-02	ENSG00000173614	ENSG00000173614	2.7.7.1		17877	protein-coding gene	gene with protein product		608700	"""nicotinamide nucleotide adenylyltransferase"", ""Leber congenital amaurosis 9"", ""Leber's congenital amaurosis 9"""	LCA9		11248244, 11027696, 22842227	Standard	XR_244792		Approved	NMNAT, PNAT1	uc001aqp.3	Q9HAN9	OTTHUMG00000001799	ENST00000377205.1:c.689T>C	chr1.hg19:g.10042608T>C	ENSP00000366410:p.Leu230Pro	159.0	0.0		97.0	4.0	NM_022787	B1AN63|Q8TAE9|Q9H247|Q9H6B6	Missense_Mutation	SNP	ENST00000377205.1	hg19	CCDS108.1	.	.	.	.	.	.	.	.	.	.	T	19.66	3.869628	0.72065	.	.	ENSG00000173614	ENST00000377205	D	0.98455	-4.94	5.01	5.01	0.66863	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.64402	D	0.000001	D	0.99239	0.9735	H	0.95504	3.68	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.98968	1.0800	10	0.87932	D	0	1.1088	15.0172	0.71594	0.0:0.0:0.0:1.0	.	230	Q9HAN9	NMNA1_HUMAN	P	230	ENSP00000366410:L230P	ENSP00000366410:L230P	L	+	2	0	NMNAT1	9965195	1.000000	0.71417	0.561000	0.28357	0.996000	0.88848	5.942000	0.70203	2.005000	0.58758	0.379000	0.24179	CTC	.	.		0.453	NMNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005029.1		
UBE4B	10277	hgsc.bcm.edu	37	1	10205093	10205093	+	Missense_Mutation	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:10205093T>A	ENST00000253251.8	+	17	2911	c.2072T>A	c.(2071-2073)cTt>cAt	p.L691H	UBE4B_ENST00000343090.6_Missense_Mutation_p.L820H|UBE4B_ENST00000377157.3_Missense_Mutation_p.L575H					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		AAAACTCAGCTTAAGGTTTGT	0.393																																					p.L820H		Atlas-SNP	.											.	UBE4B	233	.	0			c.T2459A						.						63.0	62.0	62.0					1																	10205093		2203	4300	6503	SO:0001583	missense	10277	exon18			CTCAGCTTAAGGT	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"""U-box domain containing"""	12500	protein-coding gene	gene with protein product		613565	"""ubiquitination factor E4B (homologous to yeast UFD2)"", ""ubiquitination factor E4B (UFD2 homolog, yeast)"""			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.2072T>A	chr1.hg19:g.10205093T>A	ENSP00000253251:p.Leu691His	150.0	0.0		93.0	4.0	NM_001105562		Missense_Mutation	SNP	ENST00000253251.8	hg19	CCDS110.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.219400	0.79464	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.52057	0.68;0.68;0.68	5.83	5.83	0.93111	Ubiquitin conjugation factor E4, core (1);	0.000000	0.85682	D	0.000000	T	0.56572	0.1994	M	0.82517	2.595	0.80722	D	1	B;B;B	0.33637	0.42;0.42;0.366	B;B;B	0.36186	0.188;0.219;0.118	T	0.61222	-0.7106	10	0.56958	D	0.05	-18.9981	16.1846	0.81942	0.0:0.0:0.0:1.0	.	691;820;691	A8K8S9;O95155;O95155-2	.;UBE4B_HUMAN;.	H	691;575;820	ENSP00000253251:L691H;ENSP00000366362:L575H;ENSP00000343001:L820H	ENSP00000253251:L691H	L	+	2	0	UBE4B	10127680	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	7.462000	0.80851	2.229000	0.72834	0.533000	0.62120	CTT	.	.		0.393	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048	
KAZN	23254	hgsc.bcm.edu	37	1	15430640	15430640	+	Missense_Mutation	SNP	G	G	A	rs147449416		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:15430640G>A	ENST00000376030.2	+	13	2297	c.2003G>A	c.(2002-2004)cGg>cAg	p.R668Q		NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	668	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						CACATCCTCCGGAGACACCTG	0.632																																					p.R668Q		Atlas-SNP	.											.	KAZN	57	.	0			c.G2003A						.	G	GLN/ARG	0,4406		0,0,2203	47.0	37.0	40.0		2003	5.7	1.0	1	dbSNP_134	40	1,8599		0,1,4299	no	missense	KAZN	NM_201628.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	668/776	15430640	1,13005	2203	4300	6503	SO:0001583	missense	23254	exon13			TCCTCCGGAGACA	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"""Sterile alpha motif (SAM) domain containing"""	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.2003G>A	chr1.hg19:g.15430640G>A	ENSP00000365198:p.Arg668Gln	118.0	0.0		73.0	4.0	NM_201628	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	hg19	CCDS152.2	.	.	.	.	.	.	.	.	.	.	G	32	5.130480	0.94473	0.0	1.16E-4	ENSG00000189337	ENST00000376030	T	0.38887	1.11	5.67	5.67	0.87782	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (1);	0.195189	0.32819	N	0.005614	T	0.63640	0.2528	M	0.87269	2.87	0.80722	D	1	D	0.69078	0.997	P	0.55785	0.784	T	0.70766	-0.4783	10	0.87932	D	0	-33.8907	15.2647	0.73651	0.0:0.0:1.0:0.0	.	668	Q674X7	KAZRN_HUMAN	Q	668	ENSP00000365198:R668Q	ENSP00000365198:R668Q	R	+	2	0	KAZN	15303227	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	4.598000	0.61069	2.671000	0.90904	0.585000	0.79938	CGG	.	G|1.000;A|0.000		0.632	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999	
SPEN	23013	hgsc.bcm.edu	37	1	16261624	16261624	+	Silent	SNP	C	C	A	rs151181793		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:16261624C>A	ENST00000375759.3	+	11	9093	c.8889C>A	c.(8887-8889)ccC>ccA	p.P2963P		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2963					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		TTGCTGACCCCGTCACCCTTA	0.592																																					p.P2963P		Atlas-SNP	.											SPEN,caecum,carcinoma,0,1	SPEN	374	.	0			c.C8889A						.						60.0	64.0	63.0					1																	16261624		2203	4300	6503	SO:0001819	synonymous_variant	23013	exon11			TGACCCCGTCACC		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.8889C>A	chr1.hg19:g.16261624C>A		196.0	0.0		80.0	4.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	hg19	CCDS164.1																																																																																			.	C|0.998;T|0.002		0.592	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
CLCNKA	1187	hgsc.bcm.edu	37	1	16351303	16351303	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:16351303G>T	ENST00000331433.4	+	4	294	c.275G>T	c.(274-276)cGg>cTg	p.R92L	CLCNKA_ENST00000375692.1_Missense_Mutation_p.R92L|CLCNKA_ENST00000420078.1_Missense_Mutation_p.R92L|CLCNKA_ENST00000439316.2_Intron|CLCNKA_ENST00000464764.1_Intron			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	92					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)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		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)	Niflumic Acid(DB04552)	CACCTGCTCCGGTATCTTTCC	0.637																																					p.R92L		Atlas-SNP	.											.	CLCNKA	56	.	0			c.G275T						.						134.0	101.0	112.0					1																	16351303		2203	4300	6503	SO:0001583	missense	1187	exon4			TGCTCCGGTATCT		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.275G>T	chr1.hg19:g.16351303G>T	ENSP00000332771:p.Arg92Leu	241.0	0.0		124.0	6.0	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	hg19	CCDS167.1	.	.	.	.	.	.	.	.	.	.	G	17.13	3.311349	0.60414	.	.	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000331433	D;D;D	0.92752	-3.1;-3.1;-3.1	4.0	4.0	0.46444	Chloride channel, core (2);	0.131851	0.51477	D	0.000085	D	0.91389	0.7283	M	0.75447	2.3	0.80722	D	1	B;B	0.28512	0.214;0.214	B;B	0.37304	0.198;0.246	D	0.90447	0.4436	10	0.66056	D	0.02	.	7.7785	0.29051	0.1153:0.0:0.8847:0.0	.	92;92	Q5T5Q4;P51800	.;CLCKA_HUMAN	L	92	ENSP00000364844:R92L;ENSP00000410353:R92L;ENSP00000332771:R92L	ENSP00000332771:R92L	R	+	2	0	CLCNKA	16223890	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.392000	0.66272	2.220000	0.72140	0.462000	0.41574	CGG	.	.		0.637	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
ACTL8	81569	hgsc.bcm.edu	37	1	18152877	18152877	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:18152877T>C	ENST00000375406.1	+	3	1180	c.964T>C	c.(964-966)Tcc>Ccc	p.S322P		NM_030812.2	NP_110439.2	Q9H568	ACTL8_HUMAN	actin-like 8	322					epithelial cell differentiation (GO:0030855)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	28		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00186)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;6.43e-06)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.00652)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)		TCACGTCTCCTCCACCAAGGC	0.592											OREG0013157	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S322P		Atlas-SNP	.											.	ACTL8	58	.	0			c.T964C						.						75.0	81.0	79.0					1																	18152877		2203	4300	6503	SO:0001583	missense	81569	exon3			GTCTCCTCCACCA	AK057339	CCDS183.1	1p36.2-p35	2009-03-25			ENSG00000117148	ENSG00000117148			24018	protein-coding gene	gene with protein product	"""cancer/testis antigen 57"""						Standard	NM_030812		Approved	CT57	uc001bat.3	Q9H568	OTTHUMG00000002512	ENST00000375406.1:c.964T>C	chr1.hg19:g.18152877T>C	ENSP00000364555:p.Ser322Pro	199.0	0.0	723	100.0	4.0	NM_030812	Q13104|Q96M75	Missense_Mutation	SNP	ENST00000375406.1	hg19	CCDS183.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.777503	0.31411	.	.	ENSG00000117148	ENST00000375406	D	0.94862	-3.54	4.88	-8.75	0.00834	.	0.749624	0.11425	N	0.565373	D	0.87462	0.6183	L	0.48362	1.52	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.73714	-0.3896	10	0.87932	D	0	-4.8049	3.4932	0.07645	0.2065:0.4713:0.1381:0.1841	.	322	Q9H568	ACTL8_HUMAN	P	322	ENSP00000364555:S322P	ENSP00000364555:S322P	S	+	1	0	ACTL8	18025464	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.004000	0.12878	-1.235000	0.02545	0.533000	0.62120	TCC	.	.		0.592	ACTL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007143.1	NM_030812	
VWA5B1	127731	hgsc.bcm.edu	37	1	20657405	20657405	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:20657405G>A	ENST00000375079.2	+	11	1697	c.1501G>A	c.(1501-1503)Gtg>Atg	p.V501M	VWA5B1_ENST00000289815.8_Missense_Mutation_p.V501M|VWA5B1_ENST00000289825.4_Missense_Mutation_p.V218M|VWA5B1_ENST00000375083.4_Missense_Mutation_p.V501M	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	501	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						CCACAGACTGGTGAAAGGACT	0.572																																					p.V501M		Atlas-SNP	.											.	VWA5B1	44	.	0			c.G1501A						.						86.0	79.0	81.0					1																	20657405		692	1591	2283	SO:0001583	missense	127731	exon11			AGACTGGTGAAAG	AK125833, AK057346		1p36.12	2014-02-12			ENSG00000158816	ENSG00000158816			26538	protein-coding gene	gene with protein product							Standard	NM_001039500		Approved	FLJ32784	uc009vps.2	Q5TIE3	OTTHUMG00000002835	ENST00000375079.2:c.1501G>A	chr1.hg19:g.20657405G>A	ENSP00000364220:p.Val501Met	251.0	0.0		110.0	5.0	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Missense_Mutation	SNP	ENST00000375079.2	hg19		.	.	.	.	.	.	.	.	.	.	G	26.0	4.691697	0.88735	.	.	ENSG00000158816	ENST00000375089;ENST00000289815;ENST00000375083;ENST00000289825;ENST00000375079	T;T;T;T	0.07327	3.2;3.2;3.2;3.2	5.19	5.19	0.71726	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	T	0.25158	0.0611	L	0.50847	1.595	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.97110	0.994;0.999;1.0	T	0.00370	-1.1783	10	0.72032	D	0.01	-13.5714	17.2962	0.87171	0.0:0.0:1.0:0.0	.	501;501;218	Q5TIE3;Q5TIE3-2;Q5TIE3-3	VW5B1_HUMAN;.;.	M	501;501;501;218;501	ENSP00000289815:V501M;ENSP00000364224:V501M;ENSP00000289825:V218M;ENSP00000364220:V501M	ENSP00000289815:V501M	V	+	1	0	VWA5B1	20529992	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.839000	0.69395	2.430000	0.82344	0.643000	0.83706	GTG	.	.		0.572	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
ZNF436	80818	hgsc.bcm.edu	37	1	23688528	23688528	+	Silent	SNP	G	G	T	rs144729139		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:23688528G>T	ENST00000314011.4	-	4	1483	c.1347C>A	c.(1345-1347)acC>acA	p.T449T	ZNF436_ENST00000374608.3_Silent_p.T449T	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	449					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T449T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		TCTCACATTCGGTACATTCAT	0.433																																					p.T449T		Atlas-SNP	.											.	ZNF436	49	.	1	Substitution - coding silent(1)	lung(1)	c.C1347A						.						89.0	93.0	91.0					1																	23688528		2203	4300	6503	SO:0001819	synonymous_variant	80818	exon4			ACATTCGGTACAT	AB051497	CCDS233.1	1p36	2013-01-08			ENSG00000125945	ENSG00000125945		"""Zinc fingers, C2H2-type"", ""-"""	20814	protein-coding gene	gene with protein product		611703				11214970	Standard	NM_001077195		Approved	KIAA1710, Zfp46	uc001bgt.3	Q9C0F3	OTTHUMG00000003232	ENST00000314011.4:c.1347C>A	chr1.hg19:g.23688528G>T		173.0	0.0		88.0	4.0	NM_001077195	Q658I9	Silent	SNP	ENST00000314011.4	hg19	CCDS233.1																																																																																			.	G|1.000;A|0.000		0.433	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634	
ASAP3	55616	hgsc.bcm.edu	37	1	23762411	23762411	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:23762411A>G	ENST00000336689.3	-	17	1726	c.1682T>C	c.(1681-1683)cTg>cCg	p.L561P	ASAP3_ENST00000437606.2_Missense_Mutation_p.L552P|ASAP3_ENST00000495646.1_Missense_Mutation_p.L65P	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	561					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						CAGTACCGACAGGAGGTCCCT	0.577																																					p.L561P		Atlas-SNP	.											.	ASAP3	65	.	0			c.T1682C						.						110.0	112.0	112.0					1																	23762411		2203	4300	6503	SO:0001583	missense	55616	exon17			ACCGACAGGAGGT	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.1682T>C	chr1.hg19:g.23762411A>G	ENSP00000338769:p.Leu561Pro	159.0	0.0		79.0	4.0	NM_017707	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Missense_Mutation	SNP	ENST00000336689.3	hg19	CCDS235.1	.	.	.	.	.	.	.	.	.	.	A	9.001	0.980135	0.18812	.	.	ENSG00000088280	ENST00000538685;ENST00000495646;ENST00000336689;ENST00000437606	T;T;T	0.54279	1.93;0.59;0.58	3.88	2.76	0.32466	Ankyrin repeat-containing domain (1);	0.302991	0.27168	N	0.020605	T	0.31949	0.0813	N	0.14661	0.345	0.21861	N	0.999509	B;B;B;B	0.24823	0.059;0.112;0.006;0.033	B;B;B;B	0.28305	0.018;0.056;0.088;0.021	T	0.17471	-1.0368	10	0.51188	T	0.08	.	6.1593	0.20356	0.7955:0.0:0.2045:0.0	.	552;430;84;561	Q8TDY4-3;B4DRP2;Q9NXH7;Q8TDY4	.;.;.;ASAP3_HUMAN	P	84;65;561;552	ENSP00000436150:L65P;ENSP00000338769:L561P;ENSP00000408826:L552P	ENSP00000338769:L561P	L	-	2	0	ASAP3	23634998	0.922000	0.31269	0.925000	0.36789	0.716000	0.41182	3.953000	0.56699	1.759000	0.51996	0.363000	0.22086	CTG	.	.		0.577	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707	
RPL11	6135	hgsc.bcm.edu	37	1	24022327	24022327	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:24022327C>T	ENST00000374550.3	+	5	481	c.436C>T	c.(436-438)Cgc>Tgc	p.R146C	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	146					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)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|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)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		AGACAAGAAGCGCAGGACAGG	0.527																																					p.R146C		Atlas-SNP	.											RPL11,NS,carcinoma,-1,1	RPL11	21	.	0			c.C436T						.						70.0	61.0	64.0					1																	24022327		2202	4299	6501	SO:0001583	missense	6135	exon5			AAGAAGCGCAGGA	L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"""L ribosomal proteins"""	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.436C>T	chr1.hg19:g.24022327C>T	ENSP00000363676:p.Arg146Cys	121.0	0.0		73.0	3.0	NM_000975	P25121|P39026|Q8TDH2|Q9Y674	Missense_Mutation	SNP	ENST00000374550.3	hg19	CCDS238.1	.	.	.	.	.	.	.	.	.	.	C	19.55	3.848686	0.71603	.	.	ENSG00000142676	ENST00000374550;ENST00000458455	T;T	0.78481	-1.18;-1.18	5.7	5.7	0.88788	Ribosomal protein L5 domain (2);	0.000000	0.85682	D	0.000000	D	0.84969	0.5590	M	0.91920	3.255	0.80722	D	1	B;B	0.17667	0.023;0.018	B;B	0.26969	0.072;0.075	T	0.83316	-0.0020	10	0.87932	D	0	-6.3587	19.819	0.96583	0.0:1.0:0.0:0.0	.	145;146	P62913-2;P62913	.;RL11_HUMAN	C	146;144	ENSP00000363676:R146C;ENSP00000398888:R144C	ENSP00000363676:R146C	R	+	1	0	RPL11	23894914	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.542000	0.60677	2.688000	0.91661	0.591000	0.81541	CGC	.	.		0.527	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975	
PDIK1L	149420	hgsc.bcm.edu	37	1	26448825	26448825	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:26448825A>G	ENST00000374271.4	+	4	1070	c.783A>G	c.(781-783)acA>acG	p.T261T	PDIK1L_ENST00000374269.1_Silent_p.T261T	NM_001243532.1|NM_001243533.1|NM_152835.4	NP_001230461.1|NP_001230462.1|NP_690048.1	Q8N165	PDK1L_HUMAN	PDLIM1 interacting kinase 1 like	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	7		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00239)|all_lung(284;0.00366)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000735)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)		ACACAGAGACAAAGAAGGAAC	0.438																																					p.T261T		Atlas-SNP	.											.	PDIK1L	19	.	0			c.A783G						.						97.0	100.0	99.0					1																	26448825		2203	4300	6503	SO:0001819	synonymous_variant	149420	exon3			AGAGACAAAGAAG	AF411102	CCDS274.1	1p35.1	2008-02-05			ENSG00000175087	ENSG00000175087			18981	protein-coding gene	gene with protein product		610785				14631099	Standard	NM_152835		Approved	CLIK1L	uc009vsb.3	Q8N165	OTTHUMG00000007511	ENST00000374271.4:c.783A>G	chr1.hg19:g.26448825A>G		168.0	0.0		92.0	4.0	NM_001243532	B2R777|D3DPK2|Q5T2I0|Q8NDB3	Silent	SNP	ENST00000374271.4	hg19	CCDS274.1																																																																																			.	.		0.438	PDIK1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019752.1	NM_152835	
GPATCH3	63906	hgsc.bcm.edu	37	1	27219162	27219162	+	Splice_Site	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:27219162T>C	ENST00000361720.5	-	5	1255	c.1232A>G	c.(1231-1233)aAg>aGg	p.K411R	GPN2_ENST00000374135.4_5'Flank	NM_022078.2	NP_071361.2	Q96I76	GPTC3_HUMAN	G patch domain containing 3	411	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.						nucleic acid binding (GO:0003676)			endometrium(2)|large_intestine(1)|lung(11)|skin(1)	15		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.97e-51)|OV - Ovarian serous cystadenocarcinoma(117;9.55e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|STAD - Stomach adenocarcinoma(196;0.000595)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|READ - Rectum adenocarcinoma(331;0.0419)		CTAACTCACCTTGGTGTGGCG	0.562																																					p.K411R		Atlas-SNP	.											.	GPATCH3	30	.	0			c.A1232G						.						159.0	152.0	154.0					1																	27219162		2203	4300	6503	SO:0001630	splice_region_variant	63906	exon5			CTCACCTTGGTGT	BC007767	CCDS290.1	1p35.3-p35.1	2013-01-28		2006-12-13	ENSG00000198746	ENSG00000198746		"""G patch domain containing"""	25720	protein-coding gene	gene with protein product				GPATC3			Standard	NM_022078		Approved	FLJ12455	uc001bne.3	Q96I76	OTTHUMG00000004229	ENST00000361720.5:c.1233+1A>G	chr1.hg19:g.27219162T>C		163.0	0.0		94.0	4.0	NM_022078	Q5JYH2|Q8NDJ2|Q9H9Z3	Missense_Mutation	SNP	ENST00000361720.5	hg19	CCDS290.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.5|21.5	4.154835|4.154835	0.78114|0.78114	.|.	.|.	ENSG00000198746|ENSG00000198746	ENST00000361720;ENST00000536641;ENST00000374122;ENST00000450844|ENST00000445019	T;T|.	0.32753|.	1.44;1.44|.	5.18|5.18	5.18|5.18	0.71444|0.71444	D111/G-patch (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.54902|0.54902	0.1887|0.1887	L|L	0.28400|0.28400	0.85|0.85	0.80722|0.80722	D|D	1|1	D|.	0.62365|.	0.991|.	P|.	0.62649|.	0.905|.	T|T	0.51505|0.51505	-0.8697|-0.8697	10|5	0.35671|.	T|.	0.21|.	-32.4964|-32.4964	15.1942|15.1942	0.73071|0.73071	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	411|.	Q96I76|.	GPTC3_HUMAN|.	R|G	411;393;222;29|61	ENSP00000354645:K411R;ENSP00000399036:K29R|.	ENSP00000354645:K411R|.	K|R	-|-	2|1	0|2	GPATCH3|GPATCH3	27091749|27091749	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.895000|0.895000	0.52256|0.52256	6.886000|6.886000	0.75611|0.75611	2.172000|2.172000	0.68678|0.68678	0.533000|0.533000	0.62120|0.62120	AAG|AGG	.	.		0.562	GPATCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012181.1	NM_022078	Missense_Mutation
GPATCH3	63906	hgsc.bcm.edu	37	1	27226824	27226824	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:27226824C>A	ENST00000361720.5	-	1	133	c.110G>T	c.(109-111)cGa>cTa	p.R37L		NM_022078.2	NP_071361.2	Q96I76	GPTC3_HUMAN	G patch domain containing 3	37							nucleic acid binding (GO:0003676)			endometrium(2)|large_intestine(1)|lung(11)|skin(1)	15		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.97e-51)|OV - Ovarian serous cystadenocarcinoma(117;9.55e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|STAD - Stomach adenocarcinoma(196;0.000595)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|READ - Rectum adenocarcinoma(331;0.0419)		GCGCTCTTCTCGGAACTGGCT	0.632																																					p.R37L		Atlas-SNP	.											.	GPATCH3	30	.	0			c.G110T						.						33.0	34.0	33.0					1																	27226824		2203	4300	6503	SO:0001583	missense	63906	exon1			TCTTCTCGGAACT	BC007767	CCDS290.1	1p35.3-p35.1	2013-01-28		2006-12-13	ENSG00000198746	ENSG00000198746		"""G patch domain containing"""	25720	protein-coding gene	gene with protein product				GPATC3			Standard	NM_022078		Approved	FLJ12455	uc001bne.3	Q96I76	OTTHUMG00000004229	ENST00000361720.5:c.110G>T	chr1.hg19:g.27226824C>A	ENSP00000354645:p.Arg37Leu	129.0	0.0		46.0	4.0	NM_022078	Q5JYH2|Q8NDJ2|Q9H9Z3	Missense_Mutation	SNP	ENST00000361720.5	hg19	CCDS290.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.818395	0.50633	.	.	ENSG00000198746	ENST00000361720;ENST00000536641	T	0.27402	1.67	5.5	5.5	0.81552	.	0.193744	0.45361	D	0.000371	T	0.20820	0.0501	L	0.28274	0.84	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.05971	-1.0853	10	0.19590	T	0.45	-17.9273	11.8439	0.52371	0.2156:0.7844:0.0:0.0	.	37	Q96I76	GPTC3_HUMAN	L	37	ENSP00000354645:R37L	ENSP00000354645:R37L	R	-	2	0	GPATCH3	27099411	1.000000	0.71417	0.995000	0.50966	0.879000	0.50718	3.382000	0.52463	2.854000	0.98071	0.655000	0.94253	CGA	.	.		0.632	GPATCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012181.1	NM_022078	
PTPRU	10076	hgsc.bcm.edu	37	1	29638034	29638034	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:29638034T>C	ENST00000345512.3	+	21	3083	c.2954T>C	c.(2953-2955)gTc>gCc	p.V985A	PTPRU_ENST00000428026.2_Missense_Mutation_p.V975A|PTPRU_ENST00000373779.3_Missense_Mutation_p.V975A|PTPRU_ENST00000460170.2_Missense_Mutation_p.V981A|PTPRU_ENST00000356870.3_Missense_Mutation_p.V981A|PTPRU_ENST00000415600.2_3'UTR|PTPRU_ENST00000323874.8_Missense_Mutation_p.V981A	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	985	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		TCCAGCATCGTCATGATCACC	0.637																																					p.V985A		Atlas-SNP	.											.	PTPRU	374	.	0			c.T2954C						.						117.0	101.0	106.0					1																	29638034		2203	4300	6503	SO:0001583	missense	10076	exon21			GCATCGTCATGAT	U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9683	protein-coding gene	gene with protein product	"""pi R-PTP-Psi"""	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.2954T>C	chr1.hg19:g.29638034T>C	ENSP00000334941:p.Val985Ala	178.0	0.0		89.0	4.0	NM_005704	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	hg19	CCDS334.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.592865	0.86953	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79	4.76	4.76	0.60689	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.64402	D	0.000001	T	0.65821	0.2728	M	0.90145	3.09	0.80722	D	1	P;P;P;P;P	0.42010	0.725;0.725;0.725;0.768;0.768	B;P;B;P;P	0.49853	0.26;0.49;0.404;0.624;0.624	T	0.72320	-0.4329	9	.	.	.	.	13.9164	0.63899	0.0:0.0:0.0:1.0	.	975;981;975;981;985	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	A	985;975;981;981;975;981	ENSP00000334941:V985A;ENSP00000362884:V975A;ENSP00000349333:V981A;ENSP00000314987:V981A;ENSP00000392332:V975A;ENSP00000432906:V981A	.	V	+	2	0	PTPRU	29510621	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.864000	0.87037	2.133000	0.65898	0.533000	0.62120	GTC	.	.		0.637	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1		
IQCC	55721	hgsc.bcm.edu	37	1	32672950	32672950	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:32672950A>G	ENST00000291358.6	+	5	689	c.668A>G	c.(667-669)cAa>cGa	p.Q223R	DCDC2B_ENST00000409358.1_5'Flank|IQCC_ENST00000537469.1_Missense_Mutation_p.Q303R|RP4-622L5.7_ENST00000373604.4_RNA|RP4-622L5.7_ENST00000421616.1_RNA	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	223										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)				GACCAGTCACAACCAAGCGCA	0.567																																					p.Q303R		Atlas-SNP	.											.	IQCC	46	.	0			c.A908G						.						74.0	71.0	72.0					1																	32672950		2203	4300	6503	SO:0001583	missense	55721	exon5			AGTCACAACCAAG	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.668A>G	chr1.hg19:g.32672950A>G	ENSP00000291358:p.Gln223Arg	185.0	0.0		110.0	5.0	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Missense_Mutation	SNP	ENST00000291358.6	hg19	CCDS355.1	.	.	.	.	.	.	.	.	.	.	A	11.38	1.622522	0.28889	.	.	ENSG00000160051	ENST00000537469;ENST00000291358	T;T	0.25250	1.81;1.81	3.64	2.5	0.30297	.	0.737321	0.11771	N	0.531108	T	0.18635	0.0447	L	0.32530	0.975	0.09310	N	1	B;B	0.21225	0.053;0.053	B;B	0.20767	0.031;0.018	T	0.22347	-1.0219	10	0.62326	D	0.03	0.0351	5.9218	0.19086	0.8796:0.0:0.1204:0.0	.	303;223	F5H7T8;Q4KMZ1	.;IQCC_HUMAN	R	303;223	ENSP00000442291:Q303R;ENSP00000291358:Q223R	ENSP00000291358:Q223R	Q	+	2	0	IQCC	32445537	0.026000	0.19158	0.032000	0.17829	0.013000	0.08279	1.489000	0.35562	0.752000	0.32923	0.459000	0.35465	CAA	.	.		0.567	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134	
BSDC1	55108	hgsc.bcm.edu	37	1	32834115	32834115	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:32834115T>C	ENST00000455895.2	-	10	1226	c.1193A>G	c.(1192-1194)gAc>gGc	p.D398G	BSDC1_ENST00000419121.2_Missense_Mutation_p.D342G|BSDC1_ENST00000413080.1_Missense_Mutation_p.D337G|BSDC1_ENST00000341071.7_Missense_Mutation_p.D415G|BSDC1_ENST00000463967.1_5'UTR|BSDC1_ENST00000526031.1_Missense_Mutation_p.D303G|BSDC1_ENST00000446293.2_Missense_Mutation_p.D415G	NM_001143888.1|NM_018045.6	NP_001137360.1|NP_060515.3	Q9NW68	BSDC1_HUMAN	BSD domain containing 1	398										breast(1)|central_nervous_system(2)|kidney(1)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CAAGTCAAAGTCTTTCTCCCA	0.582																																					p.D415G		Atlas-SNP	.											.	BSDC1	52	.	0			c.A1244G						.						116.0	102.0	107.0					1																	32834115		2203	4300	6503	SO:0001583	missense	55108	exon10			TCAAAGTCTTTCT	BX641056	CCDS363.2, CCDS44101.1, CCDS44102.1, CCDS44103.1, CCDS72752.1	1p35.1	2008-02-05			ENSG00000160058	ENSG00000160058			25501	protein-coding gene	gene with protein product						12477932	Standard	XM_005270985		Approved	FLJ10276, RP4-811H24.7	uc010ohg.2	Q9NW68	OTTHUMG00000007588	ENST00000455895.2:c.1193A>G	chr1.hg19:g.32834115T>C	ENSP00000412173:p.Asp398Gly	151.0	0.0		94.0	4.0	NM_001143888	B4DMS7|B4DTI7|B4DTP7|B4E2X8|Q49AT8|Q68DY6|Q6IAA3|Q6MZK1|Q6UXS1|Q9HAL9	Missense_Mutation	SNP	ENST00000455895.2	hg19	CCDS363.2	.	.	.	.	.	.	.	.	.	.	T	29.9	5.041911	0.93685	.	.	ENSG00000160058	ENST00000455895;ENST00000413080;ENST00000341071;ENST00000526031;ENST00000419121;ENST00000446293	.	.	.	5.45	5.45	0.79879	.	0.041854	0.85682	D	0.000000	T	0.69566	0.3125	L	0.55481	1.735	0.80722	D	1	D;D;D;D;D	0.65815	0.995;0.968;0.983;0.99;0.97	P;P;P;P;P	0.62560	0.904;0.732;0.864;0.864;0.543	T	0.72858	-0.4165	9	0.87932	D	0	-14.8468	15.0267	0.71674	0.0:0.0:0.0:1.0	.	303;342;415;415;398	Q9NW68-9;Q9NW68-8;Q9NW68-7;Q9NW68-3;Q9NW68	.;.;.;.;BSDC1_HUMAN	G	398;337;415;303;342;415	.	ENSP00000344816:D415G	D	-	2	0	BSDC1	32606702	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.964000	0.87933	2.205000	0.71048	0.533000	0.62120	GAC	.	.		0.582	BSDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020056.3	NM_018045	
KIAA1522	57648	hgsc.bcm.edu	37	1	33238480	33238480	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:33238480C>T	ENST00000373480.1	+	7	3203	c.3100C>T	c.(3100-3102)Ctg>Ttg	p.L1034L	YARS_ENST00000469100.1_5'Flank|KIAA1522_ENST00000373481.3_Silent_p.L1045L|KIAA1522_ENST00000401073.2_Silent_p.L1093L|KIAA1522_ENST00000294521.3_Silent_p.L142L	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	1034										breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				ACAGAAAGAGCTGGCCTGACC	0.562											OREG0013333	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1093L		Atlas-SNP	.											.	KIAA1522	68	.	0			c.C3277T						.						75.0	76.0	76.0					1																	33238480		1986	4165	6151	SO:0001819	synonymous_variant	57648	exon7			AAAGAGCTGGCCT	AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.3100C>T	chr1.hg19:g.33238480C>T		152.0	0.0	838	82.0	4.0	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Silent	SNP	ENST00000373480.1	hg19	CCDS55588.1																																																																																			.	.		0.562	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1		
ZMYM1	79830	hgsc.bcm.edu	37	1	35579987	35579987	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:35579987G>T	ENST00000373330.1	+	11	2730	c.2556G>T	c.(2554-2556)ttG>ttT	p.L852F	ZMYM1_ENST00000359858.4_Missense_Mutation_p.L852F|ZMYM1_ENST00000373329.1_3'UTR			Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM-type 1	852						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TGCTGACATTGGTTTCCAAAT	0.348																																					p.L852F		Atlas-SNP	.											.	ZMYM1	86	.	0			c.G2556T						.						82.0	69.0	73.0					1																	35579987		1831	4084	5915	SO:0001583	missense	79830	exon10			GACATTGGTTTCC	AK096206	CCDS41302.1	1p34.3	2008-05-02	2005-09-12		ENSG00000197056	ENSG00000197056		"""Zinc fingers, MYM type"""	26253	protein-coding gene	gene with protein product			"""zinc finger, MYM domain containing 1"""			12477932	Standard	XM_005271216		Approved	FLJ23151, MYM	uc001bym.3	Q5SVZ6	OTTHUMG00000004374	ENST00000373330.1:c.2556G>T	chr1.hg19:g.35579987G>T	ENSP00000362427:p.Leu852Phe	173.0	0.0		119.0	5.0	NM_024772	D3DPR7|Q7Z3Q4	Missense_Mutation	SNP	ENST00000373330.1	hg19	CCDS41302.1	.	.	.	.	.	.	.	.	.	.	G	0.823	-0.747979	0.03065	.	.	ENSG00000197056	ENST00000359858;ENST00000373329;ENST00000373330	T;T;T	0.25579	1.79;1.79;1.79	3.91	0.451	0.16629	Ribonuclease H-like (1);	1.200770	0.06331	N	0.706201	T	0.14485	0.0350	L	0.29908	0.895	0.18873	N	0.999986	P;P	0.42409	0.779;0.578	B;B	0.33690	0.168;0.12	T	0.19549	-1.0302	9	.	.	.	1.379	3.8662	0.09018	0.2631:0.0:0.5556:0.1813	.	833;852	B4DSJ9;Q5SVZ6	.;ZMYM1_HUMAN	F	852;777;852	ENSP00000352920:L852F;ENSP00000362426:L777F;ENSP00000362427:L852F	.	L	+	3	2	ZMYM1	35352574	0.006000	0.16342	0.189000	0.23252	0.064000	0.16182	0.003000	0.13083	0.093000	0.17368	0.455000	0.32223	TTG	.	.		0.348	ZMYM1-001	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012705.1	NM_024772	
GNL2	29889	hgsc.bcm.edu	37	1	38048471	38048471	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:38048471G>T	ENST00000373062.3	-	7	801	c.703C>A	c.(703-705)Cct>Act	p.P235T		NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	235	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	30		Myeloproliferative disorder(586;0.0393)				TCAATGTGAGGGGAACGAGTA	0.393																																					p.P235T		Atlas-SNP	.											.	GNL2	58	.	0			c.C703A						.						171.0	159.0	163.0					1																	38048471		2203	4300	6503	SO:0001583	missense	29889	exon7			TGTGAGGGGAACG	L05425	CCDS421.1	1p34	2008-02-05			ENSG00000134697	ENSG00000134697			29925	protein-coding gene	gene with protein product		609365				8822211	Standard	NM_013285		Approved	Ngp-1, HUMAUANTIG	uc001cbk.3	Q13823	OTTHUMG00000004322	ENST00000373062.3:c.703C>A	chr1.hg19:g.38048471G>T	ENSP00000362153:p.Pro235Thr	122.0	0.0		85.0	5.0	NM_013285	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	hg19	CCDS421.1	.	.	.	.	.	.	.	.	.	.	G	13.85	2.359782	0.41801	.	.	ENSG00000134697	ENST00000373062;ENST00000545489	T	0.14516	2.5	5.87	3.94	0.45596	.	0.329365	0.37053	N	0.002278	T	0.13628	0.0330	L	0.49640	1.575	0.44937	D	0.997951	B	0.27068	0.167	B	0.29598	0.104	T	0.05484	-1.0882	10	0.18276	T	0.48	-8.6586	11.9514	0.52956	0.0664:0.1223:0.8113:0.0	.	235	Q13823	NOG2_HUMAN	T	235;76	ENSP00000362153:P235T	ENSP00000362153:P235T	P	-	1	0	GNL2	37821058	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.276000	0.65580	0.768000	0.33290	0.591000	0.81541	CCT	.	.		0.393	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285	
MACF1	23499	hgsc.bcm.edu	37	1	39816575	39816575	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:39816575G>T	ENST00000372915.3	+	42	11186	c.11099G>T	c.(11098-11100)cGg>cTg	p.R3700L	MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000317713.7_Missense_Mutation_p.R1633L|MACF1_ENST00000567887.1_Missense_Mutation_p.R3732L|MACF1_ENST00000289893.4_Missense_Mutation_p.R2135L|MACF1_ENST00000361689.2_Missense_Mutation_p.R1633L|MACF1_ENST00000545844.1_Missense_Mutation_p.R1633L|MACF1_ENST00000564288.1_Missense_Mutation_p.R3695L|MACF1_ENST00000539005.1_Missense_Mutation_p.R1633L			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3700					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)			ACAGCTCTTCGGGAAAAGCTT	0.532																																					p.R1633L		Atlas-SNP	.											.	MACF1	909	.	0			c.G4898T						.						87.0	83.0	84.0					1																	39816575		2203	4300	6503	SO:0001583	missense	23499	exon39			CTCTTCGGGAAAA	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.11099G>T	chr1.hg19:g.39816575G>T	ENSP00000362006:p.Arg3700Leu	90.0	0.0		51.0	5.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.	.	.	.	.	.	.	.	.	.	G	15.29	2.789068	0.49997	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000530262;ENST00000289893	T;T;T;T;T;T;T	0.62105	1.28;0.05;1.28;1.28;1.28;1.28;1.1	6.06	-6.09	0.02145	.	0.634882	0.14357	N	0.324734	T	0.59459	0.2195	L	0.51422	1.61	0.38205	D	0.940317	P;P;P;B	0.49862	0.474;0.862;0.929;0.009	B;P;B;B	0.49451	0.166;0.611;0.411;0.021	T	0.66810	-0.5829	10	0.23302	T	0.38	.	17.7482	0.88427	0.7216:0.0:0.2784:0.0	.	3700;1633;1633;1598	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3	MACF1_HUMAN;.;.;.	L	1633;3700;1633;1633;1633;1782;2135	ENSP00000439537:R1633L;ENSP00000362006:R3700L;ENSP00000354573:R1633L;ENSP00000313438:R1633L;ENSP00000444364:R1633L;ENSP00000437059:R1782L;ENSP00000289893:R2135L	ENSP00000289893:R2135L	R	+	2	0	MACF1	39589162	0.240000	0.23847	0.129000	0.21949	0.899000	0.52679	0.087000	0.14958	-1.783000	0.01274	-0.781000	0.03364	CGG	.	.		0.532	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
PPIE	10450	hgsc.bcm.edu	37	1	40218983	40218983	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:40218983C>T	ENST00000324379.5	+	10	881	c.862C>T	c.(862-864)Cca>Tca	p.P288S	PPIE_ENST00000372830.1_Intron|PPIE_ENST00000356511.2_Intron	NM_006112.3	NP_006103.1	Q9UNP9	PPIE_HUMAN	peptidylprolyl isomerase E (cyclophilin E)	288	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral genome replication (GO:0045070)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|nucleotide binding (GO:0000166)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(3)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	9	all_cancers(7;1.63e-13)|all_lung(5;2.27e-16)|all_epithelial(6;1.35e-15)|Lung NSC(20;1.49e-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;1.87e-18)|Epithelial(16;2.7e-17)|all cancers(16;5.5e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GGACGGGAAGCCAAAGCAGAA	0.582																																					p.P288S		Atlas-SNP	.											.	PPIE	33	.	0			c.C862T						.						133.0	105.0	115.0					1																	40218983		2203	4300	6503	SO:0001583	missense	10450	exon10			GGGAAGCCAAAGC	AF042385	CCDS442.1, CCDS443.1, CCDS53299.1	1p32	2013-02-12			ENSG00000084072	ENSG00000084072		"""RNA binding motif (RRM) containing"""	9258	protein-coding gene	gene with protein product	"""peptidyl-prolyl cis-trans isomerase E"", ""cyclophilin 33"", ""cyclophilin E"", ""PPIase E"", ""rotamase E"", ""peptidylprolyl isomerase E, isoform 1"""	602435				9747881	Standard	NM_203456		Approved	CyP-33, MGC3736, MGC111222	uc001cdw.3	Q9UNP9	OTTHUMG00000009248	ENST00000324379.5:c.862C>T	chr1.hg19:g.40218983C>T	ENSP00000312769:p.Pro288Ser	128.0	0.0		43.0	4.0	NM_006112	B2R971|O43634|O43635|Q32Q72|Q3S611|Q5TGA0|Q5TGA2|Q5TGA3|Q9UIZ5	Missense_Mutation	SNP	ENST00000324379.5	hg19	CCDS443.1	.	.	.	.	.	.	.	.	.	.	C	17.32	3.358716	0.61403	.	.	ENSG00000084072	ENST00000324379;ENST00000372835	T;T	0.58797	0.31;0.31	4.35	4.35	0.52113	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	.	.	.	.	T	0.76983	0.4064	H	0.96833	3.89	0.80722	D	1	P;P	0.42248	0.774;0.571	P;B	0.46253	0.509;0.232	D	0.85144	0.0982	9	0.56958	D	0.05	.	17.0155	0.86418	0.0:1.0:0.0:0.0	.	209;288	B4E3F2;Q9UNP9	.;PPIE_HUMAN	S	288;237	ENSP00000312769:P288S;ENSP00000361925:P237S	ENSP00000312769:P288S	P	+	1	0	PPIE	39991570	0.994000	0.37717	0.995000	0.50966	0.996000	0.88848	2.789000	0.47813	2.422000	0.82143	0.563000	0.77884	CCA	.	.		0.582	PPIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025642.2	NM_006112	
RLF	6018	hgsc.bcm.edu	37	1	40703878	40703878	+	Silent	SNP	G	G	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:40703878G>C	ENST00000372771.4	+	8	3531	c.3504G>C	c.(3502-3504)cgG>cgC	p.R1168R		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1168					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	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;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			TCCAACATCGGTATTCCCCAT	0.328																																					p.R1168R		Atlas-SNP	.											.	RLF	152	.	0			c.G3504C						.						79.0	84.0	83.0					1																	40703878		2203	4300	6503	SO:0001819	synonymous_variant	6018	exon8			ACATCGGTATTCC		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"""Zinc fingers, C2H2-type"""	10025	protein-coding gene	gene with protein product		180610	"""rearranged L-myc fusion sequence"""			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.3504G>C	chr1.hg19:g.40703878G>C		94.0	0.0		68.0	4.0	NM_012421	Q14CQ1|Q9NU60	Silent	SNP	ENST00000372771.4	hg19	CCDS448.1																																																																																			.	.		0.328	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421	
SMAP2	64744	hgsc.bcm.edu	37	1	40881972	40881972	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:40881972T>C	ENST00000539317.1	+	8	759	c.566T>C	c.(565-567)cTt>cCt	p.L189P		NM_001198980.1	NP_001185909.1	Q8WU79	SMAP2_HUMAN	small ArfGAP2	269	Interaction with clathrin heavy chains. {ECO:0000250}.				regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			central_nervous_system(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24	Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.04e-17)			GACTCCATTCTTTCACTGTAT	0.498																																					p.L269P		Atlas-SNP	.											.	SMAP2	48	.	0			c.T806C						.						127.0	124.0	125.0					1																	40881972		2203	4300	6503	SO:0001583	missense	64744	exon8			CCATTCTTTCACT	AL137764	CCDS451.1, CCDS55592.1, CCDS55593.1, CCDS72763.1	1p35.3-p34.1	2008-09-22	2008-09-05	2008-01-09	ENSG00000084070	ENSG00000084070		"""ADP-ribosylation factor GTPase activating proteins"""	25082	protein-coding gene	gene with protein product			"""stromal membrane-associated protein 1-like"", ""stromal membrane-associated GTPase-activating protein 2"""	SMAP1L		16571680	Standard	NM_001198978		Approved		uc001cfj.3	Q8WU79	OTTHUMG00000007301	ENST00000539317.1:c.566T>C	chr1.hg19:g.40881972T>C	ENSP00000442835:p.Leu189Pro	106.0	0.0		65.0	4.0	NM_022733	B2R7T1|B7Z5B5|B7Z8V2|D3DPV2|Q5QPL2|Q96C93|Q9NST2|Q9UJL8	Missense_Mutation	SNP	ENST00000539317.1	hg19	CCDS55593.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.566921	0.86439	.	.	ENSG00000084070	ENST00000372718;ENST00000372708;ENST00000539317	T;T;T	0.65549	0.58;0.47;-0.16	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000003	T	0.79003	0.4373	M	0.76170	2.325	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.91635	0.999;0.997;0.995	T	0.81215	-0.1034	10	0.87932	D	0	-18.1823	14.7743	0.69713	0.0:0.0:0.0:1.0	.	189;239;269	B7Z5B5;Q8WU79-2;Q8WU79	.;.;SMAP2_HUMAN	P	269;239;189	ENSP00000361803:L269P;ENSP00000361793:L239P;ENSP00000442835:L189P	ENSP00000361793:L239P	L	+	2	0	SMAP2	40654559	1.000000	0.71417	0.981000	0.43875	0.979000	0.70002	7.274000	0.78538	2.371000	0.80710	0.533000	0.62120	CTT	.	.		0.498	SMAP2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022733	
CFAP57	149465	hgsc.bcm.edu	37	1	43664184	43664184	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:43664184A>G	ENST00000372492.4	+	8	1619	c.1295A>G	c.(1294-1296)gAg>gGg	p.E432G	RNA5SP46_ENST00000362370.1_RNA|WDR65_ENST00000528956.1_Missense_Mutation_p.E432G	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		432										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TACCAAGAAGAGGCATATTCC	0.393																																					p.E432G		Atlas-SNP	.											.	WDR65	76	.	0			c.A1295G						.						92.0	83.0	86.0					1																	43664184		2203	4300	6503	SO:0001583	missense	149465	exon8			AAGAAGAGGCATA																												ENST00000372492.4:c.1295A>G	chr1.hg19:g.43664184A>G	ENSP00000361570:p.Glu432Gly	93.0	0.0		73.0	4.0	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	hg19		.	.	.	.	.	.	.	.	.	.	A	24.3	4.513918	0.85389	.	.	ENSG00000243710	ENST00000372492;ENST00000528956	T;T	0.09911	2.93;2.93	5.09	5.09	0.68999	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	T	0.40791	0.1131	M	0.91768	3.24	0.53688	D	0.999976	D;D	0.71674	0.992;0.998	D;D	0.75484	0.923;0.986	T	0.49293	-0.8955	10	0.42905	T	0.14	.	14.8451	0.70254	1.0:0.0:0.0:0.0	.	432;432	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	G	432	ENSP00000361570:E432G;ENSP00000435310:E432G	ENSP00000361570:E432G	E	+	2	0	WDR65	43436771	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	8.495000	0.90481	1.916000	0.55485	0.379000	0.24179	GAG	.	.		0.393	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
ARTN	9048	hgsc.bcm.edu	37	1	44401362	44401362	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:44401362T>C	ENST00000372359.5	+	3	816	c.34T>C	c.(34-36)Tcc>Ccc	p.S12P	ARTN_ENST00000372354.3_Missense_Mutation_p.S12P|ARTN_ENST00000414809.3_Missense_Mutation_p.S12P|ARTN_ENST00000472435.1_Missense_Mutation_p.S12P|ARTN_ENST00000498139.2_Missense_Mutation_p.S12P|ARTN_ENST00000479128.1_Missense_Mutation_p.S12P|ARTN_ENST00000438616.3_5'Flank	NM_057091.2	NP_476432.2	Q5T4W7	ARTN_HUMAN	artemin	12					axon guidance (GO:0007411)|induction of positive chemotaxis (GO:0050930)|lymphocyte migration into lymphoid organs (GO:0097021)|neuroblast proliferation (GO:0007405)|peripheral nervous system development (GO:0007422)|Peyer's patch morphogenesis (GO:0061146)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	receptor binding (GO:0005102)					Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)				CTCCACGCTGTCCCACTGCCC	0.597																																					p.S12P		Atlas-SNP	.											.	ARTN	6	.	0			c.T34C						.						91.0	64.0	73.0					1																	44401362		2203	4300	6503	SO:0001583	missense	9048	exon2			ACGCTGTCCCACT	AF109401	CCDS501.1, CCDS502.1	1p33-p32	2014-01-30			ENSG00000117407	ENSG00000117407		"""Endogenous ligands"""	727	protein-coding gene	gene with protein product	"""neublastin"", ""neurotrophic factor"""	603886				9883723	Standard	NM_057090		Approved	NBN, EVN, ENOVIN	uc001ckt.3	Q5T4W7	OTTHUMG00000007705	ENST00000372359.5:c.34T>C	chr1.hg19:g.44401362T>C	ENSP00000361434:p.Ser12Pro	192.0	0.0		103.0	5.0	NM_001136215	D3DPY1|D3DPY3|O95441|O96030|Q6P6A3	Missense_Mutation	SNP	ENST00000372359.5	hg19	CCDS501.1	.	.	.	.	.	.	.	.	.	.	T	12.62	1.993505	0.35131	.	.	ENSG00000117407	ENST00000372359;ENST00000414809;ENST00000477048;ENST00000471394;ENST00000498139;ENST00000491846;ENST00000479128;ENST00000472435;ENST00000474592;ENST00000372354	D;D;T;T;D;T;T;T;T;D	0.84146	-1.81;-1.81;0.62;0.62;-1.81;0.65;0.62;0.62;0.65;-1.81	3.77	0.451	0.16629	.	1.699210	0.03814	N	0.266359	T	0.70439	0.3224	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.57277	-0.7839	10	0.33940	T	0.23	.	5.4568	0.16594	0.0:0.5345:0.0:0.4655	.	12;12	Q5T4W7-3;Q5T4W7	.;ARTN_HUMAN	P	12	ENSP00000361434:S12P;ENSP00000387435:S12P;ENSP00000434784:S12P;ENSP00000435804:S12P;ENSP00000436727:S12P;ENSP00000436149:S12P;ENSP00000434071:S12P;ENSP00000435140:S12P;ENSP00000434856:S12P;ENSP00000361429:S12P	ENSP00000361429:S12P	S	+	1	0	ARTN	44173949	0.767000	0.28508	0.002000	0.10522	0.075000	0.17131	0.732000	0.26072	0.088000	0.17205	0.533000	0.62120	TCC	.	.		0.597	ARTN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000020713.2	NM_057090	
SLC6A9	6536	hgsc.bcm.edu	37	1	44468248	44468248	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:44468248T>C	ENST00000360584.2	-	7	1204	c.1013A>G	c.(1012-1014)gAg>gGg	p.E338G	SLC6A9_ENST00000357730.2_Missense_Mutation_p.E284G|SLC6A9_ENST00000537678.1_Missense_Mutation_p.E200G|SLC6A9_ENST00000372307.3_Missense_Mutation_p.E200G|SLC6A9_ENST00000475075.2_Missense_Mutation_p.E154G|SLC6A9_ENST00000372310.3_Missense_Mutation_p.E265G|SLC6A9_ENST00000372306.3_Missense_Mutation_p.E265G	NM_201649.3	NP_964012.2	P48067	SC6A9_HUMAN	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	338					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2)	22	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	AAAGGCTCCCTCCAGGGTCAC	0.597																																					p.E338G		Atlas-SNP	.											.	SLC6A9	109	.	0			c.A1013G						.						115.0	115.0	115.0					1																	44468248		2203	4300	6503	SO:0001583	missense	6536	exon7			GCTCCCTCCAGGG	S70609	CCDS30695.1, CCDS41316.1, CCDS41317.1	1p33	2013-05-22			ENSG00000196517	ENSG00000196517		"""Solute carriers"""	11056	protein-coding gene	gene with protein product		601019				8183239, 7587377	Standard	NM_006934		Approved	GLYT1	uc001cll.4	P48067	OTTHUMG00000008294	ENST00000360584.2:c.1013A>G	chr1.hg19:g.44468248T>C	ENSP00000353791:p.Glu338Gly	140.0	0.0		73.0	4.0	NM_201649	A6NDH1|A6NII2|A6NNZ8|Q5TAB8|Q5TAB9|Q5TAC0	Missense_Mutation	SNP	ENST00000360584.2	hg19	CCDS41317.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.357665	0.82243	.	.	ENSG00000196517	ENST00000372307;ENST00000372306;ENST00000372310;ENST00000475075;ENST00000360584;ENST00000357730;ENST00000537678	T;T;T;T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85	4.51	4.51	0.55191	.	0.321665	0.36972	N	0.002311	D	0.86339	0.5909	M	0.88241	2.94	0.48571	D	0.999678	P;D;D;P;P;P	0.52996	0.837;0.957;0.957;0.905;0.947;0.565	P;P;P;P;P;B	0.60473	0.52;0.836;0.875;0.586;0.667;0.324	D	0.89187	0.3548	10	0.72032	D	0.01	.	14.2805	0.66208	0.0:0.0:0.0:1.0	.	269;265;200;265;284;338	B7Z3W8;B7Z8W5;B7Z3A9;P48067-2;P48067-3;P48067	.;.;.;.;.;SC6A9_HUMAN	G	200;265;265;154;338;284;200	ENSP00000361381:E200G;ENSP00000361380:E265G;ENSP00000361384:E265G;ENSP00000434460:E154G;ENSP00000353791:E338G;ENSP00000350362:E284G;ENSP00000442523:E200G	ENSP00000350362:E284G	E	-	2	0	SLC6A9	44240835	1.000000	0.71417	0.986000	0.45419	0.974000	0.67602	5.927000	0.70080	2.006000	0.58801	0.459000	0.35465	GAG	.	.		0.597	SLC6A9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000022825.2	NM_201649	
PLK3	1263	hgsc.bcm.edu	37	1	45266606	45266606	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:45266606A>G	ENST00000372201.4	+	2	544	c.305A>G	c.(304-306)cAt>cGt	p.H102R	PLK3_ENST00000465443.1_3'UTR	NM_004073.2	NP_004064.2	Q9H4B4	PLK3_HUMAN	polo-like kinase 3	102	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic microtubule organization (GO:0031122)|endomitotic cell cycle (GO:0007113)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi disassembly (GO:0090166)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G1/S transition checkpoint (GO:0044819)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia (GO:2000777)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell division (GO:0051302)|regulation of cytokinesis (GO:0032465)|response to osmotic stress (GO:0006970)|response to radiation (GO:0009314)|response to reactive oxygen species (GO:0000302)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi stack (GO:0005795)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					GCCAAGCCGCATCAGCGCGAG	0.672																																					p.H102R		Atlas-SNP	.											.	PLK3	41	.	0			c.A305G						.						26.0	30.0	29.0					1																	45266606		2202	4298	6500	SO:0001583	missense	1263	exon2			AGCCGCATCAGCG	AJ293866	CCDS515.1	1p34.1	2013-01-18	2010-06-24	2004-01-28	ENSG00000173846	ENSG00000173846			2154	protein-coding gene	gene with protein product		602913	"""cytokine-inducible kinase"", ""polo-like kinase 3 (Drosophila)"""	CNK		8702627	Standard	NM_004073		Approved	FNK, PRK	uc001cmn.3	Q9H4B4	OTTHUMG00000008491	ENST00000372201.4:c.305A>G	chr1.hg19:g.45266606A>G	ENSP00000361275:p.His102Arg	155.0	0.0		74.0	4.0	NM_004073	Q15767|Q5JR99|Q96CV1	Missense_Mutation	SNP	ENST00000372201.4	hg19	CCDS515.1	.	.	.	.	.	.	.	.	.	.	a	23.9	4.474547	0.84640	.	.	ENSG00000173846	ENST00000372201;ENST00000543983	T	0.23147	1.92	4.67	4.67	0.58626	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.14098	0.0341	N	0.04686	-0.185	0.80722	D	1	B	0.21753	0.06	B	0.17433	0.018	T	0.06972	-1.0797	9	0.45353	T	0.12	-9.7578	13.3485	0.60589	1.0:0.0:0.0:0.0	.	102	Q9H4B4	PLK3_HUMAN	R	102;77	ENSP00000361275:H102R	ENSP00000361275:H102R	H	+	2	0	PLK3	45039193	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.959000	0.93110	1.760000	0.52011	0.449000	0.29647	CAT	.	.		0.672	PLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023429.1	NM_004073	
ZSWIM5	57643	hgsc.bcm.edu	37	1	45484490	45484490	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:45484490A>G	ENST00000359600.5	-	14	3399	c.3194T>C	c.(3193-3195)gTg>gCg	p.V1065A		NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	1065						extracellular space (GO:0005615)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|liver(1)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					CACACTCTTCACCACCAGGGG	0.587											OREG0013450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V1065A		Atlas-SNP	.											.	ZSWIM5	72	.	0			c.T3194C						.						68.0	64.0	66.0					1																	45484490		2047	4200	6247	SO:0001583	missense	57643	exon14			CTCTTCACCACCA	AB040944	CCDS41319.1	1p34.1	2010-06-16			ENSG00000162415	ENSG00000162415		"""Zinc fingers, SWIM-type"""	29299	protein-coding gene	gene with protein product						10819331	Standard	NM_020883		Approved	KIAA1511	uc001cnd.2	Q9P217	OTTHUMG00000008950	ENST00000359600.5:c.3194T>C	chr1.hg19:g.45484490A>G	ENSP00000352614:p.Val1065Ala	195.0	0.0	932	121.0	6.0	NM_020883	Q5SXQ9	Missense_Mutation	SNP	ENST00000359600.5	hg19	CCDS41319.1	.	.	.	.	.	.	.	.	.	.	A	17.18	3.323778	0.60634	.	.	ENSG00000162415	ENST00000359600	T	0.55413	0.52	4.84	3.69	0.42338	.	0.000000	0.85682	D	0.000000	T	0.62024	0.2394	M	0.75264	2.295	0.58432	D	0.999996	P	0.45474	0.859	P	0.51415	0.669	T	0.62859	-0.6765	10	0.45353	T	0.12	-8.8877	11.509	0.50483	0.8654:0.0:0.0:0.1346	.	1065	Q9P217	ZSWM5_HUMAN	A	1065	ENSP00000352614:V1065A	ENSP00000352614:V1065A	V	-	2	0	ZSWIM5	45257077	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.910000	0.92685	0.919000	0.36945	0.459000	0.35465	GTG	.	.		0.587	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	XM_046581	
MUTYH	4595	hgsc.bcm.edu	37	1	45799158	45799158	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:45799158T>C	ENST00000372098.3	-	3	399	c.266A>G	c.(265-267)gAa>gGa	p.E89G	MUTYH_ENST00000488731.2_Intron|MUTYH_ENST00000372100.5_Missense_Mutation_p.E75G|MUTYH_ENST00000528332.2_Intron|MUTYH_ENST00000450313.1_Missense_Mutation_p.E92G|MUTYH_ENST00000372115.3_Missense_Mutation_p.E78G|MUTYH_ENST00000456914.2_Missense_Mutation_p.E64G|MUTYH_ENST00000529984.1_Intron|MUTYH_ENST00000372110.3_Missense_Mutation_p.E79G|MUTYH_ENST00000372104.1_Missense_Mutation_p.E64G|MUTYH_ENST00000528013.2_Missense_Mutation_p.E78G|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000448481.1_Missense_Mutation_p.E75G|MUTYH_ENST00000354383.6_Missense_Mutation_p.E65G|MUTYH_ENST00000355498.2_Missense_Mutation_p.E64G			Q9UIF7	MUTYH_HUMAN	mutY homolog	89					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					GGCTGTGACTTCAGCTACGTC	0.602			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.E92G		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.A275G						.						95.0	82.0	86.0					1																	45799158		2203	4300	6503	SO:0001583	missense	4595	exon3	Familial Cancer Database	MAP, MYH-associated polyposis	GTGACTTCAGCTA	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"""mutY (E. coli) homolog"", ""mutY homolog (E. coli)"""			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.266A>G	chr1.hg19:g.45799158T>C	ENSP00000361170:p.Glu89Gly	160.0	0.0		92.0	4.0	NM_001128425	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Missense_Mutation	SNP	ENST00000372098.3	hg19	CCDS520.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.248113	0.80024	.	.	ENSG00000132781	ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000450313;ENST00000372100;ENST00000435155;ENST00000528013;ENST00000483127	T;T;T;T;T;T;T;T;T;T;T;T;T	0.51817	3.08;3.09;3.08;3.09;3.08;3.08;3.08;3.08;3.08;3.09;1.82;0.79;0.69	5.86	5.86	0.93980	DNA glycosylase (1);	0.150359	0.64402	D	0.000015	T	0.60779	0.2295	M	0.64997	1.995	0.52501	D	0.99995	D;D;P;D;D	0.57899	0.967;0.981;0.894;0.967;0.967	P;P;B;P;P	0.55999	0.497;0.789;0.393;0.497;0.619	T	0.64368	-0.6424	10	0.72032	D	0.01	-14.7918	14.8146	0.70024	0.0:0.0:0.0:1.0	.	92;79;89;78;65	E5KP25;Q9UIF7-2;Q9UIF7;E5KP27;E5KP28	.;.;MUTYH_HUMAN;.;.	G	64;75;64;65;64;89;79;78;92;75;75;78;70	ENSP00000361176:E64G;ENSP00000409718:E75G;ENSP00000407590:E64G;ENSP00000346354:E65G;ENSP00000347685:E64G;ENSP00000361170:E89G;ENSP00000361182:E79G;ENSP00000361187:E78G;ENSP00000408176:E92G;ENSP00000361172:E75G;ENSP00000403655:E75G;ENSP00000433130:E78G;ENSP00000436469:E70G	ENSP00000346354:E65G	E	-	2	0	MUTYH	45571745	1.000000	0.71417	0.967000	0.41034	0.535000	0.34838	3.796000	0.55507	2.232000	0.73038	0.533000	0.62120	GAA	.	.		0.602	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222	
ELAVL4	1996	hgsc.bcm.edu	37	1	50610679	50610679	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:50610679A>G	ENST00000371823.4	+	2	284	c.60A>G	c.(58-60)acA>acG	p.T20T	ELAVL4_ENST00000371821.1_Silent_p.T25T|ELAVL4_ENST00000371824.1_Silent_p.T20T|ELAVL4_ENST00000448907.2_Silent_p.T23T|ELAVL4_ENST00000492299.1_3'UTR|ELAVL4_ENST00000371819.1_Silent_p.T25T|ELAVL4_ENST00000357083.4_Silent_p.T37T|ELAVL4_ENST00000371827.1_Silent_p.T20T	NM_001144774.1|NM_021952.3	NP_001138246.1|NP_068771.2	P26378	ELAV4_HUMAN	ELAV like neuron-specific RNA binding protein 4	20					mRNA processing (GO:0006397)|RNA processing (GO:0006396)		AU-rich element binding (GO:0017091)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	32						CATCCAATACAAGCAATGGAC	0.413																																					p.T37T		Atlas-SNP	.											.	ELAVL4	124	.	0			c.A111G						.						89.0	77.0	81.0					1																	50610679		2203	4300	6503	SO:0001819	synonymous_variant	1996	exon2			CAATACAAGCAAT	AY033998	CCDS553.1, CCDS44138.1, CCDS44139.1, CCDS44140.1, CCDS53315.1, CCDS72788.1	1p34	2013-10-03	2013-10-03		ENSG00000162374	ENSG00000162374		"""RNA binding motif (RRM) containing"""	3315	protein-coding gene	gene with protein product	"""Hu antigen D"""	168360	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)"", ""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4"""	HUD		8222755	Standard	XM_005270581		Approved	PNEM	uc001csb.2	P26378	OTTHUMG00000007877	ENST00000371823.4:c.60A>G	chr1.hg19:g.50610679A>G		132.0	0.0		79.0	5.0	NM_001144775	B1APY6|B1APY7|B7Z4G7|Q8IYD4|Q96J74|Q96J75|Q9UD24	Silent	SNP	ENST00000371823.4	hg19	CCDS553.1																																																																																			.	.		0.413	ELAVL4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000021712.1	NM_021952	
LDLRAD1	388633	hgsc.bcm.edu	37	1	54474774	54474774	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:54474774A>G	ENST00000371360.1	-	6	516	c.499T>C	c.(499-501)Tgg>Cgg	p.W167R	LDLRAD1_ENST00000371362.3_Missense_Mutation_p.W78R|LDLRAD1_ENST00000545928.1_Missense_Mutation_p.W124R|LDLRAD1_ENST00000420619.1_Missense_Mutation_p.W128R	NM_001010978.2	NP_001010978.2	Q5T700	LRAD1_HUMAN	low density lipoprotein receptor class A domain containing 1	167	LDL-receptor class A 3; atypical. {ECO:0000255|PROSITE-ProRule:PRU00124}.					integral component of membrane (GO:0016021)				large_intestine(3)|prostate(1)|skin(3)	7						CAGCGCCACCACCCAGGGCCG	0.592																																					p.W167R		Atlas-SNP	.											.	LDLRAD1	22	.	0			c.T499C						.						101.0	97.0	98.0					1																	54474774		2203	4300	6503	SO:0001583	missense	388633	exon6			GCCACCACCCAGG		CCDS30725.1, CCDS60145.1, CCDS60146.1, CCDS60147.1	1p32.3	2008-02-05	2005-10-07		ENSG00000203985	ENSG00000203985			32069	protein-coding gene	gene with protein product			"""low density lipoprotein receptor A domain containing 1"""				Standard	NM_001010978		Approved		uc001cwm.2	Q5T700	OTTHUMG00000008433	ENST00000371360.1:c.499T>C	chr1.hg19:g.54474774A>G	ENSP00000360411:p.Trp167Arg	206.0	0.0		95.0	5.0	NM_001010978	A0PJY0|B7ZME3|Q5T6Z9	Missense_Mutation	SNP	ENST00000371360.1	hg19	CCDS30725.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.871021	0.51695	.	.	ENSG00000203985	ENST00000371362;ENST00000371360;ENST00000545928;ENST00000420619	D;D;D;D	0.87103	-2.21;-2.21;-2.21;-2.21	4.5	3.31	0.37934	.	0.000000	0.52532	D	0.000074	D	0.90566	0.7043	M	0.67953	2.075	0.42889	D	0.994199	D;D	0.89917	0.996;1.0	P;D	0.76575	0.731;0.988	D	0.88188	0.2875	10	0.25106	T	0.35	-20.3964	10.4302	0.44403	0.837:0.163:0.0:0.0	.	124;167	B7ZME3;Q5T700	.;LRAD1_HUMAN	R	78;167;124;128	ENSP00000360413:W78R;ENSP00000360411:W167R;ENSP00000445871:W124R;ENSP00000411017:W128R	ENSP00000360411:W167R	W	-	1	0	LDLRAD1	54247362	0.998000	0.40836	0.994000	0.49952	0.607000	0.37147	4.376000	0.59556	1.905000	0.55150	0.533000	0.62120	TGG	.	.		0.592	LDLRAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023243.1	NM_001010978	
CDCP2	200008	hgsc.bcm.edu	37	1	54618517	54618517	+	Splice_Site	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:54618517C>T	ENST00000371330.1	-	1	926	c.79G>A	c.(79-81)Ggt>Agt	p.G27S	RP11-446E24.4_ENST00000525949.1_Intron|RP11-446E24.4_ENST00000311841.7_3'UTR	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	27						extracellular region (GO:0005576)				kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						GAGTGCCTACCTTCCATGGCT	0.627																																					p.G27S		Atlas-SNP	.											.	CDCP2	52	.	0			c.G79A						.						81.0	85.0	84.0					1																	54618517		2203	4300	6503	SO:0001630	splice_region_variant	200008	exon1			GCCTACCTTCCAT		CCDS588.2	1p32.3	2011-02-10			ENSG00000157211	ENSG00000157211			27297	protein-coding gene	gene with protein product		612320				12477932	Standard	NM_201546		Approved		uc001cwv.2	Q5VXM1	OTTHUMG00000155307	ENST00000371330.1:c.79+1G>A	chr1.hg19:g.54618517C>T		216.0	0.0		125.0	26.0	NM_201546	Q6ZWJ3	Missense_Mutation	SNP	ENST00000371330.1	hg19	CCDS588.2	.	.	.	.	.	.	.	.	.	.	C	21.0	4.080918	0.76528	.	.	ENSG00000157211	ENST00000371330	T	0.26957	1.7	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.27384	0.0672	N	0.17901	0.54	0.51767	D	0.999933	D	0.57899	0.981	P	0.53490	0.727	T	0.01591	-1.1317	9	.	.	.	-6.7344	15.5363	0.76004	0.0:1.0:0.0:0.0	.	27	Q5VXM1	CDCP2_HUMAN	S	27	ENSP00000360381:G27S	.	G	-	1	0	CDCP2	54391105	0.975000	0.34042	1.000000	0.80357	0.588000	0.36517	1.350000	0.34010	2.574000	0.86865	0.650000	0.86243	GGT	.	.		0.627	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546	Missense_Mutation
USP24	23358	hgsc.bcm.edu	37	1	55537593	55537593	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:55537593G>T	ENST00000294383.6	-	67	7693	c.7694C>A	c.(7693-7695)aCg>aAg	p.T2565K	USP24_ENST00000484447.1_5'UTR|USP24_ENST00000407756.1_Missense_Mutation_p.T2405K	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	2565					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						ATACGCTAACGTGTCCTGCAG	0.493											OREG0013507	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T2565K		Atlas-SNP	.											.	USP24	323	.	0			c.C7694A						.						67.0	64.0	65.0					1																	55537593		2062	4209	6271	SO:0001583	missense	23358	exon67			GCTAACGTGTCCT	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.7694C>A	chr1.hg19:g.55537593G>T	ENSP00000294383:p.Thr2565Lys	137.0	0.0	1008	66.0	4.0	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	hg19	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	G	25.4	4.633083	0.87660	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.04406	3.63;3.67	4.56	4.56	0.56223	.	0.000000	0.64402	D	0.000001	T	0.19725	0.0474	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00473	-1.1718	10	0.62326	D	0.03	.	17.5474	0.87866	0.0:0.0:1.0:0.0	.	2405	B7WPF4	.	K	2565;2405	ENSP00000294383:T2565K;ENSP00000385700:T2405K	ENSP00000294383:T2565K	T	-	2	0	USP24	55310181	1.000000	0.71417	0.991000	0.47740	0.817000	0.46193	9.024000	0.93689	2.374000	0.81015	0.655000	0.94253	ACG	.	.		0.493	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
FGGY	55277	hgsc.bcm.edu	37	1	60019838	60019838	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:60019838A>G	ENST00000303721.7	+	8	1016	c.842A>G	c.(841-843)gAg>gGg	p.E281G	FGGY_ENST00000371218.4_Missense_Mutation_p.E281G|FGGY_ENST00000474476.1_3'UTR|FGGY_ENST00000371210.1_5'UTR|FGGY_ENST00000371212.1_Missense_Mutation_p.E193G	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	281					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					CTCATCTGTGAGGGGCAGCCA	0.517																																					p.E281G		Atlas-SNP	.											.	FGGY	99	.	0			c.A842G						.						74.0	57.0	63.0					1																	60019838		2203	4300	6503	SO:0001583	missense	55277	exon8			TCTGTGAGGGGCA		CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.842A>G	chr1.hg19:g.60019838A>G	ENSP00000305922:p.Glu281Gly	153.0	0.0		93.0	5.0	NM_001113411	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Missense_Mutation	SNP	ENST00000303721.7	hg19	CCDS611.2	.	.	.	.	.	.	.	.	.	.	A	16.73	3.203046	0.58234	.	.	ENSG00000172456	ENST00000371218;ENST00000303721;ENST00000371212	T;T;T	0.25250	2.82;2.82;1.81	5.28	5.28	0.74379	.	0.049083	0.85682	D	0.000000	T	0.25938	0.0632	L	0.52364	1.645	0.80722	D	1	B;B;B;B	0.15141	0.004;0.012;0.002;0.004	B;B;B;B	0.17722	0.019;0.009;0.002;0.005	T	0.03706	-1.1011	9	.	.	.	-23.3108	15.3844	0.74684	1.0:0.0:0.0:0.0	.	281;193;281;281	Q96C11-3;B1AK94;F2Z2V1;Q96C11	.;.;.;FGGY_HUMAN	G	281;281;193	ENSP00000360262:E281G;ENSP00000305922:E281G;ENSP00000360256:E193G	.	E	+	2	0	FGGY	59792426	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.233000	0.78125	2.210000	0.71456	0.533000	0.62120	GAG	.	.		0.517	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411	
INADL	10207	hgsc.bcm.edu	37	1	62330060	62330060	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:62330060A>G	ENST00000371158.2	+	20	2704	c.2590A>G	c.(2590-2592)Atg>Gtg	p.M864V	INADL_ENST00000316485.6_Missense_Mutation_p.M864V	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	864					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						ATTGCAGGAAATGGATGAAGA	0.418																																					p.M864V		Atlas-SNP	.											.	INADL	179	.	0			c.A2590G						.						114.0	111.0	112.0					1																	62330060		2203	4300	6503	SO:0001583	missense	10207	exon20			CAGGAAATGGATG	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.2590A>G	chr1.hg19:g.62330060A>G	ENSP00000360200:p.Met864Val	170.0	0.0		100.0	4.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	0.282	-0.985589	0.02180	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.10960	2.94;2.82	5.48	-1.59	0.08453	.	0.326888	0.28809	N	0.014075	T	0.06188	0.0160	L	0.42245	1.32	0.20764	N	0.999857	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.35919	-0.9769	10	0.16896	T	0.51	.	2.3489	0.04279	0.1658:0.3049:0.3789:0.1504	.	864;864;864	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	V	864	ENSP00000360200:M864V;ENSP00000326199:M864V	ENSP00000255202:M864V	M	+	1	0	INADL	62102648	0.000000	0.05858	0.032000	0.17829	0.673000	0.39480	-0.584000	0.05800	-0.202000	0.10268	0.454000	0.30748	ATG	.	.		0.418	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
INADL	10207	hgsc.bcm.edu	37	1	62582321	62582321	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:62582321C>A	ENST00000371158.2	+	36	4887	c.4773C>A	c.(4771-4773)gcC>gcA	p.A1591A	INADL_ENST00000543708.1_Silent_p.A405A	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1591	PDZ 9. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TGAGAAATGCCTCACAGGAGA	0.507																																					p.A1591A		Atlas-SNP	.											.	INADL	179	.	0			c.C4773A						.						73.0	76.0	75.0					1																	62582321		1984	4156	6140	SO:0001819	synonymous_variant	10207	exon36			AAATGCCTCACAG	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4773C>A	chr1.hg19:g.62582321C>A		95.0	0.0		51.0	4.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	hg19	CCDS617.2																																																																																			.	.		0.507	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
DOCK7	85440	hgsc.bcm.edu	37	1	63099217	63099217	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:63099217T>C	ENST00000340370.5	-	10	1085	c.1068A>G	c.(1066-1068)ggA>ggG	p.G356G	DOCK7_ENST00000404627.2_Silent_p.G356G|DOCK7_ENST00000251157.5_Silent_p.G356G	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	356					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						CTGCACACTCTCCAATGTCTC	0.368																																					p.G356G		Atlas-SNP	.											.	DOCK7	184	.	0			c.A1068G						.						253.0	247.0	249.0					1																	63099217		2203	4300	6503	SO:0001819	synonymous_variant	85440	exon10			ACACTCTCCAATG		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.1068A>G	chr1.hg19:g.63099217T>C		161.0	0.0		95.0	4.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	hg19	CCDS30734.1																																																																																			.	.		0.368	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
DNAJC6	9829	hgsc.bcm.edu	37	1	65867511	65867511	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:65867511C>A	ENST00000395325.3	+	15	2161	c.2004C>A	c.(2002-2004)acC>acA	p.T668T	DNAJC6_ENST00000371069.4_Silent_p.T725T|DNAJC6_ENST00000263441.7_Silent_p.T655T	NM_014787.3	NP_055602.1	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	668	Pro-rich.				cell death (GO:0008219)|clathrin coat disassembly (GO:0072318)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytosol (GO:0005829)|synapse (GO:0045202)	protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(22)|ovary(1)|prostate(2)|skin(1)	39						GTACTCCCACCCATCAAAGCA	0.448																																					p.T725T		Atlas-SNP	.											.	DNAJC6	104	.	0			c.C2175A						.						96.0	96.0	96.0					1																	65867511		2203	4300	6503	SO:0001819	synonymous_variant	9829	exon15			TCCCACCCATCAA	AB007942	CCDS30739.1, CCDS58004.1, CCDS58005.1	1p31.3	2011-09-02			ENSG00000116675	ENSG00000116675		"""Heat shock proteins / DNAJ (HSP40)"""	15469	protein-coding gene	gene with protein product	"""auxilin"""	608375				9455484, 11147971	Standard	NM_001256864		Approved	KIAA0473	uc001dce.2	O75061	OTTHUMG00000009066	ENST00000395325.3:c.2004C>A	chr1.hg19:g.65867511C>A		110.0	0.0		73.0	4.0	NM_001256864	B7Z3V8|D3DQ65|D3DQ66|Q32M66|Q4G0K1|Q5T614|Q5T615	Silent	SNP	ENST00000395325.3	hg19	CCDS30739.1																																																																																			.	.		0.448	DNAJC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025134.1		
WLS	79971	hgsc.bcm.edu	37	1	68611689	68611689	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:68611689A>G	ENST00000262348.4	-	9	1394	c.1141T>C	c.(1141-1143)Ttc>Ctc	p.F381L	WLS_ENST00000491811.1_5'UTR|WLS_ENST00000354777.2_Missense_Mutation_p.F379L|GNG12-AS1_ENST00000413628.1_RNA|GNG12-AS1_ENST00000420587.1_RNA|WLS_ENST00000370976.3_Missense_Mutation_p.F290L|WLS_ENST00000540432.1_Missense_Mutation_p.F381L	NM_024911.6	NP_079187.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	381					anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						ACGATGATGAAGGCCATCTGG	0.527																																					p.F381L		Atlas-SNP	.											.	WLS	97	.	0			c.T1141C						.						86.0	85.0	85.0					1																	68611689		2203	4300	6503	SO:0001583	missense	79971	exon9			TGATGAAGGCCAT	BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"""wntless homolog"""	611514	"""chromosome 1 open reading frame 139"", ""G protein-coupled receptor 177"", ""wntless homolog (Drosophila)"""	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000262348.4:c.1141T>C	chr1.hg19:g.68611689A>G	ENSP00000262348:p.Phe381Leu	100.0	0.0		59.0	4.0	NM_024911	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Missense_Mutation	SNP	ENST00000262348.4	hg19	CCDS642.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.949806	0.73787	.	.	ENSG00000116729	ENST00000540432;ENST00000354777;ENST00000262348;ENST00000370976	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.35335	0.0928	L	0.59436	1.845	0.80722	D	1	B;B;B;B	0.26318	0.146;0.077;0.011;0.146	B;B;B;B	0.30316	0.034;0.114;0.027;0.034	T	0.33854	-0.9852	10	0.52906	T	0.07	-26.0661	15.6915	0.77457	1.0:0.0:0.0:0.0	.	381;290;381;379	F5H4K0;Q5JRS7;Q5T9L3;Q5T9L3-2	.;.;WLS_HUMAN;.	L	381;379;381;290	ENSP00000446112:F381L;ENSP00000346829:F379L;ENSP00000262348:F381L;ENSP00000360015:F290L	ENSP00000262348:F381L	F	-	1	0	WLS	68384277	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.962000	0.93254	2.107000	0.64212	0.533000	0.62120	TTC	.	.		0.527	WLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025368.1	NM_024911	
RABGGTB	5876	hgsc.bcm.edu	37	1	76253187	76253187	+	Silent	SNP	T	T	C	rs542064322		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:76253187T>C	ENST00000319942.3	+	2	80	c.9T>C	c.(7-9)acT>acC	p.T3T	RABGGTB_ENST00000496055.1_3'UTR|RABGGTB_ENST00000535300.1_5'UTR|RABGGTB_ENST00000370826.3_Silent_p.T3T|SNORD45B_ENST00000364617.1_RNA|SNORD45A_ENST00000384512.1_RNA|SNORD45C_ENST00000383893.1_RNA	NM_004582.3	NP_004573.2	P53611	PGTB2_HUMAN	Rab geranylgeranyltransferase, beta subunit	3					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)	19						GAAAGGGCACTCCACAGAAGG	0.383																																					p.T3T		Atlas-SNP	.											.	RABGGTB	37	.	0			c.T9C						.						131.0	118.0	123.0					1																	76253187		2203	4300	6503	SO:0001819	synonymous_variant	5876	exon2			GGGCACTCCACAG	U49245	CCDS669.1	1p31	2008-02-05			ENSG00000137955	ENSG00000137955			9796	protein-coding gene	gene with protein product		179080				8706741, 8954794	Standard	NM_004582		Approved		uc001dgy.2	P53611	OTTHUMG00000009786	ENST00000319942.3:c.9T>C	chr1.hg19:g.76253187T>C		218.0	0.0		122.0	6.0	NM_004582	Q92697	Silent	SNP	ENST00000319942.3	hg19	CCDS669.1																																																																																			.	.		0.383	RABGGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026972.1	NM_004582	
LPHN2	23266	hgsc.bcm.edu	37	1	82409131	82409131	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:82409131T>C	ENST00000370728.1	+	8	1521	c.876T>C	c.(874-876)aaT>aaC	p.N292N	LPHN2_ENST00000319517.6_Silent_p.N292N|LPHN2_ENST00000370723.1_Silent_p.N292N|LPHN2_ENST00000370727.1_Silent_p.N292N|LPHN2_ENST00000370730.1_Silent_p.N292N|LPHN2_ENST00000271029.4_Silent_p.N292N|LPHN2_ENST00000335786.5_Silent_p.N292N|LPHN2_ENST00000359929.3_Silent_p.N292N|LPHN2_ENST00000370717.2_Silent_p.N292N|LPHN2_ENST00000370721.1_Silent_p.N296N|LPHN2_ENST00000370715.1_Silent_p.N292N|LPHN2_ENST00000370713.1_Silent_p.N292N|LPHN2_ENST00000370725.1_Silent_p.N292N|LPHN2_ENST00000394879.1_Silent_p.N292N|LPHN2_ENST00000469377.2_Intron			O95490	LPHN2_HUMAN	latrophilin 2	292	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				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)|latrotoxin receptor activity (GO:0016524)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		GCCAGCTGAATCCATACACTC	0.423																																					p.N292N		Atlas-SNP	.											.	LPHN2	464	.	0			c.T876C						.						134.0	124.0	127.0					1																	82409131		2203	4300	6503	SO:0001819	synonymous_variant	23266	exon5			GCTGAATCCATAC	AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"""-"", ""GPCR / Class B : Orphans"""	18582	protein-coding gene	gene with protein product		607018	"""latrophilin 1"""	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.876T>C	chr1.hg19:g.82409131T>C		143.0	0.0		99.0	4.0	NM_012302	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Silent	SNP	ENST00000370728.1	hg19		.	.	.	.	.	.	.	.	.	.	T	4.305	0.055913	0.08291	.	.	ENSG00000117114	ENST00000449420	.	.	.	5.52	1.84	0.25277	.	.	.	.	.	T	0.40119	0.1104	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24048	-1.0171	4	.	.	.	.	7.3061	0.26449	0.0:0.5143:0.0:0.4857	.	.	.	.	T	160	.	.	I	+	2	0	LPHN2	82181719	0.958000	0.32768	1.000000	0.80357	0.985000	0.73830	0.087000	0.14958	0.347000	0.23924	0.374000	0.22700	ATC	.	.		0.423	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302	
EPHX4	253152	hgsc.bcm.edu	37	1	92528663	92528663	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:92528663G>T	ENST00000370383.4	+	7	1007	c.909G>T	c.(907-909)tgG>tgT	p.W303C		NM_173567.4	NP_775838.3	Q8IUS5	EPHX4_HUMAN	epoxide hydrolase 4	303						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			central_nervous_system(1)|large_intestine(3)|lung(8)	12						TACTACTGTGGGGAGAGAATG	0.393																																					p.W303C	GBM(140;473 1857 5172 22066 49719)	Atlas-SNP	.											.	EPHX4	46	.	0			c.G909T						.						130.0	134.0	133.0					1																	92528663		2203	4300	6503	SO:0001583	missense	253152	exon7			ACTGTGGGGAGAG	AK074822	CCDS736.1	1p22.1	2011-10-05	2009-04-06	2009-04-06	ENSG00000172031	ENSG00000172031		"""Abhydrolase domain containing"""	23758	protein-coding gene	gene with protein product			"""abhydrolase domain containing 7"""	ABHD7		12477932	Standard	NM_173567		Approved	EPHXRP, FLJ90341	uc001don.2	Q8IUS5	OTTHUMG00000010114	ENST00000370383.4:c.909G>T	chr1.hg19:g.92528663G>T	ENSP00000359410:p.Trp303Cys	207.0	0.0		94.0	4.0	NM_173567	Q8NCC6	Missense_Mutation	SNP	ENST00000370383.4	hg19	CCDS736.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.227482	0.79576	.	.	ENSG00000172031	ENST00000370383	T	0.04758	3.56	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.22475	0.0542	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.03259	-1.1055	10	0.49607	T	0.09	.	19.904	0.97001	0.0:0.0:1.0:0.0	.	303	Q8IUS5	EPHX4_HUMAN	C	303	ENSP00000359410:W303C	ENSP00000359410:W303C	W	+	3	0	EPHX4	92301251	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.366000	0.97143	2.698000	0.92095	0.650000	0.86243	TGG	.	.		0.393	EPHX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027985.1	NM_173567	
EPHX4	253152	hgsc.bcm.edu	37	1	92528734	92528734	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:92528734G>T	ENST00000370383.4	+	7	1078	c.980G>T	c.(979-981)aGg>aTg	p.R327M		NM_173567.4	NP_775838.3	Q8IUS5	EPHX4_HUMAN	epoxide hydrolase 4	327						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			central_nervous_system(1)|large_intestine(3)|lung(8)	12						AACTATTTCAGGCTAACTATT	0.388																																					p.R327M	GBM(140;473 1857 5172 22066 49719)	Atlas-SNP	.											.	EPHX4	46	.	0			c.G980T						.						88.0	93.0	91.0					1																	92528734		2203	4300	6503	SO:0001583	missense	253152	exon7			ATTTCAGGCTAAC	AK074822	CCDS736.1	1p22.1	2011-10-05	2009-04-06	2009-04-06	ENSG00000172031	ENSG00000172031		"""Abhydrolase domain containing"""	23758	protein-coding gene	gene with protein product			"""abhydrolase domain containing 7"""	ABHD7		12477932	Standard	NM_173567		Approved	EPHXRP, FLJ90341	uc001don.2	Q8IUS5	OTTHUMG00000010114	ENST00000370383.4:c.980G>T	chr1.hg19:g.92528734G>T	ENSP00000359410:p.Arg327Met	93.0	0.0		80.0	4.0	NM_173567	Q8NCC6	Missense_Mutation	SNP	ENST00000370383.4	hg19	CCDS736.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.199073	0.79015	.	.	ENSG00000172031	ENST00000370383	T	0.70399	-0.48	5.84	5.84	0.93424	.	0.043531	0.85682	D	0.000000	T	0.79221	0.4409	M	0.86268	2.805	0.53688	D	0.999975	P	0.49358	0.923	P	0.56343	0.796	T	0.82234	-0.0558	10	0.72032	D	0.01	.	13.3592	0.60646	0.0719:0.0:0.9281:0.0	.	327	Q8IUS5	EPHX4_HUMAN	M	327	ENSP00000359410:R327M	ENSP00000359410:R327M	R	+	2	0	EPHX4	92301322	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.227000	0.72282	2.756000	0.94617	0.650000	0.86243	AGG	.	.		0.388	EPHX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027985.1	NM_173567	
GLMN	11146	hgsc.bcm.edu	37	1	92713534	92713534	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:92713534T>C	ENST00000370360.3	-	17	1567	c.1486A>G	c.(1486-1488)Aca>Gca	p.T496A	GLMN_ENST00000534881.1_Missense_Mutation_p.T482A	NM_053274.2	NP_444504.1	Q92990	GLMN_HUMAN	glomulin, FKBP associated protein	496					muscle cell differentiation (GO:0042692)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of T cell proliferation (GO:0042130)|neural tube closure (GO:0001843)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of phosphorylation (GO:0042327)|regulation of gene expression, epigenetic (GO:0040029)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|vasculogenesis (GO:0001570)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul3-RING ubiquitin ligase complex (GO:0031463)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cullin-RING ubiquitin ligase complex (GO:0031461)|intracellular (GO:0005622)	hepatocyte growth factor receptor binding (GO:0005171)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase inhibitor activity (GO:0055105)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	17		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)		CCAAGTTCTGTCCATAATCCA	0.294									Multiple Glomus Tumors (of the Skin), Familial																												p.T496A		Atlas-SNP	.											GLMN,NS,carcinoma,+2,1	GLMN	37	.	0			c.A1486G						.						84.0	88.0	87.0					1																	92713534		2202	4290	6492	SO:0001583	missense	11146	exon17	Familial Cancer Database	Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma	GTTCTGTCCATAA	U73704	CCDS738.1	1p22.1	2008-02-05	2004-07-01		ENSG00000174842	ENSG00000174842			14373	protein-coding gene	gene with protein product		601749	"""venous malformation with glomus cells"""	VMGLOM		8955134	Standard	XM_005270400		Approved	FAP48, GLML, GVM, FKBPAP	uc001dor.3	Q92990	OTTHUMG00000010283	ENST00000370360.3:c.1486A>G	chr1.hg19:g.92713534T>C	ENSP00000359385:p.Thr496Ala	158.0	0.0		86.0	4.0	NM_053274	Q5VVC3|Q9BVE8	Missense_Mutation	SNP	ENST00000370360.3	hg19	CCDS738.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.568284	0.86439	.	.	ENSG00000174842	ENST00000370360;ENST00000534881	T;T	0.44482	0.92;0.92	6.17	6.17	0.99709	.	0.043410	0.85682	D	0.000000	T	0.46814	0.1412	L	0.55834	1.745	0.58432	D	0.999997	P;P	0.52463	0.924;0.953	P;P	0.55508	0.777;0.76	T	0.48747	-0.9008	10	0.72032	D	0.01	-13.1409	16.8222	0.85835	0.0:0.0:0.0:1.0	.	482;496	B4DJ85;Q92990	.;GLMN_HUMAN	A	496;482	ENSP00000359385:T496A;ENSP00000440156:T482A	ENSP00000359385:T496A	T	-	1	0	GLMN	92486122	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.378000	0.73150	2.371000	0.80710	0.533000	0.62120	ACA	.	.		0.294	GLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028358.1	NM_007070	
DPYD	1806	hgsc.bcm.edu	37	1	97770913	97770913	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:97770913G>T	ENST00000370192.3	-	18	2301	c.2201C>A	c.(2200-2202)gCc>gAc	p.A734D	DPYD-AS1_ENST00000422980.1_RNA	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	734					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	AGTGTTGGTGGCTGTAACGCC	0.468																																					p.A734D		Atlas-SNP	.											.	DPYD	219	.	0			c.C2201A						.						197.0	167.0	177.0					1																	97770913		2203	4300	6503	SO:0001583	missense	1806	exon18			TTGGTGGCTGTAA	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.2201C>A	chr1.hg19:g.97770913G>T	ENSP00000359211:p.Ala734Asp	156.0	0.0		97.0	5.0	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	hg19	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.035026	0.93575	.	.	ENSG00000188641	ENST00000370192	T	0.75938	-0.98	5.55	5.55	0.83447	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.90573	0.7045	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92729	0.6198	10	0.87932	D	0	-15.1721	19.8696	0.96845	0.0:0.0:1.0:0.0	.	734	Q12882	DPYD_HUMAN	D	734	ENSP00000359211:A734D	ENSP00000359211:A734D	A	-	2	0	DPYD	97543501	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	9.416000	0.97383	2.773000	0.95371	0.585000	0.79938	GCC	.	.		0.468	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
DBT	1629	hgsc.bcm.edu	37	1	100672056	100672056	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:100672056T>C	ENST00000370132.4	-	9	1167	c.1154A>G	c.(1153-1155)cAg>cGg	p.Q385R		NM_001918.3	NP_001909.3	P11182	ODB2_HUMAN	dihydrolipoamide branched chain transacylase E2	385					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity (GO:0043754)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(1)	19		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)		GGTGCTGAGCTGACTCACAGA	0.403																																					p.Q385R		Atlas-SNP	.											.	DBT	39	.	0			c.A1154G						.						185.0	188.0	187.0					1																	100672056		2203	4300	6503	SO:0001583	missense	1629	exon9			CTGAGCTGACTCA	BC016675	CCDS767.1	1p31	2008-02-05	2004-11-15		ENSG00000137992	ENSG00000137992			2698	protein-coding gene	gene with protein product		248610	"""dihydrolipoamide branched chain transacylase (E2 component of branched chain keto acid dehydrogenase complex; maple syrup urine disease)"""			1420314, 1429740	Standard	NM_001918		Approved		uc001dta.3	P11182	OTTHUMG00000010921	ENST00000370132.4:c.1154A>G	chr1.hg19:g.100672056T>C	ENSP00000359151:p.Gln385Arg	140.0	0.0		92.0	4.0	NM_001918	B2R811|Q5VVL8	Missense_Mutation	SNP	ENST00000370132.4	hg19	CCDS767.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.126641	0.56721	.	.	ENSG00000137992	ENST00000543138;ENST00000370132	T	0.40476	1.03	5.54	5.54	0.83059	2-oxoacid dehydrogenase acyltransferase, catalytic domain (1);Chloramphenicol acetyltransferase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.15998	0.0385	N	0.20357	0.565	0.80722	D	1	B;B	0.22211	0.008;0.066	B;B	0.23018	0.014;0.043	T	0.06625	-1.0816	10	0.21014	T	0.42	-11.8926	15.969	0.79998	0.0:0.0:0.0:1.0	.	204;385	F5H1F9;P11182	.;ODB2_HUMAN	R	204;385	ENSP00000359151:Q385R	ENSP00000359151:Q385R	Q	-	2	0	DBT	100444644	1.000000	0.71417	0.965000	0.40720	0.731000	0.41821	7.565000	0.82337	2.234000	0.73211	0.459000	0.35465	CAG	.	.		0.403	DBT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030101.2	NM_001918	
COL11A1	1301	hgsc.bcm.edu	37	1	103491374	103491374	+	Intron	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:103491374T>C	ENST00000370096.3	-	7	1210				COL11A1_ENST00000353414.4_Intron|COL11A1_ENST00000358392.2_Silent_p.K305K|COL11A1_ENST00000512756.1_Intron	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1						cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CTAGTTTGGCTTTTGCTGATG	0.368																																					p.K305K		Atlas-SNP	.											.	COL11A1	972	.	0			c.A915G						.						171.0	165.0	167.0					1																	103491374		2203	4300	6503	SO:0001627	intron_variant	1301	exon6			TTTGGCTTTTGCT	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.898-205A>G	chr1.hg19:g.103491374T>C		214.0	0.0		138.0	6.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.		0.368	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
KIAA1324	57535	hgsc.bcm.edu	37	1	109715162	109715162	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:109715162C>A	ENST00000369939.3	+	5	851	c.668C>A	c.(667-669)aCc>aAc	p.T223N	KIAA1324_ENST00000529753.1_Missense_Mutation_p.T223N	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	223					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		TGGATGAAGACCACAGAGAAA	0.498																																					p.T223N		Atlas-SNP	.											.	KIAA1324	77	.	0			c.C668A						.						78.0	75.0	76.0					1																	109715162		2203	4300	6503	SO:0001583	missense	57535	exon5			TGAAGACCACAGA	AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"""estrogen induced gene 121"""	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.668C>A	chr1.hg19:g.109715162C>A	ENSP00000358955:p.Thr223Asn	236.0	0.0		153.0	63.0	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Missense_Mutation	SNP	ENST00000369939.3	hg19	CCDS794.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.964348	0.74131	.	.	ENSG00000116299	ENST00000369939;ENST00000457623;ENST00000529753	T;T;T	0.42513	0.97;0.97;0.97	5.69	5.69	0.88448	.	0.222920	0.45867	D	0.000330	T	0.27524	0.0676	N	0.11064	0.09	0.24179	N	0.995594	D;D;D;D	0.63880	0.976;0.993;0.976;0.976	P;P;P;P	0.58520	0.84;0.753;0.84;0.794	T	0.19582	-1.0301	10	0.27785	T	0.31	-7.9859	17.586	0.87981	0.0:1.0:0.0:0.0	.	223;223;223;223	Q6UXG2-4;Q6UXG2-3;C9J810;Q6UXG2	.;.;.;K1324_HUMAN	N	223	ENSP00000358955:T223N;ENSP00000393964:T223N;ENSP00000434595:T223N	ENSP00000358955:T223N	T	+	2	0	KIAA1324	109516685	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.872000	0.48467	2.678000	0.91216	0.650000	0.86243	ACC	.	.		0.498	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775	
ATXN7L2	127002	hgsc.bcm.edu	37	1	110031709	110031709	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:110031709T>C	ENST00000369870.3	+	7	1039	c.1024T>C	c.(1024-1026)Tgt>Cgt	p.C342R		NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	342										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		CTACCCATACTGTGCACTGCC	0.622																																					p.C342R		Atlas-SNP	.											.	ATXN7L2	60	.	0			c.T1024C						.						85.0	76.0	79.0					1																	110031709		2203	4300	6503	SO:0001583	missense	127002	exon7			CCATACTGTGCAC	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.1024T>C	chr1.hg19:g.110031709T>C	ENSP00000358886:p.Cys342Arg	128.0	0.0		91.0	4.0	NM_153340		Missense_Mutation	SNP	ENST00000369870.3	hg19	CCDS30794.1	.	.	.	.	.	.	.	.	.	.	T	17.10	3.303442	0.60195	.	.	ENSG00000162650	ENST00000369870;ENST00000541125	T	0.30714	1.52	5.97	4.85	0.62838	.	0.000000	0.64402	D	0.000002	T	0.13114	0.0318	L	0.50333	1.59	0.80722	D	1	B	0.25441	0.126	B	0.20767	0.031	T	0.04870	-1.0921	10	0.27082	T	0.32	-5.2976	9.2673	0.37650	0.0:0.0817:0.0:0.9183	.	342	Q5T6C5	AT7L2_HUMAN	R	342	ENSP00000358886:C342R	ENSP00000358886:C342R	C	+	1	0	ATXN7L2	109833232	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.145000	0.50623	2.288000	0.76882	0.533000	0.62120	TGT	.	.		0.622	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340	
EPS8L3	79574	hgsc.bcm.edu	37	1	110294654	110294654	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:110294654G>A	ENST00000361965.4	-	15	1503	c.1397C>T	c.(1396-1398)cCa>cTa	p.P466L	EPS8L3_ENST00000361852.4_Missense_Mutation_p.P436L|RP4-735C1.4_ENST00000431955.1_RNA|EPS8L3_ENST00000369805.3_Missense_Mutation_p.P467L	NM_133181.3	NP_573444.2	Q8TE67	ES8L3_HUMAN	EPS8-like 3	466	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.					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)		CAGTTCCCGTGGGTTCCTAGC	0.597																																					p.P467L		Atlas-SNP	.											.	EPS8L3	73	.	0			c.C1400T						.						105.0	106.0	105.0					1																	110294654		2203	4300	6503	SO:0001583	missense	79574	exon15			TCCCGTGGGTTCC	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.1397C>T	chr1.hg19:g.110294654G>A	ENSP00000355255:p.Pro466Leu	236.0	0.0		186.0	75.0	NM_139053	A8K833|Q5T8Q6|Q5T8Q7|Q5T8Q8|Q96E47|Q9H719	Missense_Mutation	SNP	ENST00000361965.4	hg19	CCDS814.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.872393	0.51695	.	.	ENSG00000198758	ENST00000361852;ENST00000369805;ENST00000361965	T;T;T	0.33216	1.42;1.42;1.42	5.57	4.64	0.57946	Src homology-3 domain (4);	0.852789	0.10775	N	0.635539	T	0.28995	0.0720	M	0.85299	2.745	0.35830	D	0.825258	P;B;P	0.42296	0.666;0.434;0.775	B;B;B	0.42282	0.23;0.242;0.382	T	0.25950	-1.0117	10	0.44086	T	0.13	-0.0164	11.7056	0.51595	0.0:0.0:0.8235:0.1765	.	436;466;467	Q8TE67-2;Q8TE67;Q8TE67-3	.;ES8L3_HUMAN;.	L	436;467;466	ENSP00000354551:P436L;ENSP00000358820:P467L;ENSP00000355255:P466L	ENSP00000354551:P436L	P	-	2	0	EPS8L3	110096177	0.114000	0.22134	0.814000	0.32528	0.820000	0.46376	1.671000	0.37513	1.318000	0.45170	0.655000	0.94253	CCA	.	.		0.597	EPS8L3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032234.1	NM_024526	
CHIA	27159	hgsc.bcm.edu	37	1	111862847	111862847	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:111862847C>T	ENST00000369740.1	+	12	1293	c.1190C>T	c.(1189-1191)cCa>cTa	p.P397L	CHIA_ENST00000343320.6_Missense_Mutation_p.P397L|CHIA_ENST00000451398.2_Missense_Mutation_p.P236L|CHIA_ENST00000483391.1_Missense_Mutation_p.P236L|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000430615.1_Missense_Mutation_p.P289L|CHIA_ENST00000353665.6_Missense_Mutation_p.P236L	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	397					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TGCACGGCTCCAGCTCAGCCC	0.572																																					p.P397L		Atlas-SNP	.											.	CHIA	115	.	0			c.C1190T						.						67.0	67.0	67.0					1																	111862847		2203	4300	6503	SO:0001583	missense	27159	exon12			CGGCTCCAGCTCA	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.1190C>T	chr1.hg19:g.111862847C>T	ENSP00000358755:p.Pro397Leu	104.0	0.0		82.0	4.0	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	hg19	CCDS41368.1	.	.	.	.	.	.	.	.	.	.	C	13.88	2.370086	0.42003	.	.	ENSG00000134216	ENST00000422815;ENST00000483391;ENST00000369740;ENST00000343320;ENST00000451398;ENST00000353665;ENST00000489524;ENST00000430615	T;T;T;T;T;T;T;T	0.06068	4.05;3.69;3.35;3.35;3.69;3.69;3.48;3.9	5.07	5.07	0.68467	.	1.360170	0.06346	U	0.708911	T	0.05823	0.0152	M	0.71036	2.16	0.22684	N	0.998854	B	0.33000	0.393	B	0.29862	0.108	T	0.21930	-1.0231	10	0.59425	D	0.04	-1.3337	15.9825	0.80121	0.0:1.0:0.0:0.0	.	397	Q9BZP6	CHIA_HUMAN	L	341;236;397;397;236;236;236;289	ENSP00000387671:P341L;ENSP00000436946:P236L;ENSP00000358755:P397L;ENSP00000341828:P397L;ENSP00000390476:P236L;ENSP00000338970:P236L;ENSP00000433309:P236L;ENSP00000391132:P289L	ENSP00000341828:P397L	P	+	2	0	CHIA	111664370	0.000000	0.05858	0.005000	0.12908	0.049000	0.14656	0.622000	0.24433	2.628000	0.89032	0.655000	0.94253	CCA	.	.		0.572	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
ATP5F1	515	hgsc.bcm.edu	37	1	111998810	111998810	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:111998810T>C	ENST00000369722.3	+	4	932	c.326T>C	c.(325-327)aTg>aCg	p.M109T	ATP5F1_ENST00000483994.1_Missense_Mutation_p.M48T|ATP5F1_ENST00000369721.4_3'UTR	NM_001688.4	NP_001679.2	P24539	AT5F1_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit B1	109					ATP catabolic process (GO:0006200)|ATP synthesis coupled proton transport (GO:0015986)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	8		all_cancers(81;8.16e-06)|all_epithelial(167;5.63e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		CTAGGTGTAATGGTCTATGGA	0.378																																					p.M109T		Atlas-SNP	.											.	ATP5F1	20	.	0			c.T326C						.						143.0	143.0	143.0					1																	111998810		2203	4297	6500	SO:0001583	missense	515	exon4			GTGTAATGGTCTA	X60221	CCDS836.1	1p13.2	2012-10-12	2010-06-11		ENSG00000116459	ENSG00000116459		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	840	protein-coding gene	gene with protein product		603270	"""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit b, isoform 1"", ""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit B1"""			1831354	Standard	XM_005270929		Approved		uc001ebc.3	P24539	OTTHUMG00000011745	ENST00000369722.3:c.326T>C	chr1.hg19:g.111998810T>C	ENSP00000358737:p.Met109Thr	113.0	0.0		90.0	4.0	NM_001688	Q9BQ68|Q9BRU8	Missense_Mutation	SNP	ENST00000369722.3	hg19	CCDS836.1	.	.	.	.	.	.	.	.	.	.	T	6.407	0.443303	0.12164	.	.	ENSG00000116459	ENST00000369722;ENST00000483994	T;T	0.28069	1.63;1.63	5.37	4.23	0.50019	.	0.431403	0.27420	N	0.019450	T	0.08758	0.0217	L	0.29908	0.895	0.23762	N	0.996912	B;B	0.15473	0.013;0.013	B;B	0.18561	0.022;0.022	T	0.25152	-1.0140	9	.	.	.	.	11.699	0.51560	0.1327:0.0:0.0:0.8673	.	109;109	Q08ET0;P24539	.;AT5F1_HUMAN	T	109;48	ENSP00000358737:M109T;ENSP00000420366:M48T	.	M	+	2	0	ATP5F1	111800333	0.864000	0.29904	0.003000	0.11579	0.000000	0.00434	5.684000	0.68197	0.964000	0.38108	-0.301000	0.09380	ATG	.	.		0.378	ATP5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032455.1	NM_001688	
TTF2	8458	hgsc.bcm.edu	37	1	117641477	117641477	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:117641477G>T	ENST00000369466.4	+	22	3336	c.3292G>T	c.(3292-3294)Gct>Tct	p.A1098S	TTF2_ENST00000480701.1_3'UTR	NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	1098	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		TGAAGATCAAGCTTGTGACCG	0.453																																					p.A1098S		Atlas-SNP	.											.	TTF2	92	.	0			c.G3292T						.						148.0	136.0	140.0					1																	117641477		2203	4300	6503	SO:0001583	missense	8458	exon22			GATCAAGCTTGTG	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 6"""	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.3292G>T	chr1.hg19:g.117641477G>T	ENSP00000358478:p.Ala1098Ser	124.0	0.0		81.0	4.0	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	hg19	CCDS892.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.034997	0.93575	.	.	ENSG00000116830	ENST00000369466;ENST00000427271	T;T	0.74209	-0.82;-0.82	5.22	5.22	0.72569	Helicase, C-terminal (3);	0.000000	0.37809	N	0.001922	D	0.85944	0.5815	M	0.88377	2.95	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85642	0.1277	10	0.38643	T	0.18	-15.5364	16.6163	0.84917	0.0:0.0:1.0:0.0	.	1098	Q9UNY4	TTF2_HUMAN	S	1098;79	ENSP00000358478:A1098S;ENSP00000408111:A79S	ENSP00000358478:A1098S	A	+	1	0	TTF2	117443000	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.301000	0.96167	2.594000	0.87642	0.462000	0.41574	GCT	.	.		0.453	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3		
POLR3C	10623	hgsc.bcm.edu	37	1	145598543	145598543	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:145598543T>C	ENST00000334163.3	-	8	1110	c.950A>G	c.(949-951)gAt>gGt	p.D317G	POLR3C_ENST00000471254.1_5'UTR|POLR3C_ENST00000369294.1_Missense_Mutation_p.D317G	NM_006468.6	NP_006459.3	Q9BUI4	RPC3_HUMAN	polymerase (RNA) III (DNA directed) polypeptide C (62kD)	317					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		Epithelial(2;7.55e-13)			TACTGGATCATCTGCCAGCAG	0.388																																					p.D317G		Atlas-SNP	.											.	POLR3C	41	.	0			c.A950G						.						137.0	135.0	136.0					1																	145598543		2203	4300	6503	SO:0001583	missense	10623	exon8			GGATCATCTGCCA	AJ238234	CCDS72864.1	1q21	2013-01-21			ENSG00000186141	ENSG00000186141		"""RNA polymerase subunits"""	30076	protein-coding gene	gene with protein product						9171375, 12391170	Standard	NM_006468		Approved	RPC62, RPC3	uc001eoh.3	Q9BUI4	OTTHUMG00000013753	ENST00000334163.3:c.950A>G	chr1.hg19:g.145598543T>C	ENSP00000334564:p.Asp317Gly	90.0	0.0		69.0	4.0	NM_006468	O15317|Q9Y3R6	Missense_Mutation	SNP	ENST00000334163.3	hg19	CCDS921.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.538596	0.85917	.	.	ENSG00000186141	ENST00000334163;ENST00000369294	T;T	0.48522	0.81;0.81	6.17	6.17	0.99709	RNA polymerase III Rpc82, C -terminal (1);	0.090873	0.85682	D	0.000000	T	0.49677	0.1571	M	0.63843	1.955	0.80722	D	1	P;P;P	0.51449	0.637;0.934;0.945	P;P;P	0.57468	0.458;0.725;0.821	T	0.47560	-0.9108	10	0.31617	T	0.26	-21.036	13.214	0.59844	0.0:0.0:0.0:1.0	.	317;317;317	E9PHH9;Q9BUI4;Q53F76	.;RPC3_HUMAN;.	G	317	ENSP00000334564:D317G;ENSP00000358300:D317G	ENSP00000334564:D317G	D	-	2	0	POLR3C	144309900	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.085000	0.76875	2.371000	0.80710	0.533000	0.62120	GAT	.	.		0.388	POLR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038542.1	NM_006468	
ILF2	3608	hgsc.bcm.edu	37	1	153635509	153635509	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:153635509T>C	ENST00000361891.4	-	12	1032	c.907A>G	c.(907-909)Acc>Gcc	p.T303A	ILF2_ENST00000480213.1_5'UTR	NM_001267809.1|NM_004515.3	NP_001254738.1|NP_004506.2	Q12905	ILF2_HUMAN	interleukin enhancer binding factor 2	303	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				immune response (GO:0006955)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)			cervix(1)|kidney(1)|lung(4)|skin(1)	7	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGTTCTAGGGTCATGACTGTG	0.498																																					p.T303A		Atlas-SNP	.											.	ILF2	25	.	0			c.A907G						.						88.0	85.0	86.0					1																	153635509		2203	4300	6503	SO:0001583	missense	3608	exon12			CTAGGGTCATGAC	U10323	CCDS1050.1, CCDS72919.1	1q21.3	2012-12-04	2012-12-04		ENSG00000143621	ENSG00000143621			6037	protein-coding gene	gene with protein product		603181	"""interleukin enhancer binding factor 2, 45kD"", ""interleukin enhancer binding factor 2, 45kDa"""			7519613	Standard	NM_004515		Approved	NF45	uc001fcr.4	Q12905	OTTHUMG00000037087	ENST00000361891.4:c.907A>G	chr1.hg19:g.153635509T>C	ENSP00000355011:p.Thr303Ala	162.0	0.0		122.0	5.0	NM_004515	A6NDB0|B2R8G7|Q5SR10|Q5SR11|Q7L7R3|Q9BWD4|Q9P1N0	Missense_Mutation	SNP	ENST00000361891.4	hg19	CCDS1050.1	.	.	.	.	.	.	.	.	.	.	T	18.70	3.680666	0.68042	.	.	ENSG00000143621	ENST00000361891	T	0.50548	0.74	5.28	5.28	0.74379	DZF (2);	0.044922	0.85682	D	0.000000	T	0.50650	0.1628	M	0.85630	2.765	0.80722	D	1	B;B	0.33528	0.363;0.416	B;B	0.43990	0.311;0.438	T	0.60845	-0.7182	10	0.72032	D	0.01	-12.3981	11.5378	0.50648	0.0:0.0:0.0:1.0	.	303;303	F4ZW62;Q12905	.;ILF2_HUMAN	A	303	ENSP00000355011:T303A	ENSP00000355011:T303A	T	-	1	0	ILF2	151902133	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.160000	0.64929	2.225000	0.72522	0.533000	0.62120	ACC	.	.		0.498	ILF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090040.1	NM_004515	
DENND4B	9909	hgsc.bcm.edu	37	1	153903522	153903522	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:153903522T>C	ENST00000361217.4	-	25	4433	c.4015A>G	c.(4015-4017)Acc>Gcc	p.T1339A	DENND4B_ENST00000474386.1_5'UTR	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	1339					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)			GGATCAGGGGTTAGCCAAGGA	0.572																																					p.T1339A		Atlas-SNP	.											.	DENND4B	210	.	0			c.A4015G						.						26.0	30.0	29.0					1																	153903522		2004	4169	6173	SO:0001583	missense	9909	exon25			CAGGGGTTAGCCA	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.4015A>G	chr1.hg19:g.153903522T>C	ENSP00000354597:p.Thr1339Ala	110.0	0.0		70.0	4.0	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	T	7.862	0.726343	0.15439	.	.	ENSG00000198837	ENST00000361217	T	0.06068	3.35	5.14	2.77	0.32553	.	0.689341	0.13633	N	0.373562	T	0.00875	0.0029	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.48364	-0.9042	10	0.40728	T	0.16	-2.4136	5.4973	0.16809	0.0:0.1716:0.1604:0.6679	.	1339	O75064	DEN4B_HUMAN	A	1339	ENSP00000354597:T1339A	ENSP00000354597:T1339A	T	-	1	0	DENND4B	152170146	0.001000	0.12720	0.007000	0.13788	0.804000	0.45430	-0.031000	0.12287	0.974000	0.38366	0.455000	0.32223	ACC	.	.		0.572	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	
SLC39A1	27173	hgsc.bcm.edu	37	1	153935029	153935029	+	Missense_Mutation	SNP	G	G	A	rs3211049		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:153935029G>A	ENST00000368623.3	-	1	922	c.163C>T	c.(163-165)Cca>Tca	p.P55S	SLC39A1_ENST00000368621.1_Missense_Mutation_p.P55S|SLC39A1_ENST00000537590.1_5'UTR|SLC39A1_ENST00000310483.6_Missense_Mutation_p.P55S|SLC39A1_ENST00000461071.1_5'UTR|SLC39A1_ENST00000356205.4_Missense_Mutation_p.P55S			Q9NY26	S39A1_HUMAN	solute carrier family 39 (zinc transporter), member 1	55				P -> T (in Ref. 1; CAB59979/CAB59980). {ECO:0000305}.	cation transport (GO:0006812)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic cation transmembrane transporter activity (GO:0022890)|zinc ion transmembrane transporter activity (GO:0005385)			kidney(2)|large_intestine(2)|lung(7)|urinary_tract(1)	12	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)	Colorectal(1306;0.019)		TTAGCTCCTGGCCGGCGCAGC	0.632																																					p.P55S		Atlas-SNP	.											.	SLC39A1	24	.	0			c.C163T						.						37.0	44.0	41.0					1																	153935029		2203	4300	6503	SO:0001583	missense	27173	exon2			CTCCTGGCCGGCG	BC007886	CCDS1055.1, CCDS72920.1	1q21	2013-05-22		2002-02-15	ENSG00000143570	ENSG00000143570		"""Solute carriers"""	12876	protein-coding gene	gene with protein product		604740	"""zinc/iron regulated transporter-like"""	ZIRTL		10610721, 10681536	Standard	NM_014437		Approved	ZIP1	uc031ppi.1	Q9NY26	OTTHUMG00000037158	ENST00000368623.3:c.163C>T	chr1.hg19:g.153935029G>A	ENSP00000357612:p.Pro55Ser	179.0	0.0		118.0	5.0	NM_001271957	B4DDY7|Q5T4K1|Q8N2H7|Q9BTV0|Q9UBI7|Q9Y2Z7|Q9Y380	Missense_Mutation	SNP	ENST00000368623.3	hg19	CCDS1055.1	.	.	.	.	.	.	.	.	.	.	G	1.547	-0.540142	0.04053	.	.	ENSG00000143570	ENST00000356205;ENST00000368623;ENST00000368621;ENST00000310483;ENST00000543075;ENST00000429040;ENST00000413622;ENST00000417348	T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96	5.64	-0.156	0.13391	.	0.369343	0.24506	N	0.037935	T	0.06050	0.0157	N	0.12746	0.255	0.23816	N	0.996769	B	0.02656	0.0	B	0.12156	0.007	T	0.36866	-0.9730	10	0.20046	T	0.44	-2.6953	3.6124	0.08065	0.0792:0.2628:0.389:0.269	.	55	Q9NY26	S39A1_HUMAN	S	55;55;55;55;44;55;55;55	ENSP00000348535:P55S;ENSP00000357612:P55S;ENSP00000357610:P55S;ENSP00000309710:P55S;ENSP00000392950:P55S;ENSP00000392229:P55S;ENSP00000407717:P55S	ENSP00000309710:P55S	P	-	1	0	SLC39A1	152201653	0.000000	0.05858	0.283000	0.24790	0.287000	0.27160	-0.205000	0.09411	0.004000	0.14682	0.655000	0.94253	CCA	.	.		0.632	SLC39A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090284.1	NM_014437	
CREB3L4	148327	hgsc.bcm.edu	37	1	153945673	153945673	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:153945673T>C	ENST00000368607.3	+	7	1012	c.746T>C	c.(745-747)gTg>gCg	p.V249A	CREB3L4_ENST00000271889.4_Missense_Mutation_p.V249A|JTB_ENST00000471173.1_5'Flank|CREB3L4_ENST00000368600.3_Missense_Mutation_p.V229A|CREB3L4_ENST00000405694.3_Missense_Mutation_p.V102A|CREB3L4_ENST00000368603.1_Missense_Mutation_p.V249A|CREB3L4_ENST00000468845.1_3'UTR	NM_001255978.1|NM_001255980.1|NM_130898.3	NP_001242907.1|NP_001242909.1|NP_570968.1	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like 4	249	bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(3)	13	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CATTCTAGGGTGGCAGCCTGT	0.512																																					p.V249A		Atlas-SNP	.											.	CREB3L4	36	.	0			c.T746C						.						63.0	64.0	63.0					1																	153945673		2203	4300	6503	SO:0001583	missense	148327	exon7			CTAGGGTGGCAGC	AF394167	CCDS1056.1, CCDS58029.1	1q21.2	2013-01-10			ENSG00000143578	ENSG00000143578		"""basic leucine zipper proteins"""	18854	protein-coding gene	gene with protein product		607138					Standard	NM_130898		Approved	AIbZIP, CREB4, CREB3, hJAL, ATCE1	uc001fdr.3	Q8TEY5	OTTHUMG00000037159	ENST00000368607.3:c.746T>C	chr1.hg19:g.153945673T>C	ENSP00000357596:p.Val249Ala	124.0	0.0		100.0	4.0	NM_001255978	D3DV62|Q5T4L0|Q86YW6	Missense_Mutation	SNP	ENST00000368607.3	hg19	CCDS1056.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.738148	0.49045	.	.	ENSG00000143578	ENST00000405694;ENST00000368607;ENST00000271889;ENST00000368603;ENST00000368600	T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21	5.26	4.13	0.48395	Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1);	0.242965	0.32671	N	0.005787	T	0.27967	0.0689	L	0.35542	1.07	0.41438	D	0.987902	B;B	0.32409	0.046;0.37	B;B	0.30316	0.068;0.114	T	0.20907	-1.0261	10	0.59425	D	0.04	-12.8755	9.3244	0.37984	0.0:0.0849:0.0:0.9151	.	229;249	Q5T4L0;Q8TEY5	.;CR3L4_HUMAN	A	102;249;249;249;229	ENSP00000385104:V102A;ENSP00000357596:V249A;ENSP00000271889:V249A;ENSP00000357592:V249A;ENSP00000357589:V229A	ENSP00000271889:V249A	V	+	2	0	CREB3L4	152212297	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.545000	0.36169	1.008000	0.39264	0.533000	0.62120	GTG	.	.		0.512	CREB3L4-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090291.1	NM_130898	
UBAP2L	9898	hgsc.bcm.edu	37	1	154218760	154218760	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:154218760C>A	ENST00000361546.2	+	10	965	c.923C>A	c.(922-924)cCt>cAt	p.P308H	UBAP2L_ENST00000271877.7_Missense_Mutation_p.P319H|UBAP2L_ENST00000343815.6_Missense_Mutation_p.P308H|UBAP2L_ENST00000428931.1_Missense_Mutation_p.P308H			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	308					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|prostate(1)|urinary_tract(2)	50	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TCTCAGGCTCCTTCTCTGGCC	0.488																																					p.P308H		Atlas-SNP	.											.	UBAP2L	197	.	0			c.C923A						.						129.0	124.0	125.0					1																	154218760		2203	4300	6503	SO:0001583	missense	9898	exon11			AGGCTCCTTCTCT	BC003170	CCDS1063.1, CCDS44229.1, CCDS72925.1	1q21.3	2008-02-05			ENSG00000143569	ENSG00000143569			29877	protein-coding gene	gene with protein product						8590280, 11230159	Standard	NM_014847		Approved	NICE-4, KIAA0144	uc001fep.4	Q14157	OTTHUMG00000035983	ENST00000361546.2:c.923C>A	chr1.hg19:g.154218760C>A	ENSP00000355343:p.Pro308His	114.0	0.0		78.0	4.0	NM_001127320	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	hg19	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.855341	0.71719	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000271877;ENST00000368504;ENST00000361546	T;T;T;T;T	0.44083	2.71;2.72;2.73;0.93;2.72	5.29	5.29	0.74685	.	0.116551	0.64402	D	0.000014	T	0.29389	0.0732	N	0.08118	0	0.32691	N	0.514171	P;D;P;P;P	0.69078	0.838;0.997;0.899;0.899;0.838	B;D;P;P;B	0.66716	0.276;0.946;0.466;0.466;0.364	T	0.33189	-0.9878	10	0.56958	D	0.05	-9.7163	11.5156	0.50520	0.0:0.9194:0.0:0.0806	.	222;319;301;308;308	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	H	308;308;319;319;308	ENSP00000345308:P308H;ENSP00000389445:P308H;ENSP00000271877:P319H;ENSP00000357490:P319H;ENSP00000355343:P308H	ENSP00000271877:P319H	P	+	2	0	UBAP2L	152485384	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.331000	0.59273	2.752000	0.94435	0.655000	0.94253	CCT	.	.		0.488	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847	
ATP8B2	57198	hgsc.bcm.edu	37	1	154317184	154317184	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:154317184C>A	ENST00000368489.3	+	21	2308	c.2308C>A	c.(2308-2310)Ctt>Att	p.L770I		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	756					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	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)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TCAGGACAAGCTTTCTTCTTC	0.532											OREG0013835	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L770I		Atlas-SNP	.											.	ATP8B2	158	.	0			c.C2308A						.						146.0	136.0	139.0					1																	154317184		2203	4300	6503	SO:0001583	missense	57198	exon21			GACAAGCTTTCTT	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"""ATPases / P-type"""	13534	protein-coding gene	gene with protein product		605867	"""ATPase, class I, type 8B, member 2"""			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.2308C>A	chr1.hg19:g.154317184C>A	ENSP00000357475:p.Leu770Ile	100.0	0.0	1762	76.0	4.0	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	hg19	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	C	5.724	0.318030	0.10845	.	.	ENSG00000143515	ENST00000368489	T	0.09817	2.94	5.62	2.52	0.30459	.	1.074510	0.07109	N	0.841811	T	0.02304	0.0071	N	0.11892	0.195	0.19575	N	0.999964	B	0.28470	0.213	B	0.29862	0.108	T	0.47911	-0.9080	10	0.31617	T	0.26	.	10.7602	0.46259	0.1356:0.474:0.3904:0.0	.	770	P98198-3	.	I	770	ENSP00000357475:L770I	ENSP00000357475:L770I	L	+	1	0	ATP8B2	152583808	0.000000	0.05858	0.003000	0.11579	0.257000	0.26127	0.640000	0.24705	0.694000	0.31654	0.591000	0.81541	CTT	.	.		0.532	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452	
IL6R	3570	hgsc.bcm.edu	37	1	154437808	154437808	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:154437808A>G	ENST00000368485.3	+	10	1796	c.1359A>G	c.(1357-1359)ccA>ccG	p.P453P	IL6R_ENST00000344086.4_3'UTR	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	453					acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)		IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	CCAGGGACCCACGGAGCCCTT	0.582																																					p.P453P		Atlas-SNP	.											.	IL6R	47	.	0			c.A1359G						.						67.0	70.0	69.0					1																	154437808		2203	4300	6503	SO:0001819	synonymous_variant	3570	exon10			GGACCCACGGAGC	X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6019	protein-coding gene	gene with protein product		147880					Standard	NM_000565		Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.1359A>G	chr1.hg19:g.154437808A>G		197.0	0.0		105.0	5.0	NM_000565	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	Silent	SNP	ENST00000368485.3	hg19	CCDS1067.1																																																																																			.	.		0.582	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087911.1	NM_000565	
TDRD10	126668	hgsc.bcm.edu	37	1	154515291	154515291	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:154515291A>G	ENST00000368480.3	+	8	582	c.497A>G	c.(496-498)gAa>gGa	p.E166G	TDRD10_ENST00000479937.1_3'UTR|TDRD10_ENST00000368482.4_Missense_Mutation_p.E166G			Q5VZ19	TDR10_HUMAN	tudor domain containing 10	166							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	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)			GTCCCGTTGGAAATGAGGTGA	0.512																																					p.E166G		Atlas-SNP	.											.	TDRD10	48	.	0			c.A497G						.						83.0	74.0	77.0					1																	154515291		2203	4300	6503	SO:0001583	missense	126668	exon8			CGTTGGAAATGAG	AL713777	CCDS30878.2, CCDS41406.1	1q21.3	2013-02-12			ENSG00000163239	ENSG00000163239		"""Tudor domain containing"", ""RNA binding motif (RRM) containing"""	25316	protein-coding gene	gene with protein product						12975309	Standard	NM_182499		Approved	DKFZp434M202	uc009wow.3	Q5VZ19	OTTHUMG00000037264	ENST00000368480.3:c.497A>G	chr1.hg19:g.154515291A>G	ENSP00000357465:p.Glu166Gly	166.0	0.0		93.0	4.0	NM_182499	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Missense_Mutation	SNP	ENST00000368480.3	hg19	CCDS41406.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.801146	0.50315	.	.	ENSG00000163239	ENST00000368482;ENST00000368480	T;T	0.38240	1.19;1.15	3.27	3.27	0.37495	.	0.000000	0.36002	U	0.002843	T	0.14313	0.0346	L	0.32530	0.975	0.23862	N	0.996631	P;P	0.48694	0.914;0.801	B;P	0.45558	0.404;0.485	T	0.03384	-1.1042	10	0.37606	T	0.19	-6.3717	7.9501	0.30010	1.0:0.0:0.0:0.0	.	166;166	Q5VZ19;Q5VZ19-2	TDR10_HUMAN;.	G	166	ENSP00000357467:E166G;ENSP00000357465:E166G	ENSP00000357465:E166G	E	+	2	0	TDRD10	152781915	0.998000	0.40836	0.959000	0.39883	0.861000	0.49209	1.022000	0.30052	1.375000	0.46248	0.369000	0.22263	GAA	.	.		0.512	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499	
DCST2	127579	hgsc.bcm.edu	37	1	155005955	155005955	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:155005955G>T	ENST00000368424.3	-	1	281	c.223C>A	c.(223-225)Cag>Aag	p.Q75K	DCST1_ENST00000368419.2_5'Flank|DCST1_ENST00000392480.1_5'Flank|DCST1_ENST00000295542.1_5'Flank|DCST2_ENST00000295536.5_Missense_Mutation_p.Q75K|DCST1_ENST00000423025.2_5'Flank	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	75						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|prostate(1)|skin(1)	38	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GCTCGGACCTGGCGAGAGAAT	0.657																																					p.Q75K		Atlas-SNP	.											.	DCST2	80	.	0			c.C223A						.						48.0	46.0	47.0					1																	155005955		2203	4300	6503	SO:0001583	missense	127579	exon1			GGACCTGGCGAGA	AK057496	CCDS1082.2	1q22	2008-02-05		2005-08-09	ENSG00000163354	ENSG00000163354			26562	protein-coding gene	gene with protein product							Standard	NM_144622		Approved	FLJ32934	uc001fgm.3	Q5T1A1	OTTHUMG00000037371	ENST00000368424.3:c.223C>A	chr1.hg19:g.155005955G>T	ENSP00000357409:p.Gln75Lys	173.0	0.0		88.0	5.0	NM_144622	Q2M2R2|Q8N810|Q96M03	Missense_Mutation	SNP	ENST00000368424.3	hg19	CCDS1082.2	.	.	.	.	.	.	.	.	.	.	G	8.969	0.972544	0.18736	.	.	ENSG00000163354	ENST00000368424;ENST00000295536	T;T	0.23552	1.9;1.93	5.44	4.33	0.51752	.	0.968381	0.08463	N	0.942162	T	0.05686	0.0149	L	0.38175	1.15	0.20403	N	0.99991	B	0.19331	0.035	B	0.14023	0.01	T	0.43065	-0.9414	10	0.02654	T	1	-31.6972	7.057	0.25106	0.0995:0.0:0.7252:0.1753	.	75	Q5T1A1	DCST2_HUMAN	K	75	ENSP00000357409:Q75K;ENSP00000295536:Q75K	ENSP00000295536:Q75K	Q	-	1	0	DCST2	153272579	0.870000	0.30015	1.000000	0.80357	0.867000	0.49689	2.247000	0.43151	2.564000	0.86499	0.561000	0.74099	CAG	.	.		0.657	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622	
ARHGEF2	9181	hgsc.bcm.edu	37	1	155927648	155927648	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:155927648T>C	ENST00000361247.4	-	13	1670	c.1571A>G	c.(1570-1572)cAg>cGg	p.Q524R	ARHGEF2_ENST00000313695.7_Missense_Mutation_p.Q496R|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.Q523R|ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.Q525R|ARHGEF2_ENST00000462460.2_Missense_Mutation_p.Q569R|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.Q496R	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	524	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					GATTAGATTCTGCAGCGATAC	0.522																																					p.Q524R	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.A1571G						.						89.0	64.0	72.0					1																	155927648		2203	4300	6503	SO:0001583	missense	9181	exon13			AGATTCTGCAGCG	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	682	protein-coding gene	gene with protein product		607560	"""rho/rac guanine nucleotide exchange factor (GEF) 2"""			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.1571A>G	chr1.hg19:g.155927648T>C	ENSP00000354837:p.Gln524Arg	131.0	0.0		101.0	5.0	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	hg19	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.579088	0.86645	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000313667	T;T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93;-0.93	5.28	5.28	0.74379	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.45606	D	0.000343	T	0.74884	0.3775	L	0.55834	1.745	0.49389	D	0.999789	P;D;P	0.57257	0.883;0.979;0.858	P;P;P	0.57846	0.771;0.828;0.535	T	0.78677	-0.2111	10	0.66056	D	0.02	-39.65	13.1991	0.59756	0.0:0.0:0.0:1.0	.	568;524;523	D3DVA5;Q92974;Q92974-2	.;ARHG2_HUMAN;.	R	496;524;525;496;523	ENSP00000315325:Q496R;ENSP00000354837:Q524R;ENSP00000357298:Q525R;ENSP00000357299:Q496R;ENSP00000314787:Q523R	ENSP00000314787:Q523R	Q	-	2	0	ARHGEF2	154194272	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.632000	0.54287	2.213000	0.71641	0.528000	0.53228	CAG	.	.		0.522	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723	
INSRR	3645	hgsc.bcm.edu	37	1	156813015	156813015	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:156813015A>G	ENST00000368195.3	-	17	3303	c.2907T>C	c.(2905-2907)ccT>ccC	p.P969P	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	969					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)					CCCATTCATCAGGGACATACA	0.572																																					p.P969P		Atlas-SNP	.											.	INSRR	309	.	0			c.T2907C						.						56.0	50.0	52.0					1																	156813015		2203	4300	6503	SO:0001819	synonymous_variant	3645	exon17			TTCATCAGGGACA	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.2907T>C	chr1.hg19:g.156813015A>G		131.0	0.0		75.0	4.0	NM_014215	O60724|Q5VZS3	Silent	SNP	ENST00000368195.3	hg19	CCDS1160.1																																																																																			.	.		0.572	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215	
PEAR1	375033	hgsc.bcm.edu	37	1	156879570	156879570	+	Missense_Mutation	SNP	C	C	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:156879570C>G	ENST00000338302.3	+	13	1664	c.1439C>G	c.(1438-1440)cCc>cGc	p.P480R	PEAR1_ENST00000292357.7_Missense_Mutation_p.P480R			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	480					recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					TGCTCTGTGCCCTGCCCACCC	0.627																																					p.P480R		Atlas-SNP	.											.	PEAR1	118	.	0			c.C1439G						.						55.0	52.0	53.0					1																	156879570		2203	4300	6503	SO:0001583	missense	375033	exon12			CTGTGCCCTGCCC	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.1439C>G	chr1.hg19:g.156879570C>G	ENSP00000344465:p.Pro480Arg	105.0	0.0		82.0	4.0	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	hg19	CCDS30892.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.184356	0.78677	.	.	ENSG00000187800	ENST00000338302;ENST00000292357	D;D	0.85955	-2.05;-2.05	5.16	5.16	0.70880	EGF-like region, conserved site (1);	0.135578	0.34245	N	0.004137	T	0.74809	0.3765	N	0.05574	-0.02	0.47441	D	0.999423	D	0.59767	0.986	P	0.58454	0.839	T	0.74731	-0.3566	10	0.17832	T	0.49	.	16.1843	0.81939	0.0:1.0:0.0:0.0	.	480	Q5VY43	PEAR1_HUMAN	R	480	ENSP00000344465:P480R;ENSP00000292357:P480R	ENSP00000292357:P480R	P	+	2	0	PEAR1	155146194	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.575000	0.67430	2.679000	0.91253	0.561000	0.74099	CCC	.	.		0.627	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
OR6K2	81448	hgsc.bcm.edu	37	1	158670333	158670333	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:158670333A>G	ENST00000359610.2	-	1	153	c.110T>C	c.(109-111)tTc>tCc	p.F37S		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	37						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					AACAACAATGAAAGCATAGAT	0.443																																					p.F37S		Atlas-SNP	.											.	OR6K2	104	.	0			c.T110C						.						110.0	107.0	108.0					1																	158670333		2203	4300	6503	SO:0001583	missense	81448	exon1			ACAATGAAAGCAT	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"""GPCR / Class A : Olfactory receptors"""	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.110T>C	chr1.hg19:g.158670333A>G	ENSP00000352626:p.Phe37Ser	132.0	0.0		87.0	5.0	NM_001005279	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	hg19	CCDS30902.1	.	.	.	.	.	.	.	.	.	.	A	12.07	1.827340	0.32329	.	.	ENSG00000196171	ENST00000359610	T	0.00428	7.44	4.47	4.47	0.54385	.	0.000000	0.40064	N	0.001188	T	0.00440	0.0014	L	0.54323	1.7	0.26318	N	0.977725	D	0.89917	1.0	D	0.91635	0.999	T	0.50676	-0.8800	10	0.87932	D	0	-15.1693	12.8974	0.58108	1.0:0.0:0.0:0.0	.	37	Q8NGY2	OR6K2_HUMAN	S	37	ENSP00000352626:F37S	ENSP00000352626:F37S	F	-	2	0	OR6K2	156936957	0.923000	0.31300	0.346000	0.25655	0.184000	0.23303	3.836000	0.55813	1.854000	0.53819	0.533000	0.62120	TTC	.	.		0.443	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279	
ITLN2	142683	hgsc.bcm.edu	37	1	160919847	160919847	+	Missense_Mutation	SNP	G	G	T	rs201391588		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:160919847G>T	ENST00000368029.3	-	6	767	c.710C>A	c.(709-711)cCg>cAg	p.P237Q	ITLN2_ENST00000494442.1_5'UTR|RP11-544M22.1_ENST00000356006.3_RNA	NM_080878.2	NP_543154.1	Q8WWU7	ITLN2_HUMAN	intelectin 2	237	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	19	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			TTGACCATACGGTGAGTAATA	0.398																																					p.P237Q		Atlas-SNP	.											.	ITLN2	35	.	0			c.C710A						.						130.0	116.0	121.0					1																	160919847		2203	4300	6503	SO:0001583	missense	142683	exon6			CCATACGGTGAGT	AY065973	CCDS1212.1	1q22-q23.5	2013-02-06			ENSG00000158764	ENSG00000158764		"""Fibrinogen C domain containing"""	20599	protein-coding gene	gene with protein product		609874				11181563	Standard	NM_080878		Approved	HL-2	uc001fxd.3	Q8WWU7	OTTHUMG00000028605	ENST00000368029.3:c.710C>A	chr1.hg19:g.160919847G>T	ENSP00000357008:p.Pro237Gln	129.0	0.0		93.0	4.0	NM_080878	Q17RR2|Q5VYI0	Missense_Mutation	SNP	ENST00000368029.3	hg19	CCDS1212.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.829002	0.32329	.	.	ENSG00000158764	ENST00000368029	T	0.21932	1.98	4.72	4.72	0.59763	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (1);	0.000000	0.53938	U	0.000056	T	0.24236	0.0587	M	0.85373	2.75	0.36106	D	0.844452	P;P	0.52842	0.886;0.956	B;P	0.44359	0.433;0.447	T	0.37572	-0.9700	10	0.72032	D	0.01	-0.81	15.5105	0.75776	0.0:0.0:1.0:0.0	.	236;237	A6NI51;Q8WWU7	.;ITLN2_HUMAN	Q	237	ENSP00000357008:P237Q	ENSP00000357008:P237Q	P	-	2	0	ITLN2	159186471	0.989000	0.36119	0.431000	0.26735	0.005000	0.04900	2.768000	0.47645	2.285000	0.76669	0.561000	0.74099	CCG	.	.		0.398	ITLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071465.1	NM_080878	
C1orf111	284680	hgsc.bcm.edu	37	1	162344320	162344320	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:162344320A>G	ENST00000367935.5	-	3	383	c.304T>C	c.(304-306)Ttc>Ctc	p.F102L	RP11-565P22.6_ENST00000431696.1_Intron	NM_182581.3	NP_872387.2	Q5T0L3	CA111_HUMAN	chromosome 1 open reading frame 111	102										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	11	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)			GCACACACGAAGTAGCTGTAG	0.577																																					p.F102L		Atlas-SNP	.											.	C1orf111	26	.	0			c.T304C						.						121.0	120.0	120.0					1																	162344320		2203	4300	6503	SO:0001583	missense	284680	exon3			ACACGAAGTAGCT	BC032957	CCDS1238.1	1q23.3	2008-02-05			ENSG00000171722	ENSG00000171722			27648	protein-coding gene	gene with protein product						12477932	Standard	NM_182581		Approved		uc001gbx.2	Q5T0L3	OTTHUMG00000031375	ENST00000367935.5:c.304T>C	chr1.hg19:g.162344320A>G	ENSP00000356912:p.Phe102Leu	142.0	0.0		83.0	4.0	NM_182581	Q6X961|Q8NEC3	Missense_Mutation	SNP	ENST00000367935.5	hg19	CCDS1238.1	.	.	.	.	.	.	.	.	.	.	A	19.70	3.877366	0.72294	.	.	ENSG00000171722	ENST00000367935	T	0.37915	1.17	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000005	T	0.49304	0.1549	M	0.73598	2.24	0.33288	D	0.563115	D	0.67145	0.996	D	0.77557	0.99	T	0.59669	-0.7411	9	0.87932	D	0	-19.8356	12.0718	0.53620	1.0:0.0:0.0:0.0	.	102	Q5T0L3	CA111_HUMAN	L	102	ENSP00000356912:F102L	ENSP00000356912:F102L	F	-	1	0	C1orf111	160610944	1.000000	0.71417	0.993000	0.49108	0.708000	0.40852	3.692000	0.54727	1.859000	0.53934	0.533000	0.62120	TTC	.	.		0.577	C1orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076791.2	NM_182581	
RXRG	6258	hgsc.bcm.edu	37	1	165398198	165398198	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:165398198G>A	ENST00000359842.5	-	2	357	c.55C>T	c.(55-57)Cct>Tct	p.P19S		NM_001256570.1|NM_006917.4	NP_001243499.1|NP_008848.1	P48443	RXRG_HUMAN	retinoid X receptor, gamma	19	Modulating. {ECO:0000250}.				gene expression (GO:0010467)|heart development (GO:0007507)|neuron differentiation (GO:0030182)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|skeletal muscle tissue development (GO:0007519)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	9-cis retinoic acid receptor activity (GO:0004886)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.P19T(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(22)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	38	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tretinoin(DB00755)	GTGTGGCCAGGGGAGCCTGTA	0.572																																					p.P19S		Atlas-SNP	.											RXRG,NS,carcinoma,0,1	RXRG	91	.	1	Substitution - Missense(1)	lung(1)	c.C55T						.						44.0	40.0	41.0					1																	165398198		2203	4300	6503	SO:0001583	missense	6258	exon2			GGCCAGGGGAGCC	U38480	CCDS1248.1, CCDS72970.1	1q22-q23	2013-01-16			ENSG00000143171	ENSG00000143171		"""Nuclear hormone receptors"""	10479	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 3"""	180247				8034312	Standard	NR_033824		Approved	NR2B3	uc001gda.3	P48443	OTTHUMG00000034626	ENST00000359842.5:c.55C>T	chr1.hg19:g.165398198G>A	ENSP00000352900:p.Pro19Ser	140.0	0.0		93.0	4.0	NM_006917	A6NIP1|Q6IBU7	Missense_Mutation	SNP	ENST00000359842.5	hg19	CCDS1248.1	.	.	.	.	.	.	.	.	.	.	G	11.95	1.790428	0.31685	.	.	ENSG00000143171	ENST00000359842	D	0.91894	-2.93	4.56	3.65	0.41850	.	0.846178	0.10999	N	0.610725	T	0.79423	0.4443	L	0.27053	0.805	0.43439	D	0.995615	B	0.02656	0.0	B	0.01281	0.0	T	0.70475	-0.4861	9	0.54805	T	0.06	.	11.3765	0.49730	0.0887:0.0:0.9113:0.0	.	19	P48443	RXRG_HUMAN	S	19	ENSP00000352900:P19S	ENSP00000352900:P19S	P	-	1	0	RXRG	163664822	0.999000	0.42202	0.989000	0.46669	0.928000	0.56348	1.311000	0.33562	1.142000	0.42291	0.561000	0.74099	CCT	.	.		0.572	RXRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083794.2	NM_006917	
TIPRL	261726	hgsc.bcm.edu	37	1	168169255	168169255	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:168169255G>T	ENST00000367833.2	+	7	935	c.790G>T	c.(790-792)Gac>Tac	p.D264Y		NM_152902.3	NP_690866.1	O75663	TIPRL_HUMAN	TOR signaling pathway regulator	264	Interaction with PPP2CA.				DNA damage checkpoint (GO:0000077)|negative regulation of protein phosphatase type 2A activity (GO:0034048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|kidney(1)|large_intestine(1)|ovary(2)|skin(1)	6	all_hematologic(923;0.215)					TAACCCAGCAGACTCACAAAA	0.363																																					p.D264Y		Atlas-SNP	.											.	TIPRL	16	.	0			c.G790T						.						61.0	60.0	60.0					1																	168169255		2203	4299	6502	SO:0001583	missense	261726	exon7			CCAGCAGACTCAC	AB097034	CCDS1270.1, CCDS30935.1	1q23.2	2014-03-07	2014-03-07		ENSG00000143155	ENSG00000143155			30231	protein-coding gene	gene with protein product		611807	"""TIP41, TOR signaling pathway regulator-like (S. cerevisiae)"""			12761501	Standard	NM_001031800		Approved	MGC3794, dJ69E11.3, TIP41	uc001gfg.3	O75663	OTTHUMG00000034646	ENST00000367833.2:c.790G>T	chr1.hg19:g.168169255G>T	ENSP00000356807:p.Asp264Tyr	101.0	0.0		91.0	4.0	NM_152902	B2R8V3|Q5HYB2|Q8IZ86	Missense_Mutation	SNP	ENST00000367833.2	hg19	CCDS1270.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.527741	0.27299	.	.	ENSG00000143155	ENST00000367833	.	.	.	5.91	5.0	0.66597	.	0.543934	0.21397	N	0.075209	T	0.30262	0.0759	L	0.47716	1.5	0.32833	D	0.504357	B	0.31790	0.34	B	0.31016	0.123	T	0.32745	-0.9895	8	0.56958	D	0.05	-10.2752	11.6011	0.51003	0.1431:0.0:0.8569:0.0	.	264	O75663	TIPRL_HUMAN	Y	264	.	ENSP00000356807:D264Y	D	+	1	0	TIPRL	166435879	0.010000	0.17322	0.999000	0.59377	0.549000	0.35272	0.634000	0.24614	1.504000	0.48704	0.655000	0.94253	GAC	.	.		0.363	TIPRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083822.1	NM_152902	
CCDC181	57821	hgsc.bcm.edu	37	1	169388397	169388397	+	Splice_Site	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:169388397C>A	ENST00000367806.3	-	4	1221	c.1069G>T	c.(1069-1071)Gaa>Taa	p.E357*	CCDC181_ENST00000545005.1_Splice_Site_p.E357*|CCDC181_ENST00000367805.3_Splice_Site_p.E357*|CCDC181_ENST00000491570.1_5'UTR	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	357						nucleus (GO:0005634)											CGTCGCTCTTCCTAGTAAAAG	0.308																																					p.E357X		Atlas-SNP	.											.	C1orf114	67	.	0			c.G1069T						.						45.0	42.0	43.0					1																	169388397		2202	4295	6497	SO:0001630	splice_region_variant	57821	exon4			GCTCTTCCTAGTA	AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 114"""	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.1069-1G>T	chr1.hg19:g.169388397C>A		91.0	0.0		59.0	4.0	NM_021179	O60780|Q53FD5|Q5TID9|Q8TC48	Nonsense_Mutation	SNP	ENST00000367806.3	hg19		.	.	.	.	.	.	.	.	.	.	C	37	6.585705	0.97684	.	.	ENSG00000117477	ENST00000367805;ENST00000367806;ENST00000545005	.	.	.	5.98	5.98	0.97165	.	0.348808	0.31859	N	0.006945	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-8.2959	20.0532	0.97636	0.0:1.0:0.0:0.0	.	.	.	.	X	357	.	ENSP00000356779:E357X	E	-	1	0	C1orf114	167655021	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.070000	0.71220	2.835000	0.97688	0.650000	0.86243	GAA	.	.		0.308	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179	Nonsense_Mutation
F5	2153	hgsc.bcm.edu	37	1	169512354	169512354	+	Splice_Site	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:169512354T>C	ENST00000367797.3	-	13	2177		c.e13-2		F5_ENST00000367796.3_Splice_Site	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)						blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	TCCAAGTTCCTACAGAAGAGA	0.383																																					.		Atlas-SNP	.											.	F5	301	.	0			c.1976-2A>G						.						50.0	50.0	50.0					1																	169512354		2202	4300	6502	SO:0001630	splice_region_variant	2153	exon14			AGTTCCTACAGAA	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.1976-2A>G	chr1.hg19:g.169512354T>C		103.0	0.0		73.0	23.0	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Splice_Site	SNP	ENST00000367797.3	hg19	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	T	17.22	3.333513	0.60853	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	.	.	.	5.98	4.82	0.62117	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9103	0.58177	0.0:0.0:0.1358:0.8642	.	.	.	.	.	-1	.	.	.	-	.	.	F5	167778978	1.000000	0.71417	0.806000	0.32338	0.751000	0.42716	6.275000	0.72594	1.035000	0.39972	0.482000	0.46254	.	.	.		0.383	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	Intron
DNM3	26052	hgsc.bcm.edu	37	1	171958288	171958288	+	Splice_Site	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:171958288G>T	ENST00000355305.5	+	4	746	c.589G>T	c.(589-591)Ggt>Tgt	p.G197C	DNM3_ENST00000520906.1_Splice_Site_p.G197C|DNM3_ENST00000358155.4_Splice_Site_p.G197C|DNM3_ENST00000367733.2_Splice_Site_p.G197C|DNM3_ENST00000367731.1_Splice_Site_p.G197C			Q9UQ16	DYN3_HUMAN	dynamin 3	197	Dynamin-type G.				endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TGATCCTCAAGGTGAGTGTGT	0.378																																					p.G197C		Atlas-SNP	.											.	DNM3	85	.	0			c.G589T						.						50.0	47.0	48.0					1																	171958288		1912	4143	6055	SO:0001630	splice_region_variant	26052	exon4			CCTCAAGGTGAGT	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"""Pleckstrin homology (PH) domain containing"""	29125	protein-coding gene	gene with protein product	"""Dyna III"""	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.589+1G>T	chr1.hg19:g.171958288G>T		131.0	0.0		76.0	4.0	NM_001136127	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	hg19		.	.	.	.	.	.	.	.	.	.	G	26.5	4.743055	0.89663	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000367733;ENST00000355305;ENST00000367731;ENST00000520906;ENST00000523513	D;D;D;D;D;D	0.97404	-4.23;-4.23;-4.23;-4.23;-4.23;-4.37	5.9	5.9	0.94986	.	0.047955	0.85682	D	0.000000	D	0.99417	0.9794	H	0.99834	4.825	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.85130	0.997;0.997;0.995;0.997	D	0.98227	1.0481	10	0.87932	D	0	.	18.8427	0.92190	0.0:0.0:1.0:0.0	.	197;197;197;197	E5RHK8;Q9UQ16-2;Q9UQ16-3;Q6P2G1	.;.;.;.	C	197;197;197;197;197;197;87	ENSP00000350876:G197C;ENSP00000356707:G197C;ENSP00000347457:G197C;ENSP00000356705:G197C;ENSP00000429701:G197C;ENSP00000429416:G87C	ENSP00000347457:G197C	G	+	1	0	DNM3	170224911	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	9.793000	0.99091	2.788000	0.95919	0.650000	0.86243	GGT	.	.		0.378	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569	Missense_Mutation
PAPPA2	60676	hgsc.bcm.edu	37	1	176564279	176564279	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:176564279C>T	ENST00000367662.3	+	3	2703	c.1539C>T	c.(1537-1539)taC>taT	p.Y513Y	PAPPA2_ENST00000367661.3_Silent_p.Y513Y	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	513	Metalloprotease.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.Y513*(2)		NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TCTCCCAGTACAATGGATACT	0.532																																					p.Y513Y		Atlas-SNP	.											PAPPA2_ENST00000367661,NS,carcinoma,0,2	PAPPA2	665	.	2	Substitution - Nonsense(2)	lung(2)	c.C1539T						.						55.0	55.0	55.0					1																	176564279		1979	4172	6151	SO:0001819	synonymous_variant	60676	exon3			CCAGTACAATGGA	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1539C>T	chr1.hg19:g.176564279C>T		68.0	1.0		61.0	3.0	NM_021936	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	hg19	CCDS41438.1																																																																																			.	.		0.532	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		
ZNF648	127665	hgsc.bcm.edu	37	1	182026597	182026597	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:182026597G>T	ENST00000339948.3	-	2	756	c.549C>A	c.(547-549)tcC>tcA	p.S183S		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	183					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(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						AGTTCCCTGCGGACGTGTCTA	0.587																																					p.S183S	NSCLC(71;908 1374 5429 20458 35642)	Atlas-SNP	.											.	ZNF648	111	.	0			c.C549A						.						58.0	63.0	61.0					1																	182026597		2203	4300	6503	SO:0001819	synonymous_variant	127665	exon2			CCCTGCGGACGTG	AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"""Zinc fingers, C2H2-type"""	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.549C>A	chr1.hg19:g.182026597G>T		152.0	0.0		96.0	6.0	NM_001009992	B2RP16	Silent	SNP	ENST00000339948.3	hg19	CCDS30952.1																																																																																			.	.		0.587	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597	
LAMC1	3915	hgsc.bcm.edu	37	1	183111868	183111868	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:183111868C>T	ENST00000258341.4	+	28	5030	c.4773C>T	c.(4771-4773)gaC>gaT	p.D1591D	RP11-181K3.4_ENST00000457852.3_RNA	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1591	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	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)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						ATCTGGAGGACATCAGGAAGA	0.522																																					p.D1591D		Atlas-SNP	.											.	LAMC1	176	.	0			c.C4773T						.						130.0	113.0	118.0					1																	183111868		2203	4300	6503	SO:0001819	synonymous_variant	3915	exon28			GGAGGACATCAGG	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.4773C>T	chr1.hg19:g.183111868C>T		113.0	0.0		95.0	4.0	NM_002293	Q5VYE7	Silent	SNP	ENST00000258341.4	hg19	CCDS1351.1																																																																																			.	.		0.522	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
HMCN1	83872	hgsc.bcm.edu	37	1	186031705	186031705	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:186031705A>G	ENST00000271588.4	+	48	7715	c.7486A>G	c.(7486-7488)Agt>Ggt	p.S2496G	HMCN1_ENST00000367492.2_Missense_Mutation_p.S2496G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2496	Ig-like C2-type 23.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AGAGAAACAGAGTGTTACGCT	0.408																																					p.S2496G		Atlas-SNP	.											.	HMCN1	797	.	0			c.A7486G						.						106.0	100.0	102.0					1																	186031705		2203	4300	6503	SO:0001583	missense	83872	exon48			AAACAGAGTGTTA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.7486A>G	chr1.hg19:g.186031705A>G	ENSP00000271588:p.Ser2496Gly	123.0	0.0		86.0	5.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	14.97	2.694899	0.48202	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.70164	-0.46;-0.46	5.51	3.15	0.36227	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.177069	0.64402	D	0.000007	T	0.66934	0.2840	M	0.75777	2.31	0.28600	N	0.909212	B	0.24823	0.112	B	0.37015	0.239	T	0.59193	-0.7500	10	0.24483	T	0.36	.	8.9866	0.35997	0.7857:0.0:0.2143:0.0	.	2496	Q96RW7	HMCN1_HUMAN	G	2496	ENSP00000271588:S2496G;ENSP00000356462:S2496G	ENSP00000271588:S2496G	S	+	1	0	HMCN1	184298328	0.998000	0.40836	0.976000	0.42696	0.985000	0.73830	3.670000	0.54569	0.921000	0.36994	0.482000	0.46254	AGT	.	.		0.408	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
HMCN1	83872	hgsc.bcm.edu	37	1	186157064	186157064	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:186157064G>A	ENST00000271588.4	+	106	16693	c.16464G>A	c.(16462-16464)atG>atA	p.M5488I	HMCN1_ENST00000367492.2_Missense_Mutation_p.M5371I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5488					response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CCAATCGCATGTGCTTCAACA	0.517																																					p.M5488I		Atlas-SNP	.											.	HMCN1	797	.	0			c.G16464A						.						345.0	248.0	280.0					1																	186157064		2203	4300	6503	SO:0001583	missense	83872	exon106			TCGCATGTGCTTC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.16464G>A	chr1.hg19:g.186157064G>A	ENSP00000271588:p.Met5488Ile	186.0	0.0		119.0	6.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	19.22	3.784983	0.70222	.	.	ENSG00000143341	ENST00000271588;ENST00000367492;ENST00000414277	T;T;T	0.75367	-0.03;-0.02;-0.93	5.72	5.72	0.89469	EGF-like calcium-binding, conserved site (1);Growth factor, receptor (1);Epidermal growth factor-like (1);	0.035367	0.85682	D	0.000000	T	0.70290	0.3207	L	0.48362	1.52	0.39946	D	0.974476	B	0.30406	0.278	B	0.26517	0.07	T	0.68239	-0.5461	10	0.39692	T	0.17	.	19.8968	0.96969	0.0:0.0:1.0:0.0	.	5488	Q96RW7	HMCN1_HUMAN	I	5488;5371;163	ENSP00000271588:M5488I;ENSP00000356462:M5371I;ENSP00000406205:M163I	ENSP00000271588:M5488I	M	+	3	0	HMCN1	184423687	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	9.807000	0.99171	2.691000	0.91804	0.655000	0.94253	ATG	.	.		0.517	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
IGFN1	91156	hgsc.bcm.edu	37	1	201186487	201186487	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:201186487C>T	ENST00000335211.4	+	17	9798	c.9668C>T	c.(9667-9669)gCa>gTa	p.A3223V	IGFN1_ENST00000295591.8_Missense_Mutation_p.A383V	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	766						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ACATGGACAGCACCTCGGGGC	0.652																																					p.A3223V		Atlas-SNP	.											.	IGFN1	220	.	0			c.C9668T						.						63.0	64.0	64.0					1																	201186487		2203	4300	6503	SO:0001583	missense	91156	exon17			GGACAGCACCTCG	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.9668C>T	chr1.hg19:g.201186487C>T	ENSP00000334714:p.Ala3223Val	235.0	0.0		182.0	23.0	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	hg19	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607853	0.87258	.	.	ENSG00000163395	ENST00000335211;ENST00000295591	T;T	0.58940	0.3;0.3	4.68	4.68	0.58851	.	0.227102	0.37393	N	0.002106	T	0.63271	0.2497	L	0.58969	1.84	0.38149	D	0.938696	P	0.39520	0.676	P	0.48488	0.579	T	0.63642	-0.6591	10	0.24483	T	0.36	.	15.7862	0.78306	0.0:1.0:0.0:0.0	.	3223	F8WAI1	.	V	3223;383	ENSP00000334714:A3223V;ENSP00000295591:A383V	ENSP00000295591:A383V	A	+	2	0	IGFN1	199453110	0.885000	0.30320	0.114000	0.21550	0.008000	0.06430	4.271000	0.58902	2.129000	0.65627	0.561000	0.74099	GCA	.	.		0.652	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
LGR6	59352	hgsc.bcm.edu	37	1	202287998	202287998	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:202287998C>T	ENST00000367278.3	+	18	2656	c.2567C>T	c.(2566-2568)gCc>gTc	p.A856V	LGR6_ENST00000439764.2_Missense_Mutation_p.A717V|LGR6_ENST00000255432.7_Missense_Mutation_p.A804V	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	856					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						TATGCTGCGGCCGGGGAGCTG	0.632																																					p.A856V		Atlas-SNP	.											.	LGR6	102	.	0			c.C2567T						.						48.0	58.0	54.0					1																	202287998		2203	4300	6503	SO:0001583	missense	59352	exon18			CTGCGGCCGGGGA	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"""GPCR / Class A : Orphans"""	19719	protein-coding gene	gene with protein product		606653	"""leucine-rich repeat-containing G protein-coupled receptor 6"""			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.2567C>T	chr1.hg19:g.202287998C>T	ENSP00000356247:p.Ala856Val	167.0	0.0		94.0	4.0	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Missense_Mutation	SNP	ENST00000367278.3	hg19	CCDS30971.1	.	.	.	.	.	.	.	.	.	.	C	10.12	1.263462	0.23051	.	.	ENSG00000133067	ENST00000367278;ENST00000255432;ENST00000439764	T;T;T	0.59638	0.25;0.65;0.68	4.18	3.27	0.37495	.	0.384683	0.21905	N	0.067385	T	0.43255	0.1239	L	0.40543	1.245	0.09310	N	0.999999	P;B;B	0.38078	0.617;0.202;0.128	B;B;B	0.30855	0.121;0.098;0.101	T	0.36720	-0.9736	10	0.51188	T	0.08	.	10.7001	0.45922	0.0:0.8359:0.0:0.1641	.	717;804;856	Q9HBX8-1;Q9HBX8-2;Q9HBX8	.;.;LGR6_HUMAN	V	856;804;717	ENSP00000356247:A856V;ENSP00000255432:A804V;ENSP00000387869:A717V	ENSP00000255432:A804V	A	+	2	0	LGR6	200554621	0.922000	0.31269	0.013000	0.15412	0.216000	0.24613	2.333000	0.43912	1.121000	0.41925	0.485000	0.47835	GCC	.	.		0.632	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
LAX1	54900	hgsc.bcm.edu	37	1	203741220	203741220	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:203741220G>T	ENST00000442561.2	+	4	725	c.335G>T	c.(334-336)cGc>cTc	p.R112L	LAX1_ENST00000367217.5_Missense_Mutation_p.R96L|LAX1_ENST00000367215.1_3'UTR	NM_017773.3	NP_060243.2	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1	112					antigen receptor-mediated signaling pathway (GO:0050851)|B cell activation (GO:0042113)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)			central_nervous_system(2)|endometrium(3)|large_intestine(2)|lung(13)|prostate(1)|stomach(1)|urinary_tract(2)	24	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			AGGAGTATGCGCATTTTCAGT	0.488																																					p.R112L		Atlas-SNP	.											.	LAX1	48	.	0			c.G335T						.						139.0	128.0	132.0					1																	203741220		2203	4300	6503	SO:0001583	missense	54900	exon4			GTATGCGCATTTT	AK000347	CCDS1441.2, CCDS44297.1	1q32.1	2008-02-05			ENSG00000122188	ENSG00000122188			26005	protein-coding gene	gene with protein product	"""LAT-like membrane associated protein"", ""linker for activation of x cells"""					12359715	Standard	NM_017773		Approved	LAX, FLJ20340	uc001haa.3	Q8IWV1	OTTHUMG00000035908	ENST00000442561.2:c.335G>T	chr1.hg19:g.203741220G>T	ENSP00000406970:p.Arg112Leu	107.0	0.0		67.0	4.0	NM_017773	B7Z744|J3KP69|Q6NSZ6|Q9NXB4	Missense_Mutation	SNP	ENST00000442561.2	hg19	CCDS1441.2	.	.	.	.	.	.	.	.	.	.	G	13.10	2.137429	0.37728	.	.	ENSG00000122188	ENST00000442561;ENST00000367217	.	.	.	4.56	3.64	0.41730	.	0.217303	0.32935	N	0.005472	T	0.49457	0.1558	L	0.53249	1.67	0.09310	N	1	D;D	0.63046	0.992;0.992	P;P	0.56278	0.795;0.72	T	0.38564	-0.9655	9	0.62326	D	0.03	-3.9142	9.0249	0.36222	0.1046:0.0:0.8954:0.0	.	96;112	B7Z744;Q8IWV1	.;LAX1_HUMAN	L	112;96	.	ENSP00000356186:R96L	R	+	2	0	LAX1	202007843	0.024000	0.19004	0.005000	0.12908	0.071000	0.16799	0.720000	0.25896	1.033000	0.39918	0.655000	0.94253	CGC	.	.		0.488	LAX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087468.3	NM_017773	
SOX13	9580	hgsc.bcm.edu	37	1	204083543	204083543	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:204083543A>G	ENST00000367204.1	+	3	423	c.314A>G	c.(313-315)aAc>aGc	p.N105S	SOX13_ENST00000367203.4_3'UTR	NM_005686.2	NP_005677.2	Q9UN79	SOX13_HUMAN	SRY (sex determining region Y)-box 13	105					anatomical structure morphogenesis (GO:0009653)|regulation of gamma-delta T cell differentiation (GO:0045586)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	13	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			CTGGACTTCAACCGAAATTTG	0.537																																					p.N105S		Atlas-SNP	.											.	SOX13	38	.	0			c.A314G						.						52.0	51.0	52.0					1																	204083543		1949	4153	6102	SO:0001583	missense	9580	exon3			ACTTCAACCGAAA		CCDS44299.1	1q32	2008-07-18			ENSG00000143842	ENSG00000143842		"""SRY (sex determining region Y)-boxes"""	11192	protein-coding gene	gene with protein product	"""islet cell antibody 12"", ""SRY-related HMG-box gene 13"", ""type 1 diabetes autoantigen"", ""SRY-box 13"""	604748				10198172	Standard	NM_005686		Approved	Sox-13, ICA12, MGC117216	uc001ham.3	Q9UN79	OTTHUMG00000036050	ENST00000367204.1:c.314A>G	chr1.hg19:g.204083543A>G	ENSP00000356172:p.Asn105Ser	166.0	0.0		92.0	4.0	NM_005686	B4E2B0|O95275|O95826|Q3KQV7|Q5SXX1|Q9UHW7	Missense_Mutation	SNP	ENST00000367204.1	hg19	CCDS44299.1	.	.	.	.	.	.	.	.	.	.	A	5.148	0.212914	0.09757	.	.	ENSG00000143842	ENST00000367204;ENST00000528591	D	0.97505	-4.41	4.65	3.5	0.40072	.	0.221487	0.45867	N	0.000321	D	0.92289	0.7554	L	0.35414	1.06	0.25626	N	0.986358	B;B	0.12630	0.0;0.006	B;B	0.15052	0.001;0.012	T	0.81484	-0.0912	10	0.19590	T	0.45	.	6.9016	0.24285	0.8813:0.0:0.1187:0.0	.	105;87	Q9UN79;Q5SXX2	SOX13_HUMAN;.	S	105	ENSP00000356172:N105S	ENSP00000356172:N105S	N	+	2	0	SOX13	202350166	1.000000	0.71417	0.993000	0.49108	0.945000	0.59286	2.984000	0.49353	0.622000	0.30249	0.460000	0.39030	AAC	.	.		0.537	SOX13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087881.2	NM_005686	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204403607	204403607	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:204403607G>T	ENST00000367187.3	-	25	4202	c.3646C>A	c.(3646-3648)Cgc>Agc	p.R1216S	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.R1188S|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1216	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CCCAGGAAGCGGCCAAAATCA	0.522																																					p.R1216S		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C3646A						.						80.0	62.0	68.0					1																	204403607		2203	4300	6503	SO:0001583	missense	5287	exon25			GGAAGCGGCCAAA	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.3646C>A	chr1.hg19:g.204403607G>T	ENSP00000356155:p.Arg1216Ser	135.0	0.0		99.0	4.0	NM_002646	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	hg19	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.946665	0.92593	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.75367	-0.93;-0.93	5.69	5.69	0.88448	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.173359	0.47093	D	0.000249	T	0.80132	0.4567	L	0.50333	1.59	0.41599	D	0.988844	P;D	0.58620	0.888;0.983	P;P	0.59948	0.711;0.866	T	0.81716	-0.0806	10	0.87932	D	0	.	12.6528	0.56772	0.0:0.0:0.7285:0.2715	.	1188;1216	F5GWN5;O00750	.;P3C2B_HUMAN	S	1216;1188	ENSP00000356155:R1216S;ENSP00000400561:R1188S	ENSP00000356155:R1216S	R	-	1	0	PIK3C2B	202670230	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.790000	0.62453	2.692000	0.91855	0.563000	0.77884	CGC	.	.		0.522	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
NFASC	23114	hgsc.bcm.edu	37	1	204938107	204938107	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:204938107A>G	ENST00000401399.1	+	9	1199	c.1000A>G	c.(1000-1002)Aag>Gag	p.K334E	NFASC_ENST00000513543.1_Missense_Mutation_p.K345E|NFASC_ENST00000367169.4_Missense_Mutation_p.K334E|NFASC_ENST00000338586.6_Missense_Mutation_p.K334E|NFASC_ENST00000367172.4_Missense_Mutation_p.K334E|NFASC_ENST00000338515.6_Missense_Mutation_p.K334E|NFASC_ENST00000339876.6_Missense_Mutation_p.K334E|NFASC_ENST00000367170.4_Missense_Mutation_p.K334E|NFASC_ENST00000404076.1_Missense_Mutation_p.K328E|NFASC_ENST00000367171.4_Missense_Mutation_p.K334E|NFASC_ENST00000360049.4_Missense_Mutation_p.K345E|NFASC_ENST00000403080.1_Missense_Mutation_p.K334E|NFASC_ENST00000539706.1_Missense_Mutation_p.K345E|NFASC_ENST00000404907.1_Missense_Mutation_p.K345E			O94856	NFASC_HUMAN	neurofascin	334					axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GGTGAGAGTAAAGGGTACGTT	0.527																																					p.K345E		Atlas-SNP	.											.	NFASC	396	.	0			c.A1033G						.						64.0	69.0	67.0					1																	204938107		2203	4300	6503	SO:0001583	missense	23114	exon10			AGAGTAAAGGGTA	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.1000A>G	chr1.hg19:g.204938107A>G	ENSP00000385637:p.Lys334Glu	188.0	0.0		89.0	4.0	NM_015090	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	hg19	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	A	19.80	3.894541	0.72639	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08	5.8	5.8	0.92144	.	0.000000	0.56097	D	0.000027	T	0.73466	0.3590	N	0.04746	-0.17	0.80722	D	1	D;B;D;P;D;P;D	0.89917	1.0;0.322;1.0;0.815;1.0;0.517;1.0	D;B;D;P;D;B;D	0.91635	0.994;0.05;0.967;0.601;0.996;0.074;0.999	T	0.69899	-0.5020	10	0.07175	T	0.84	.	15.8152	0.78595	1.0:0.0:0.0:0.0	.	345;345;430;334;334;345;334	O94856-11;O94856-8;B4DRH7;F8W791;O94856-9;O94856-3;O94856-2	.;.;.;.;.;.;.	E	334;334;334;334;334;334;345;345;345;334;334;328;334;345;345;321	ENSP00000356140:K334E;ENSP00000356139:K334E;ENSP00000356138:K334E;ENSP00000342128:K334E;ENSP00000344786:K334E;ENSP00000343509:K334E;ENSP00000438614:K345E;ENSP00000353154:K345E;ENSP00000356137:K334E;ENSP00000384875:K334E;ENSP00000385676:K328E;ENSP00000385637:K334E;ENSP00000384061:K345E;ENSP00000425908:K345E;ENSP00000415031:K321E	ENSP00000295776:K345E	K	+	1	0	NFASC	203204730	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.444000	0.80532	2.213000	0.71641	0.528000	0.53228	AAG	.	.		0.527	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
NUAK2	81788	hgsc.bcm.edu	37	1	205273191	205273191	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:205273191T>C	ENST00000367157.3	-	7	1400	c.1274A>G	c.(1273-1275)gAc>gGc	p.D425G		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CTCCGGAGGGTCCTCCTGTAC	0.627																																					p.D425G		Atlas-SNP	.											.	NUAK2	107	.	0			c.A1274G						.						73.0	69.0	70.0					1																	205273191		2203	4300	6503	SO:0001583	missense	81788	exon7			GGAGGGTCCTCCT	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"""SNF1/AMP activated protein kinase"""	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.1274A>G	chr1.hg19:g.205273191T>C	ENSP00000356125:p.Asp425Gly	115.0	0.0		81.0	4.0	NM_030952		Missense_Mutation	SNP	ENST00000367157.3	hg19	CCDS1453.1	.	.	.	.	.	.	.	.	.	.	T	0.014	-1.582617	0.00879	.	.	ENSG00000163545	ENST00000367157	T	0.72394	-0.65	4.84	0.918	0.19386	.	0.448909	0.18701	N	0.133563	T	0.44664	0.1304	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18241	-1.0343	10	0.15066	T	0.55	.	4.8344	0.13456	0.0:0.2661:0.1515:0.5824	.	425	Q9H093	NUAK2_HUMAN	G	425	ENSP00000356125:D425G	ENSP00000356125:D425G	D	-	2	0	NUAK2	203539814	0.000000	0.05858	0.021000	0.16686	0.032000	0.12392	0.193000	0.17116	-0.108000	0.12066	0.334000	0.21626	GAC	.	.		0.627	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952	
INTS7	25896	hgsc.bcm.edu	37	1	212139822	212139822	+	Missense_Mutation	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:212139822T>A	ENST00000366994.3	-	16	2237	c.2133A>T	c.(2131-2133)ttA>ttT	p.L711F	INTS7_ENST00000366992.3_Missense_Mutation_p.L711F|INTS7_ENST00000469606.1_5'UTR|INTS7_ENST00000366993.3_Missense_Mutation_p.L711F|INTS7_ENST00000440600.2_Missense_Mutation_p.L662F	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	711					cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		GAGATATCAGTAAACAGCTCT	0.348																																					p.L711F		Atlas-SNP	.											.	INTS7	68	.	0			c.A2133T						.						80.0	86.0	84.0					1																	212139822		2203	4300	6503	SO:0001583	missense	25896	exon16			TATCAGTAAACAG	AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"""chromosome 1 open reading frame 73"""	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.2133A>T	chr1.hg19:g.212139822T>A	ENSP00000355961:p.Leu711Phe	111.0	0.0		90.0	39.0	NM_015434	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Missense_Mutation	SNP	ENST00000366994.3	hg19	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.652261	0.47362	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992;ENST00000440600	T;T;T;T	0.49139	0.79;0.81;0.8;0.8	4.98	-3.46	0.04767	.	0.000000	0.64402	D	0.000001	T	0.22244	0.0536	L	0.27053	0.805	0.49687	D	0.999817	B;B;B;B	0.27229	0.172;0.046;0.046;0.046	B;B;B;B	0.25291	0.04;0.04;0.04;0.059	T	0.11131	-1.0600	10	0.09843	T	0.71	-12.6108	4.9809	0.14164	0.1385:0.5431:0.1413:0.1771	.	662;711;711;711	B4DLZ6;Q9NVH2-3;Q9NVH2-2;Q9NVH2	.;.;.;INT7_HUMAN	F	711;711;711;662	ENSP00000355961:L711F;ENSP00000355960:L711F;ENSP00000355959:L711F;ENSP00000388908:L662F	ENSP00000355959:L711F	L	-	3	2	INTS7	210206445	0.997000	0.39634	0.994000	0.49952	0.996000	0.88848	0.448000	0.21726	-0.262000	0.09392	0.454000	0.30748	TTA	.	.		0.348	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434	
USH2A	7399	hgsc.bcm.edu	37	1	215963585	215963585	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:215963585T>C	ENST00000307340.3	-	51	10384	c.9998A>G	c.(9997-9999)gAt>gGt	p.D3333G	USH2A_ENST00000366943.2_Missense_Mutation_p.D3333G	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3333					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GCATATGGTATCTGACATATT	0.378										HNSCC(13;0.011)																											p.D3333G		Atlas-SNP	.											.	USH2A	1168	.	0			c.A9998G						.						122.0	114.0	117.0					1																	215963585		2203	4300	6503	SO:0001583	missense	7399	exon51			ATGGTATCTGACA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9998A>G	chr1.hg19:g.215963585T>C	ENSP00000305941:p.Asp3333Gly	156.0	0.0		122.0	5.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	12.64	1.999505	0.35320	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.13420	2.6;2.59	5.91	5.91	0.95273	Fibronectin, type III (2);	0.143817	0.31370	N	0.007773	T	0.12305	0.0299	L	0.53249	1.67	0.30027	N	0.813858	P	0.43094	0.799	B	0.33339	0.162	T	0.17137	-1.0379	10	0.33141	T	0.24	.	11.387	0.49791	0.0:0.0697:0.0:0.9303	.	3333	O75445	USH2A_HUMAN	G	3333	ENSP00000305941:D3333G;ENSP00000355910:D3333G	ENSP00000305941:D3333G	D	-	2	0	USH2A	214030208	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.843000	0.48238	2.254000	0.74563	0.533000	0.62120	GAT	.	.		0.378	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
EPRS	2058	hgsc.bcm.edu	37	1	220203778	220203778	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:220203778T>C	ENST00000366923.3	-	6	842	c.573A>G	c.(571-573)ccA>ccG	p.P191P		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	191	Glutamate--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	TCTCCGCACCTGGAAGCTCAA	0.398																																					p.P191P		Atlas-SNP	.											.	EPRS	140	.	0			c.A573G						.						90.0	89.0	89.0					1																	220203778		2203	4300	6503	SO:0001819	synonymous_variant	2058	exon6			CGCACCTGGAAGC	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"""Aminoacyl tRNA synthetases / Class I"", ""Aminoacyl tRNA synthetases / Class II"""	3418	protein-coding gene	gene with protein product	"""glutamate tRNA ligase"", ""proline tRNA ligase"""	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.573A>G	chr1.hg19:g.220203778T>C		92.0	0.0		62.0	4.0	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Silent	SNP	ENST00000366923.3	hg19	CCDS31027.1																																																																																			.	.		0.398	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446	
TLR5	7100	hgsc.bcm.edu	37	1	223286028	223286028	+	Nonsense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:223286028G>A	ENST00000540964.1	-	4	807	c.346C>T	c.(346-348)Cag>Tag	p.Q116*	TLR5_ENST00000342210.6_Nonsense_Mutation_p.Q116*			O60602	TLR5_HUMAN	toll-like receptor 5	116					cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		AACAGTCCCTGAAAAGCATCT	0.413																																					p.Q116X		Atlas-SNP	.											.	TLR5	86	.	0			c.C346T						.						94.0	92.0	92.0					1																	223286028		2203	4300	6503	SO:0001587	stop_gained	7100	exon6			GTCCCTGAAAAGC		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"""Toll/interleukin-1 receptor-like protein 3"""	603031	"""systemic lupus erythematosus susceptibility 1"""	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.346C>T	chr1.hg19:g.223286028G>A	ENSP00000440643:p.Gln116*	156.0	0.0		121.0	5.0	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Nonsense_Mutation	SNP	ENST00000540964.1	hg19	CCDS31033.1	.	.	.	.	.	.	.	.	.	.	G	36	5.741443	0.96873	.	.	ENSG00000187554	ENST00000540964;ENST00000366881;ENST00000342210	.	.	.	5.03	5.03	0.67393	.	0.460355	0.21479	N	0.073863	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3781	0.66892	0.0:0.2626:0.7374:0.0	.	.	.	.	X	116	.	ENSP00000340089:Q116X	Q	-	1	0	TLR5	221352651	0.956000	0.32656	0.563000	0.28383	0.969000	0.65631	2.578000	0.46051	2.483000	0.83821	0.655000	0.94253	CAG	.	.		0.413	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268	
TLR5	7100	hgsc.bcm.edu	37	1	223286221	223286221	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:223286221G>T	ENST00000540964.1	-	4	614	c.153C>A	c.(151-153)ctC>ctA	p.L51L	TLR5_ENST00000342210.6_Silent_p.L51L			O60602	TLR5_HUMAN	toll-like receptor 5	51					cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		AGCTCAGCAGGAGCCTCTCAG	0.532																																					p.L51L		Atlas-SNP	.											.	TLR5	86	.	0			c.C153A						.						65.0	66.0	65.0					1																	223286221		2203	4300	6503	SO:0001819	synonymous_variant	7100	exon6			CAGCAGGAGCCTC		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"""Toll/interleukin-1 receptor-like protein 3"""	603031	"""systemic lupus erythematosus susceptibility 1"""	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.153C>A	chr1.hg19:g.223286221G>T		122.0	0.0		123.0	5.0	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Silent	SNP	ENST00000540964.1	hg19	CCDS31033.1																																																																																			.	.		0.532	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268	
CDC42BPA	8476	hgsc.bcm.edu	37	1	227216408	227216408	+	Missense_Mutation	SNP	C	C	T	rs369641713		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:227216408C>T	ENST00000366769.3	-	29	5568	c.4277G>A	c.(4276-4278)cGa>cAa	p.R1426Q	CDC42BPA_ENST00000366765.3_Missense_Mutation_p.R1439Q|CDC42BPA_ENST00000366766.2_Missense_Mutation_p.R1461Q|CDC42BPA_ENST00000366767.3_Missense_Mutation_p.R1345Q|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.R1406Q|CDC42BPA_ENST00000366764.2_Missense_Mutation_p.R1398Q|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.R1426Q	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TCTAGATCTTCGGCCCTGGCA	0.423																																					p.R1426Q		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.G4277A						.	C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	123.0	110.0	115.0		4277,4034	4.6	1.0	1		115	0,8600		0,0,4300	no	missense,missense	CDC42BPA	NM_003607.3,NM_014826.4	43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	1426/1720,1345/1639	227216408	1,13005	2203	4300	6503	SO:0001583	missense	8476	exon29			GATCTTCGGCCCT	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"""myotonic dystrophy kinase-related Cdc42-binding kinase"""	603412	"""CDC42-binding protein kinase alpha (DMPK-like)"""				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.4277G>A	chr1.hg19:g.227216408C>T	ENSP00000355731:p.Arg1426Gln	166.0	0.0		85.0	4.0	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	hg19	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496204	0.85069	2.27E-4	0.0	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000366762;ENST00000535525;ENST00000366765	T;T;T;T;T;T;T	0.05081	3.5;3.5;3.5;3.5;3.5;3.5;3.5	5.53	4.62	0.57501	.	0.060172	0.64402	D	0.000003	T	0.28599	0.0708	M	0.84773	2.715	0.58432	D	0.999996	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.994;0.999;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.87578	0.996;0.998;0.958;0.952;0.997;0.973;0.983;0.986	T	0.10245	-1.0638	10	0.72032	D	0.01	.	14.5294	0.67915	0.0:0.9296:0.0:0.0704	.	1406;1398;741;323;1345;1426;1461;628	F5H5N0;Q5VT25-4;E9PEF7;Q5T7A7;Q5VT25-3;Q5VT25-5;Q5VT25-2;Q5T799	.;.;.;.;.;.;.;.	Q	1426;1345;1426;1461;1398;741;1406;1439	ENSP00000355731:R1426Q;ENSP00000355729:R1345Q;ENSP00000335341:R1426Q;ENSP00000355728:R1461Q;ENSP00000355726:R1398Q;ENSP00000443275:R1406Q;ENSP00000355727:R1439Q	ENSP00000335341:R1426Q	R	-	2	0	CDC42BPA	225283031	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	6.034000	0.70933	1.484000	0.48361	0.585000	0.79938	CGA	.	.		0.423	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	
PGBD5	79605	hgsc.bcm.edu	37	1	230486728	230486728	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:230486728A>G	ENST00000525115.1	-	3	686	c.663T>C	c.(661-663)tgT>tgC	p.C221C	PGBD5_ENST00000321327.2_Silent_p.C320C|PGBD5_ENST00000391860.1_Silent_p.C175C			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	221						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		CAGTGGAAGAACATTGTCTGA	0.567																																					p.C290C		Atlas-SNP	.											.	PGBD5	73	.	0			c.T870C						.						115.0	110.0	112.0					1																	230486728		2203	4300	6503	SO:0001819	synonymous_variant	79605	exon3			GGAAGAACATTGT	AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.663T>C	chr1.hg19:g.230486728A>G		123.0	0.0		93.0	4.0	NM_001258311	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Silent	SNP	ENST00000525115.1	hg19																																																																																				.	.		0.567	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554	
NID1	4811	hgsc.bcm.edu	37	1	236157008	236157008	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:236157008A>G	ENST00000264187.6	-	13	2774	c.2692T>C	c.(2692-2694)Tgc>Cgc	p.C898R	NID1_ENST00000366595.3_Missense_Mutation_p.C765R	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	898	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	CGATCCACGCACCAGCAGTAG	0.701																																					p.C898R		Atlas-SNP	.											.	NID1	196	.	0			c.T2692C						.						21.0	22.0	22.0					1																	236157008		2200	4297	6497	SO:0001583	missense	4811	exon13			CCACGCACCAGCA	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.2692T>C	chr1.hg19:g.236157008A>G	ENSP00000264187:p.Cys898Arg	161.0	0.0		77.0	4.0	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	hg19	CCDS1608.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.880061	0.91740	.	.	ENSG00000116962	ENST00000264187;ENST00000366595	D;D	0.87491	-2.26;-2.26	5.69	5.69	0.88448	Thyroglobulin type-1 (6);	0.000000	0.85682	D	0.000000	D	0.96278	0.8786	H	0.98351	4.21	0.80722	D	1	D;P	0.89917	1.0;0.931	D;P	0.91635	0.999;0.739	D	0.97936	1.0323	10	0.87932	D	0	.	15.5931	0.76554	1.0:0.0:0.0:0.0	.	765;898	P14543-2;P14543	.;NID1_HUMAN	R	898;765	ENSP00000264187:C898R;ENSP00000355554:C765R	ENSP00000264187:C898R	C	-	1	0	NID1	234223631	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	8.751000	0.91628	2.162000	0.67917	0.454000	0.30748	TGC	.	.		0.701	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
EDARADD	128178	hgsc.bcm.edu	37	1	236645629	236645629	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:236645629C>T	ENST00000334232.4	+	6	495	c.328C>T	c.(328-330)Ccc>Tcc	p.P110S	EDARADD_ENST00000359362.5_Missense_Mutation_p.P100S	NM_145861.2	NP_665860.2	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain	110					cell differentiation (GO:0030154)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	cytoplasm (GO:0005737)		p.P110T(1)		endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|stomach(1)	12	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GCTCCGGGCCCCCACCATAAG	0.478																																					p.P110S		Atlas-SNP	.											EDARADD,NS,carcinoma,0,1	EDARADD	31	.	1	Substitution - Missense(1)	lung(1)	c.C328T						.						82.0	79.0	80.0					1																	236645629		2203	4300	6503	SO:0001583	missense	128178	exon6			CGGGCCCCCACCA	AY028914	CCDS1610.1, CCDS31065.1	1q42.3	2013-05-22			ENSG00000186197	ENSG00000186197			14341	protein-coding gene	gene with protein product		606603				11780064	Standard	NM_145861		Approved		uc001hxu.1	Q8WWZ3	OTTHUMG00000039954	ENST00000334232.4:c.328C>T	chr1.hg19:g.236645629C>T	ENSP00000335076:p.Pro110Ser	143.0	0.0		73.0	4.0	NM_145861	A2VCK5|A8K7B5|B1AL54|B9ZVW5|Q5VYJ7	Missense_Mutation	SNP	ENST00000334232.4	hg19	CCDS1610.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.160516	0.57368	.	.	ENSG00000186197	ENST00000334232;ENST00000359362	T;D	0.82433	-1.04;-1.61	5.22	5.22	0.72569	.	0.000000	0.64402	U	0.000001	D	0.84678	0.5525	M	0.70275	2.135	0.52099	D	0.999943	P;P	0.42692	0.787;0.787	B;B	0.43251	0.322;0.413	D	0.84472	0.0600	9	.	.	.	.	18.9765	0.92738	0.0:1.0:0.0:0.0	.	100;110	A8K7B5;Q8WWZ3	.;EDAD_HUMAN	S	110;100	ENSP00000335076:P110S;ENSP00000352320:P100S	.	P	+	1	0	EDARADD	234712252	1.000000	0.71417	0.981000	0.43875	0.401000	0.30781	5.547000	0.67249	2.720000	0.93068	0.655000	0.94253	CCC	.	.		0.478	EDARADD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000096368.1	NM_145861	
RYR2	6262	hgsc.bcm.edu	37	1	237947885	237947885	+	Silent	SNP	C	C	T	rs267598440		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:237947885C>T	ENST00000366574.2	+	90	13190	c.12873C>T	c.(12871-12873)ttC>ttT	p.F4291F	RYR2_ENST00000542537.1_Silent_p.F4275F|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000360064.6_Silent_p.F4297F	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4291					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)			GGAGTATTTTCATGACCCTCT	0.478																																					p.F4291F		Atlas-SNP	.											.	RYR2	1273	.	0			c.C12873T						.						77.0	75.0	76.0					1																	237947885		1903	4117	6020	SO:0001819	synonymous_variant	6262	exon90			TATTTTCATGACC	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.12873C>T	chr1.hg19:g.237947885C>T		69.0	0.0		42.0	4.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.478	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
KMO	8564	hgsc.bcm.edu	37	1	241718930	241718930	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:241718930A>G	ENST00000366559.4	+	5	642	c.331A>G	c.(331-333)Aga>Gga	p.R111G	KMO_ENST00000366557.4_Missense_Mutation_p.R111G|KMO_ENST00000484628.1_3'UTR|KMO_ENST00000366558.3_Missense_Mutation_p.R111G	NM_003679.4	NP_003670.2			kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)											NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			TTCTGTAAGCAGAGAAAATCT	0.313																																					p.R111G		Atlas-SNP	.											.	KMO	69	.	0			c.A331G						.						91.0	93.0	92.0					1																	241718930		2202	4298	6500	SO:0001583	missense	8564	exon5			GTAAGCAGAGAAA	AF056032	CCDS1618.1	1q42-q44	2010-11-23			ENSG00000117009	ENSG00000117009	1.14.13.9		6381	protein-coding gene	gene with protein product		603538				9237672	Standard	NM_003679		Approved		uc009xgp.3	O15229	OTTHUMG00000039635	ENST00000366559.4:c.331A>G	chr1.hg19:g.241718930A>G	ENSP00000355517:p.Arg111Gly	94.0	0.0		84.0	4.0	NM_003679		Missense_Mutation	SNP	ENST00000366559.4	hg19	CCDS1618.1	.	.	.	.	.	.	.	.	.	.	A	19.66	3.869480	0.72065	.	.	ENSG00000117009	ENST00000366559;ENST00000366558;ENST00000366557	T;T;T	0.51071	0.72;0.72;0.72	5.54	5.54	0.83059	Monooxygenase, FAD-binding (1);	0.000000	0.85682	D	0.000000	T	0.79317	0.4425	H	0.97465	4.01	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.999	D	0.86406	0.1745	10	0.87932	D	0	.	13.6034	0.62033	1.0:0.0:0.0:0.0	.	111;111;111	O15229;A8K693;O15229-2	KMO_HUMAN;.;.	G	111	ENSP00000355517:R111G;ENSP00000355516:R111G;ENSP00000355515:R111G	ENSP00000355515:R111G	R	+	1	2	KMO	239785553	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.383000	0.66219	2.093000	0.63338	0.482000	0.46254	AGA	.	.		0.313	KMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095612.1	NM_003679	
WDR64	128025	hgsc.bcm.edu	37	1	241886642	241886642	+	Silent	SNP	C	C	A	rs145843472		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:241886642C>A	ENST00000366552.2	+	9	1275	c.1068C>A	c.(1066-1068)acC>acA	p.T356T	WDR64_ENST00000437684.2_Silent_p.T356T	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	356										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			ATATCAGCACCAAGCCAGTAG	0.453																																					p.T356T		Atlas-SNP	.											.	WDR64	234	.	0			c.C1068A						.						113.0	105.0	107.0					1																	241886642		2203	4300	6503	SO:0001819	synonymous_variant	128025	exon9			CAGCACCAAGCCA	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"""WD repeat domain containing"""	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1068C>A	chr1.hg19:g.241886642C>A		110.0	0.0		76.0	4.0	NM_144625	B1ANT0|Q7Z573|Q96LY9	Silent	SNP	ENST00000366552.2	hg19																																																																																				.	C|1.000;T|0.000		0.453	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625	
CNST	163882	hgsc.bcm.edu	37	1	246810803	246810803	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr1:246810803T>C	ENST00000366513.4	+	9	1569	c.1300T>C	c.(1300-1302)Ttg>Ctg	p.L434L	CNST_ENST00000483271.1_3'UTR|CNST_ENST00000366512.3_Silent_p.L434L	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	434					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						GACAGAGCCGTTGATTTCACC	0.507											OREG0014367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L434L		Atlas-SNP	.											.	CNST	73	.	0			c.T1300C						.						192.0	207.0	202.0					1																	246810803		2203	4300	6503	SO:0001819	synonymous_variant	163882	exon9			GAGCCGTTGATTT	AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26486	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 64"""	613439	"""chromosome 1 open reading frame 71"""	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.1300T>C	chr1.hg19:g.246810803T>C		121.0	0.0	2468	94.0	4.0	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Silent	SNP	ENST00000366513.4	hg19	CCDS1628.1																																																																																			.	.		0.507	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609	
SNTG2	54221	hgsc.bcm.edu	37	2	1168816	1168816	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:1168816T>C	ENST00000308624.5	+	8	667	c.538T>C	c.(538-540)Tcc>Ccc	p.S180P	SNTG2_ENST00000407292.1_Intron|SNTG2_ENST00000467759.1_3'UTR	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	180					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		CAGTGGGGCCTCCTCTCCCCT	0.473																																					p.S180P		Atlas-SNP	.											.	SNTG2	125	.	0			c.T538C						.						146.0	152.0	150.0					2																	1168816		1964	4141	6105	SO:0001583	missense	54221	exon8			GGGGCCTCCTCTC	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.538T>C	chr2.hg19:g.1168816T>C	ENSP00000311837:p.Ser180Pro	128.0	0.0		121.0	5.0	NM_018968	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	hg19	CCDS46220.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.461101	0.63513	.	.	ENSG00000172554	ENST00000308624	T	0.43294	0.95	4.73	4.73	0.59995	.	0.060105	0.64402	D	0.000002	T	0.56630	0.1998	M	0.72894	2.215	0.80722	D	1	D	0.64830	0.994	P	0.58077	0.832	T	0.58940	-0.7547	10	0.45353	T	0.12	.	12.4711	0.55787	0.0:0.0:0.0:1.0	.	180	Q9NY99	SNTG2_HUMAN	P	180	ENSP00000311837:S180P	ENSP00000311837:S180P	S	+	1	0	SNTG2	1158816	1.000000	0.71417	0.646000	0.29493	0.628000	0.37860	5.105000	0.64591	1.748000	0.51833	0.523000	0.50628	TCC	.	.		0.473	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968	
GREB1	9687	hgsc.bcm.edu	37	2	11778934	11778934	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:11778934A>G	ENST00000381486.2	+	32	5985	c.5685A>G	c.(5683-5685)aaA>aaG	p.K1895K	GREB1_ENST00000234142.5_Splice_Site_p.K1895K|GREB1_ENST00000396123.1_Splice_Site_p.K893K	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1895						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		ATTTTCTGAAAGGTAACTTTT	0.463																																					p.K1895K	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.A5685G						.						114.0	102.0	106.0					2																	11778934		1881	4119	6000	SO:0001630	splice_region_variant	9687	exon32			TCTGAAAGGTAAC		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.5686+1A>G	chr2.hg19:g.11778934A>G		178.0	0.0		141.0	6.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	hg19	CCDS42655.1																																																																																			.	.		0.463	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	Silent
NBAS	51594	hgsc.bcm.edu	37	2	15694236	15694236	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:15694236C>A	ENST00000281513.5	-	4	261	c.236G>T	c.(235-237)gGa>gTa	p.G79V	NBAS_ENST00000441750.1_Missense_Mutation_p.G79V	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	79					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						GCGAACCAGTCCATCAGGGAG	0.368																																					p.G79V		Atlas-SNP	.											.	NBAS	246	.	0			c.G236T						.						102.0	100.0	101.0					2																	15694236		2203	4300	6503	SO:0001583	missense	51594	exon4			ACCAGTCCATCAG	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.236G>T	chr2.hg19:g.15694236C>A	ENSP00000281513:p.Gly79Val	124.0	0.0		124.0	5.0	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.468217	0.43839	.	.	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.09445	2.98;3.13	5.33	4.45	0.53987	.	0.057690	0.64402	D	0.000001	T	0.24736	0.0600	L	0.51422	1.61	0.43959	D	0.996633	D	0.89917	1.0	D	0.70227	0.968	T	0.00677	-1.1614	10	0.87932	D	0	.	10.9663	0.47414	0.0:0.9114:0.0:0.0886	.	79	A2RRP1	NBAS_HUMAN	V	79	ENSP00000413201:G79V;ENSP00000281513:G79V	ENSP00000281513:G79V	G	-	2	0	NBAS	15611687	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	4.005000	0.57075	1.238000	0.43771	0.305000	0.20034	GGA	.	.		0.368	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
UBXN2A	165324	hgsc.bcm.edu	37	2	24199877	24199877	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:24199877C>A	ENST00000309033.4	+	4	463	c.219C>A	c.(217-219)acC>acA	p.T73T	UBXN2A_ENST00000446425.2_3'UTR|UBXN2A_ENST00000535786.1_Silent_p.T73T|UBXN2A_ENST00000404924.1_Silent_p.T73T	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	73	SEP. {ECO:0000255|PROSITE- ProRule:PRU00732}.				regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)				endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						ACGGATTCACCGTCAACGACG	0.398																																					p.T73T		Atlas-SNP	.											UBXN2A,colon,carcinoma,0,1	UBXN2A	20	.	0			c.C219A						.						81.0	80.0	80.0					2																	24199877		2203	4300	6503	SO:0001819	synonymous_variant	165324	exon4			ATTCACCGTCAAC	BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960		"""UBX domain containing"""	27265	protein-coding gene	gene with protein product			"""UBX domain containing 4"""	UBXD4		12477932	Standard	NM_181713		Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.219C>A	chr2.hg19:g.24199877C>A		82.0	0.0		52.0	3.0	NM_181713	A8K577|B7ZKP8|Q569G8	Silent	SNP	ENST00000309033.4	hg19	CCDS1704.1																																																																																			.	.		0.398	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246824.2	NM_181713	
HADHB	3032	hgsc.bcm.edu	37	2	26502146	26502146	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:26502146A>G	ENST00000317799.5	+	9	878	c.774A>G	c.(772-774)gaA>gaG	p.E258E	HADHB_ENST00000537713.1_Silent_p.E243E|HADHB_ENST00000545822.1_Silent_p.E236E|HADHB_ENST00000405867.3_Intron|HADHB_ENST00000494615.1_3'UTR	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	258					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACAGGATGAAGGACTCCTTT	0.473																																					p.E258E		Atlas-SNP	.											.	HADHB	50	.	0			c.A774G						.						98.0	92.0	94.0					2																	26502146		2203	4300	6503	SO:0001819	synonymous_variant	3032	exon9			GGATGAAGGACTC		CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"""mitochondrial trifunctional protein, beta subunit"""	143450	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"""			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.774A>G	chr2.hg19:g.26502146A>G		131.0	0.0		83.0	4.0	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Silent	SNP	ENST00000317799.5	hg19	CCDS1722.1																																																																																			.	.		0.473	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183	
OTOF	9381	hgsc.bcm.edu	37	2	26699053	26699053	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:26699053T>C	ENST00000272371.2	-	23	2935	c.2809A>G	c.(2809-2811)Aag>Gag	p.K937E	OTOF_ENST00000402415.3_Missense_Mutation_p.K247E|OTOF_ENST00000338581.6_Missense_Mutation_p.K190E|OTOF_ENST00000339598.3_Missense_Mutation_p.K190E|OTOF_ENST00000403946.3_Missense_Mutation_p.K937E	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	937					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGGCTGCCTTGACCTCCTGG	0.657																																					p.K937E	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.A2809G						.						35.0	35.0	35.0					2																	26699053		2200	4297	6497	SO:0001583	missense	9381	exon23			CTGCCTTGACCTC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2809A>G	chr2.hg19:g.26699053T>C	ENSP00000272371:p.Lys937Glu	56.0	0.0		51.0	4.0	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	T	18.06	3.539003	0.65085	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;T;T	0.80214	-1.11;-1.12;-1.08;-1.35;-1.35	5.41	4.24	0.50183	.	0.377728	0.31989	N	0.006744	T	0.77725	0.4173	L	0.49126	1.545	0.58432	D	0.999992	P;B;P;B	0.52061	0.799;0.042;0.95;0.356	B;B;P;B	0.48334	0.255;0.037;0.574;0.138	T	0.72711	-0.4211	10	0.22706	T	0.39	-38.1605	10.695	0.45894	0.1432:0.0:0.0:0.8568	.	937;190;247;190	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	E	190;190;247;937;937	ENSP00000345137:K190E;ENSP00000344521:K190E;ENSP00000383906:K247E;ENSP00000272371:K937E;ENSP00000385255:K937E	ENSP00000272371:K937E	K	-	1	0	OTOF	26552557	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.084000	0.71335	0.878000	0.35920	0.459000	0.35465	AAG	.	.		0.657	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
DPYSL5	56896	hgsc.bcm.edu	37	2	27147810	27147810	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:27147810A>G	ENST00000288699.6	+	3	475	c.317A>G	c.(316-318)gAg>gGg	p.E106G	DPYSL5_ENST00000401478.1_Missense_Mutation_p.E106G	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	106					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)|signal transduction (GO:0007165)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			breast(1)|endometrium(5)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCGACAAGGAGACCTCCCTT	0.637																																					p.E106G		Atlas-SNP	.											.	DPYSL5	69	.	0			c.A317G						.						92.0	80.0	84.0					2																	27147810		2203	4300	6503	SO:0001583	missense	56896	exon3			ACAAGGAGACCTC	AF264015	CCDS1730.1	2p23.3	2008-02-05			ENSG00000157851	ENSG00000157851			20637	protein-coding gene	gene with protein product		608383				10851247, 11034345	Standard	NM_020134		Approved	CRMP5, Ulip6, CRMP-5, CRAM	uc002rhu.4	Q9BPU6	OTTHUMG00000097071	ENST00000288699.6:c.317A>G	chr2.hg19:g.27147810A>G	ENSP00000288699:p.Glu106Gly	101.0	0.0		81.0	4.0	NM_001253724	Q8TCL6|Q9NQC4|Q9NRY9	Missense_Mutation	SNP	ENST00000288699.6	hg19	CCDS1730.1	.	.	.	.	.	.	.	.	.	.	A	6.794	0.515436	0.12944	.	.	ENSG00000157851	ENST00000450961;ENST00000288699;ENST00000401478;ENST00000431402;ENST00000434719	T;D;D;T;T	0.89343	-0.95;-2.5;-2.5;-0.92;-0.94	4.96	4.96	0.65561	Amidohydrolase 1 (1);	0.262941	0.43110	D	0.000611	T	0.60560	0.2278	N	0.00150	-1.985	0.40576	D	0.981343	B	0.02656	0.0	B	0.04013	0.001	T	0.68383	-0.5423	10	0.02654	T	1	-31.3377	13.9042	0.63823	1.0:0.0:0.0:0.0	.	106	Q9BPU6	DPYL5_HUMAN	G	106	ENSP00000407174:E106G;ENSP00000288699:E106G;ENSP00000385549:E106G;ENSP00000399581:E106G;ENSP00000413075:E106G	ENSP00000288699:E106G	E	+	2	0	DPYSL5	27001314	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	4.858000	0.62947	1.993000	0.58246	0.482000	0.46254	GAG	.	.		0.637	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	NM_020134	
MAPRE3	22924	hgsc.bcm.edu	37	2	27248785	27248785	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:27248785A>G	ENST00000233121.2	+	6	860	c.662A>G	c.(661-663)aAg>aGg	p.K221R	MAPRE3_ENST00000405074.3_Missense_Mutation_p.K206R|MAPRE3_ENST00000402218.1_Missense_Mutation_p.K206R			Q9UPY8	MARE3_HUMAN	microtubule-associated protein, RP/EB family, member 3	221	APC-binding.|DCTN1-binding.|EB1 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00576}.				mitotic nuclear division (GO:0007067)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule plus-end binding (GO:1903033)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|upper_aerodigestive_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGCTGGAGAAGGAACGTGAC	0.532																																					p.K221R		Atlas-SNP	.											.	MAPRE3	40	.	0			c.A662G						.						113.0	100.0	104.0					2																	27248785		2203	4300	6503	SO:0001583	missense	22924	exon6			TGGAGAAGGAACG	Y11174	CCDS1731.1	2p23.3-p23.1	2008-06-04			ENSG00000084764	ENSG00000084764			6892	protein-coding gene	gene with protein product		605788				9233623	Standard	NM_012326		Approved	RP3, EB3	uc002rhw.3	Q9UPY8	OTTHUMG00000097067	ENST00000233121.2:c.662A>G	chr2.hg19:g.27248785A>G	ENSP00000233121:p.Lys221Arg	96.0	0.0		86.0	4.0	NM_012326	B7WPK5|O00265|Q6FHB0|Q6FI15|Q9BZP7|Q9BZP8	Missense_Mutation	SNP	ENST00000233121.2	hg19	CCDS1731.1	.	.	.	.	.	.	.	.	.	.	a	23.3	4.402264	0.83230	.	.	ENSG00000084764	ENST00000233121;ENST00000405074;ENST00000402218	T;T;T	0.49139	0.79;0.81;0.81	5.68	4.49	0.54785	EB1, C-terminal (2);	0.090131	0.64402	D	0.000003	T	0.59418	0.2192	L	0.60067	1.865	0.80722	D	1	P;P	0.49961	0.552;0.93	P;P	0.59643	0.584;0.861	T	0.59841	-0.7378	10	0.59425	D	0.04	-17.9221	11.0054	0.47631	0.86:0.0:0.0:0.14	.	206;221	Q9UPY8-2;Q9UPY8	.;MARE3_HUMAN	R	221;206;206	ENSP00000233121:K221R;ENSP00000383915:K206R;ENSP00000385715:K206R	ENSP00000233121:K221R	K	+	2	0	MAPRE3	27102289	1.000000	0.71417	0.978000	0.43139	0.764000	0.43329	9.262000	0.95591	0.932000	0.37266	0.529000	0.55759	AAG	.	.		0.532	MAPRE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214183.1	NM_012326	
TMEM214	54867	hgsc.bcm.edu	37	2	27258486	27258486	+	Missense_Mutation	SNP	G	G	A	rs375315795		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:27258486G>A	ENST00000238788.9	+	4	589	c.527G>A	c.(526-528)cGg>cAg	p.R176Q	TMEM214_ENST00000404032.3_Intron	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	176					apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CTGGTGAGCCGGGAGCTACGT	0.562																																					p.R176Q		Atlas-SNP	.											.	TMEM214	41	.	0			c.G527A						.	G	,GLN/ARG	1,3907		0,1,1953	87.0	91.0	90.0		,527	1.7	0.7	2		90	0,8296		0,0,4148	no	intron,missense	TMEM214	NM_001083590.1,NM_017727.4	,43	0,1,6101	AA,AG,GG		0.0,0.0256,0.0082	,benign	,176/690	27258486	1,12203	1954	4148	6102	SO:0001583	missense	54867	exon4			TGAGCCGGGAGCT		CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.527G>A	chr2.hg19:g.27258486G>A	ENSP00000238788:p.Arg176Gln	88.0	0.0		59.0	15.0	NM_017727	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Missense_Mutation	SNP	ENST00000238788.9	hg19	CCDS42664.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816211	0.50527	2.56E-4	0.0	ENSG00000119777	ENST00000238788	T	0.43294	0.95	5.67	1.66	0.24008	.	0.405771	0.25372	N	0.031153	T	0.31513	0.0799	L	0.51422	1.61	0.80722	D	1	B	0.13594	0.008	B	0.04013	0.001	T	0.07102	-1.0790	10	0.41790	T	0.15	-5.0376	5.3239	0.15895	0.4238:0.1366:0.4395:0.0	.	176	Q6NUQ4	TM214_HUMAN	Q	176	ENSP00000238788:R176Q	ENSP00000238788:R176Q	R	+	2	0	TMEM214	27111990	1.000000	0.71417	0.698000	0.30274	0.956000	0.61745	1.941000	0.40233	0.011000	0.14865	0.561000	0.74099	CGG	.	.		0.562	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727	
YPEL5	51646	hgsc.bcm.edu	37	2	30381672	30381672	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:30381672A>G	ENST00000379520.3	+	5	833	c.329A>G	c.(328-330)gAg>gGg	p.E110G	YPEL5_ENST00000495673.1_3'UTR|YPEL5_ENST00000261353.4_Missense_Mutation_p.E110G|YPEL5_ENST00000402003.3_Missense_Mutation_p.E110G|YPEL5_ENST00000379519.3_Missense_Mutation_p.E110G|YPEL5_ENST00000402708.1_Missense_Mutation_p.E110G	NM_001127401.1	NP_001120873.1	P62699	YPEL5_HUMAN	yippee-like 5 (Drosophila)	110										NS(1)|endometrium(1)|kidney(1)|lung(3)|prostate(1)	7	Acute lymphoblastic leukemia(172;0.155)					CGAGAGAGTGAGGGCTTTGAG	0.448																																					p.E110G		Atlas-SNP	.											.	YPEL5	16	.	0			c.A329G						.						103.0	80.0	88.0					2																	30381672		2203	4300	6503	SO:0001583	missense	51646	exon4			AGAGTGAGGGCTT	AF135161	CCDS1771.1	2p23	2004-06-28			ENSG00000119801	ENSG00000119801			18329	protein-coding gene	gene with protein product		609726					Standard	NM_016061		Approved	CGI-127	uc002rmz.4	P62699	OTTHUMG00000097839	ENST00000379520.3:c.329A>G	chr2.hg19:g.30381672A>G	ENSP00000368835:p.Glu110Gly	84.0	0.0		76.0	4.0	NM_001127400	D6W568|Q65Z97|Q8R174|Q9D6M1|Q9UMX7|Q9Y3C9	Missense_Mutation	SNP	ENST00000379520.3	hg19	CCDS1771.1	.	.	.	.	.	.	.	.	.	.	.	16.99	3.274272	0.59649	.	.	ENSG00000119801	ENST00000379520;ENST00000379519;ENST00000261353;ENST00000402003;ENST00000402708	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.42200	0.1192	N	0.11818	0.18	0.80722	D	1	B	0.29188	0.236	B	0.30029	0.11	T	0.41179	-0.9523	9	0.48119	T	0.1	-1.1754	15.0511	0.71872	1.0:0.0:0.0:0.0	.	110	P62699	YPEL5_HUMAN	G	110	.	ENSP00000261353:E110G	E	+	2	0	YPEL5	30235176	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.090000	0.94144	2.145000	0.66743	0.533000	0.62120	GAG	.	.		0.448	YPEL5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215128.1	NM_016061	
HEATR5B	54497	hgsc.bcm.edu	37	2	37246965	37246965	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:37246965G>T	ENST00000233099.5	-	26	4186	c.4091C>A	c.(4090-4092)gCg>gAg	p.A1364E	HEATR5B_ENST00000354531.2_Missense_Mutation_p.A1364E	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1364						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				GCAAGCTTTCGCTATTATATC	0.308																																					p.A1364E		Atlas-SNP	.											HEATR5B,NS,carcinoma,0,1	HEATR5B	185	.	0			c.C4091A						.						77.0	83.0	81.0					2																	37246965		2203	4300	6503	SO:0001583	missense	54497	exon26			GCTTTCGCTATTA	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.4091C>A	chr2.hg19:g.37246965G>T	ENSP00000233099:p.Ala1364Glu	51.0	0.0		39.0	2.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	G	32	5.118482	0.94385	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.52057	0.68;0.68	5.73	5.73	0.89815	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68109	0.2965	M	0.65320	2	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.64884	-0.6302	10	0.42905	T	0.14	-20.3084	19.9026	0.96993	0.0:0.0:1.0:0.0	.	1364	Q9P2D3	HTR5B_HUMAN	E	1364	ENSP00000233099:A1364E;ENSP00000346531:A1364E	ENSP00000233099:A1364E	A	-	2	0	HEATR5B	37100469	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.763000	0.98947	2.707000	0.92482	0.643000	0.83706	GCG	.	.		0.308	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
FBXO11	80204	hgsc.bcm.edu	37	2	48132835	48132835	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:48132835G>A	ENST00000403359.3	-	1	97	c.25C>T	c.(25-27)Cgg>Tgg	p.R9W	FBXO11_ENST00000378314.3_5'Flank|AC079807.2_ENST00000439870.1_RNA|AC079807.2_ENST00000417692.1_RNA|AC079807.2_ENST00000432064.1_RNA|FBXO11_ENST00000316377.4_5'Flank	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	9					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTGGGTCTCCGGTTGGCGGCT	0.726			"""Mis, F, D"""		DLBCL																																p.R9W		Atlas-SNP	.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11	127	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.C25T						.						3.0	3.0	3.0					2																	48132835		756	1788	2544	SO:0001583	missense	80204	exon1			GTCTCCGGTTGGC	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"""Ubiquitin protein ligase E3 component n-recognins"", ""F-boxes /  ""other"""""	13590	protein-coding gene	gene with protein product	"""ubiquitin protein ligase E3 component n-recognin 6"""	607871	"""F-box only protein 11"""			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.25C>T	chr2.hg19:g.48132835G>A	ENSP00000384823:p.Arg9Trp	111.0	0.0		86.0	4.0	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	hg19	CCDS54357.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.364292	0.41902	.	.	ENSG00000138081	ENST00000403359	T	0.55413	0.52	2.23	2.23	0.28157	.	.	.	.	.	T	0.34308	0.0893	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.26643	-1.0097	7	0.87932	D	0	-8.703	6.137	0.20239	0.0:0.0:0.6988:0.3012	.	.	.	.	W	9	ENSP00000384823:R9W	ENSP00000384823:R9W	R	-	1	2	FBXO11	47986339	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.517000	0.35867	1.225000	0.43566	0.491000	0.48974	CGG	.	.		0.726	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133	
CLHC1	130162	hgsc.bcm.edu	37	2	55433452	55433452	+	Silent	SNP	A	A	G	rs151168260		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:55433452A>G	ENST00000401408.1	-	9	1305	c.960T>C	c.(958-960)agT>agC	p.S320S	CLHC1_ENST00000407122.1_Silent_p.S320S|CLHC1_ENST00000494539.1_Intron|CLHC1_ENST00000406437.2_Intron|CLHC1_ENST00000406076.1_Silent_p.S198S	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	320																	TTCTTCTAGGACTGTTTGCTG	0.313																																					p.S320S		Atlas-SNP	.											.	.	.	.	0			c.T960C						.	A	,	0,4404		0,0,2202	104.0	105.0	104.0		594,960	3.3	1.0	2	dbSNP_134	104	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous	C2orf63	NM_001135598.1,NM_152385.2	,	0,1,6500	GG,GA,AA		0.0116,0.0,0.0077	,	198/465,320/587	55433452	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	130162	exon9			TCTAGGACTGTTT		CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 63"""	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.960T>C	chr2.hg19:g.55433452A>G		97.0	0.0		97.0	4.0	NM_152385	B2RDV1|Q53R93|Q8N403	Silent	SNP	ENST00000401408.1	hg19	CCDS33201.1																																																																																			.	A|1.000;G|0.000		0.313	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385	
ARHGAP25	9938	hgsc.bcm.edu	37	2	69043419	69043419	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:69043419A>G	ENST00000295381.3	+	7	1223		c.e7-1		ARHGAP25_ENST00000544262.1_3'UTR|ARHGAP25_ENST00000409202.3_Splice_Site|ARHGAP25_ENST00000409030.3_Splice_Site|ARHGAP25_ENST00000467265.1_Splice_Site|ARHGAP25_ENST00000497079.1_Splice_Site|ARHGAP25_ENST00000409220.1_Splice_Site|ARHGAP25_ENST00000479844.1_5'Flank	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25						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(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						ATCTCTTCCCAGGCTCAGCAG	0.493																																					.		Atlas-SNP	.											.	ARHGAP25	175	.	0			c.688-2A>G						.						97.0	90.0	93.0					2																	69043419		2203	4300	6503	SO:0001630	splice_region_variant	9938	exon6			CTTCCCAGGCTCA	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.805-1A>G	chr2.hg19:g.69043419A>G		88.0	0.0		78.0	4.0	NM_001166277	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Splice_Site	SNP	ENST00000295381.3	hg19		.	.	.	.	.	.	.	.	.	.	A	23.0	4.361753	0.82353	.	.	ENSG00000163219	ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000497079;ENST00000543533;ENST00000497259	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4228	0.75025	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARHGAP25	68896923	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.938000	0.92943	2.241000	0.73720	0.477000	0.44152	.	.	.		0.493	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	Intron
C2orf42	54980	hgsc.bcm.edu	37	2	70408789	70408789	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:70408789A>G	ENST00000264434.2	-	3	708	c.329T>C	c.(328-330)cTg>cCg	p.L110P	C2orf42_ENST00000420306.1_Missense_Mutation_p.L110P|C2orf42_ENST00000470096.1_5'UTR	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	110										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						TCCAGAGCTCAGCTGAGTGAT	0.562																																					p.L110P		Atlas-SNP	.											.	C2orf42	30	.	0			c.T329C						.						85.0	74.0	78.0					2																	70408789		2203	4300	6503	SO:0001583	missense	54980	exon3			GAGCTCAGCTGAG	AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.329T>C	chr2.hg19:g.70408789A>G	ENSP00000264434:p.Leu110Pro	120.0	0.0		100.0	4.0	NM_017880	D6W5G3|Q9H629	Missense_Mutation	SNP	ENST00000264434.2	hg19	CCDS1899.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.913753	0.72983	.	.	ENSG00000115998	ENST00000264434;ENST00000420306;ENST00000447804;ENST00000417865;ENST00000419381;ENST00000457952	T;T	0.49720	0.77;0.77	4.96	4.96	0.65561	.	0.075820	0.49916	D	0.000128	T	0.50939	0.1645	L	0.43152	1.355	0.80722	D	1	D	0.54207	0.965	P	0.53649	0.731	T	0.42682	-0.9437	10	0.27082	T	0.32	-9.575	13.6431	0.62265	1.0:0.0:0.0:0.0	.	110	Q9NWW7	CB042_HUMAN	P	110	ENSP00000264434:L110P;ENSP00000404515:L110P	ENSP00000264434:L110P	L	-	2	0	C2orf42	70262293	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.090000	0.89526	2.082000	0.62665	0.397000	0.26171	CTG	.	.		0.562	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880	
TIA1	7072	hgsc.bcm.edu	37	2	70441567	70441567	+	Silent	SNP	T	T	C	rs373531585		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:70441567T>C	ENST00000433529.2	-	12	1158	c.948A>G	c.(946-948)gcA>gcG	p.A316A	TIA1_ENST00000282574.4_Silent_p.A315A|C2orf42_ENST00000470096.1_Intron|TIA1_ENST00000415783.2_Silent_p.A305A|TIA1_ENST00000445587.1_Intron|TIA1_ENST00000482876.1_5'Flank	NM_022173.2	NP_071505.2	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein	316					apoptotic process (GO:0006915)|negative regulation of cytokine biosynthetic process (GO:0042036)|negative regulation of translation (GO:0017148)|regulation of mRNA splicing, via spliceosome (GO:0048024)	cytoplasmic stress granule (GO:0010494)|nuclear stress granule (GO:0097165)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	17						CAATTTGTTGTGCATTTCCAT	0.383																																					p.A316A		Atlas-SNP	.											.	TIA1	37	.	0			c.A948G						.						109.0	92.0	98.0					2																	70441567		2203	4300	6503	SO:0001819	synonymous_variant	7072	exon12			TTGTTGTGCATTT		CCDS1900.1, CCDS1901.1	2p13	2013-02-12	2001-11-28		ENSG00000116001	ENSG00000116001		"""RNA binding motif (RRM) containing"""	11802	protein-coding gene	gene with protein product	"""T-cell-restricted intracellular antigen-1"", ""nucleolysin TIA-1 isoform p40"""	603518	"""TIA1 cytotoxic granule-associated RNA-binding protein"""			8176212, 12486009	Standard	NM_022173		Approved		uc002sgj.4	P31483	OTTHUMG00000129644	ENST00000433529.2:c.948A>G	chr2.hg19:g.70441567T>C		152.0	0.0		123.0	5.0	NM_022173	Q53SS9	Silent	SNP	ENST00000433529.2	hg19	CCDS1901.1																																																																																			.	.		0.383	TIA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251842.2	NM_022037	
DYSF	8291	hgsc.bcm.edu	37	2	71892352	71892352	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:71892352C>T	ENST00000258104.3	+	46	5395	c.5118C>T	c.(5116-5118)tgC>tgT	p.C1706C	DYSF_ENST00000409762.1_Silent_p.C1723C|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000413539.2_Silent_p.C1737C|DYSF_ENST00000409366.1_Silent_p.C1728C|DYSF_ENST00000409744.1_Silent_p.C1714C|DYSF_ENST00000394120.2_Silent_p.C1707C|DYSF_ENST00000409582.3_Silent_p.C1744C|DYSF_ENST00000409651.1_Silent_p.C1738C|DYSF_ENST00000410020.3_Silent_p.C1745C|DYSF_ENST00000429174.2_Silent_p.C1727C|DYSF_ENST00000410041.1_Silent_p.C1724C	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1706					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						ACCTCTTCTGCCAGCAGCATA	0.537																																					p.C1745C		Atlas-SNP	.											.	DYSF	536	.	0			c.C5235T						.						103.0	104.0	104.0					2																	71892352		2203	4300	6503	SO:0001819	synonymous_variant	8291	exon47			CTTCTGCCAGCAG	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.5118C>T	chr2.hg19:g.71892352C>T		83.0	0.0		57.0	4.0	NM_001130987	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	hg19	CCDS1918.1																																																																																			.	.		0.537	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
DCTN1	1639	hgsc.bcm.edu	37	2	74590545	74590545	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:74590545G>A	ENST00000361874.3	-	28	3538	c.3221C>T	c.(3220-3222)cCt>cTt	p.P1074L	DCTN1_ENST00000407639.2_Missense_Mutation_p.P940L|DCTN1_ENST00000495643.1_5'Flank|RP11-287D1.3_ENST00000451608.2_5'Flank|DCTN1_ENST00000394003.3_Missense_Mutation_p.P1067L|DCTN1_ENST00000409438.1_Missense_Mutation_p.P935L|DCTN1_ENST00000409567.3_Missense_Mutation_p.P1049L|DCTN1_ENST00000409240.1_Missense_Mutation_p.P1032L|DCTN1_ENST00000409868.1_Missense_Mutation_p.P1052L	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	1074					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						AGCCTGCCCAGGGATGGCTCC	0.577																																					p.P1074L		Atlas-SNP	.											.	DCTN1	110	.	0			c.C3221T						.						19.0	19.0	19.0					2																	74590545		2202	4300	6502	SO:0001583	missense	1639	exon28			TGCCCAGGGATGG		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.3221C>T	chr2.hg19:g.74590545G>A	ENSP00000354791:p.Pro1074Leu	64.0	0.0		50.0	4.0	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	hg19	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	G	4.597	0.110890	0.08831	.	.	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.78481	-0.78;-0.96;-0.78;-0.78;-1.18;-0.96;-0.96	4.72	4.72	0.59763	.	0.192725	0.25683	N	0.028992	T	0.60856	0.2301	N	0.05230	-0.09	0.21445	N	0.999685	B;B;B;B;B;B;B	0.12013	0.001;0.0;0.003;0.0;0.0;0.005;0.0	B;B;B;B;B;B;B	0.19391	0.001;0.0;0.011;0.003;0.0;0.025;0.0	T	0.50775	-0.8788	10	0.32370	T	0.25	-3.8028	16.6006	0.84815	0.0:0.0:1.0:0.0	.	1049;1032;1074;1067;940;935;1057	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4;A8MWX9	.;.;DCTN1_HUMAN;.;.;.;.	L	1074;1067;1057;940;935;1032;1052;1049	ENSP00000354791:P1074L;ENSP00000377571:P1067L;ENSP00000384844:P940L;ENSP00000387270:P935L;ENSP00000386406:P1032L;ENSP00000387327:P1052L;ENSP00000386843:P1049L	ENSP00000354791:P1074L	P	-	2	0	DCTN1	74444053	0.404000	0.25328	0.669000	0.29828	0.678000	0.39670	2.786000	0.47790	2.424000	0.82194	0.643000	0.83706	CCT	.	.		0.577	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
CTNNA2	1496	hgsc.bcm.edu	37	2	80101205	80101205	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:80101205C>A	ENST00000402739.4	+	5	594	c.589C>A	c.(589-591)Ctg>Atg	p.L197M	CTNNA2_ENST00000361291.4_Missense_Mutation_p.L231M|CTNNA2_ENST00000541047.1_Missense_Mutation_p.L197M|CTNNA2_ENST00000496558.1_Missense_Mutation_p.L197M|CTNNA2_ENST00000466387.1_Missense_Mutation_p.L197M|CTNNA2_ENST00000540488.1_Missense_Mutation_p.L197M	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	197					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CACACAGGAGCTGAAGGATCC	0.483																																					p.L197M		Atlas-SNP	.											.	CTNNA2	462	.	0			c.C589A						.						39.0	41.0	40.0					2																	80101205		1984	4172	6156	SO:0001583	missense	1496	exon6			CAGGAGCTGAAGG		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.589C>A	chr2.hg19:g.80101205C>A	ENSP00000384638:p.Leu197Met	60.0	0.0		72.0	4.0	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	hg19		.	.	.	.	.	.	.	.	.	.	C	19.20	3.782220	0.70222	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488	T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	5.7	3.89	0.44902	Vinculin, conserved site (1);	0.000000	0.64402	D	0.000005	D	0.82365	0.5021	M	0.92122	3.275	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.994;0.997	D	0.86239	0.1642	10	0.72032	D	0.01	.	12.5675	0.56318	0.0:0.863:0.0:0.137	.	197;197;197	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	M	197;197;231;197;197;197	ENSP00000418191:L197M;ENSP00000419295:L197M;ENSP00000355398:L231M;ENSP00000384638:L197M;ENSP00000444675:L197M;ENSP00000441705:L197M	ENSP00000355398:L231M	L	+	1	2	CTNNA2	79954713	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	4.079000	0.57613	1.413000	0.46997	0.650000	0.86243	CTG	.	.		0.483	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
CAPG	822	hgsc.bcm.edu	37	2	85628289	85628289	+	Splice_Site	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:85628289T>C	ENST00000409921.1	-	5	581	c.515A>G	c.(514-516)cAg>cGg	p.Q172R	CAPG_ENST00000409670.1_Splice_Site_p.Q172R|CAPG_ENST00000483659.1_5'UTR|CAPG_ENST00000263867.4_Splice_Site_p.Q172R|CAPG_ENST00000409724.1_Splice_Site_p.Q172R			Q9BPX3	CND3_HUMAN	capping protein (actin filament), gelsolin-like	0					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)	11						CCTACCCACCTGGCCCAGGTC	0.592																																					p.Q172R		Atlas-SNP	.											.	CAPG	32	.	0			c.A515G						.						126.0	119.0	121.0					2																	85628289		2203	4300	6503	SO:0001630	splice_region_variant	822	exon5			CCCACCTGGCCCA	M94345	CCDS1974.1, CCDS58715.1	2p11.2	2008-06-04			ENSG00000042493	ENSG00000042493			1474	protein-coding gene	gene with protein product	"""macrophage capping protein"""	153615		AFCP		1322908, 12754261	Standard	NM_001747		Approved	MCP	uc010fgi.2	P40121	OTTHUMG00000130183	ENST00000409921.1:c.516+1A>G	chr2.hg19:g.85628289T>C		159.0	0.0		144.0	6.0	NM_001256140	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000409921.1	hg19	CCDS58715.1	.	.	.	.	.	.	.	.	.	.	T	14.69	2.610289	0.46527	.	.	ENSG00000042493	ENST00000542681;ENST00000263867;ENST00000409921;ENST00000409670;ENST00000409724;ENST00000439385;ENST00000449030;ENST00000447219;ENST00000409275	T;T;T;T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47;0.47;0.47;0.47	5.97	2.21	0.28008	Gelsolin domain (1);	0.316113	0.38720	N	0.001581	T	0.31389	0.0795	N	0.17594	0.5	0.35580	D	0.80621	B;B;B	0.15930	0.001;0.0;0.015	B;B;B	0.21917	0.002;0.001;0.037	T	0.14727	-1.0462	10	0.35671	T	0.21	.	5.3512	0.16036	0.0:0.1584:0.1483:0.6933	.	151;172;172	B4DU58;B8ZZS7;P40121	.;.;CAPG_HUMAN	R	151;172;172;172;172;172;172;172;172	ENSP00000263867:Q172R;ENSP00000387063:Q172R;ENSP00000386315:Q172R;ENSP00000386965:Q172R;ENSP00000391923:Q172R;ENSP00000403330:Q172R;ENSP00000398232:Q172R;ENSP00000386596:Q172R	ENSP00000263867:Q172R	Q	-	2	0	CAPG	85481800	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.744000	0.38268	0.495000	0.27882	0.533000	0.62120	CAG	.	.		0.592	CAPG-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329383.1	NM_001747	Missense_Mutation
RPIA	22934	hgsc.bcm.edu	37	2	89036184	89036184	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:89036184C>T	ENST00000283646.4	+	7	784	c.729C>T	c.(727-729)gtC>gtT	p.V243V		NM_144563.2	NP_653164.2	P49247	RPIA_HUMAN	ribose 5-phosphate isomerase A	243					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|ribose phosphate metabolic process (GO:0019693)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	monosaccharide binding (GO:0048029)|ribose-5-phosphate isomerase activity (GO:0004751)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18		Acute lymphoblastic leukemia(2;0.000456)|all_hematologic(2;0.00287)				GAATGGCTGTCAACAAGGCTG	0.572																																					p.V243V		Atlas-SNP	.											.	RPIA	35	.	0			c.C729T						.						133.0	146.0	142.0					2																	89036184		2030	4187	6217	SO:0001819	synonymous_variant	22934	exon7			GGCTGTCAACAAG	L35035	CCDS2004.2	2p11.2	2008-07-31	2008-07-31		ENSG00000153574	ENSG00000153574	5.3.1.6		10297	protein-coding gene	gene with protein product	"""ribose 5-phosphate epimerase"""	180430				7758956	Standard	NM_144563		Approved		uc002ste.3	P49247	OTTHUMG00000130333	ENST00000283646.4:c.729C>T	chr2.hg19:g.89036184C>T		94.0	0.0		70.0	4.0	NM_144563	Q541P9|Q96BJ6	Silent	SNP	ENST00000283646.4	hg19	CCDS2004.2																																																																																			.	.		0.572	RPIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252683.2		
ZNF514	84874	hgsc.bcm.edu	37	2	95815310	95815310	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:95815310T>C	ENST00000295208.2	-	5	1382	c.920A>G	c.(919-921)cAg>cGg	p.Q307R	ZNF514_ENST00000411425.1_Missense_Mutation_p.Q307R|MRPS5_ENST00000475040.1_5'Flank	NM_032788.1	NP_116177.1	Q96K75	ZN514_HUMAN	zinc finger protein 514	307					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)			large_intestine(4)|lung(6)|urinary_tract(1)	11						ATGAGTCCTCTGATGCTTAAT	0.438																																					p.Q307R		Atlas-SNP	.											.	ZNF514	34	.	0			c.A920G						.						66.0	70.0	69.0					2																	95815310		2203	4300	6503	SO:0001583	missense	84874	exon5			GTCCTCTGATGCT	AL832263	CCDS2011.1	2q11.2	2013-01-08			ENSG00000144026	ENSG00000144026		"""Zinc fingers, C2H2-type"", ""-"""	25894	protein-coding gene	gene with protein product							Standard	NM_032788		Approved	FLJ14457	uc002sue.1	Q96K75	OTTHUMG00000130391	ENST00000295208.2:c.920A>G	chr2.hg19:g.95815310T>C	ENSP00000295208:p.Gln307Arg	142.0	0.0		119.0	5.0	NM_032788	Q5JPJ3	Missense_Mutation	SNP	ENST00000295208.2	hg19	CCDS2011.1	.	.	.	.	.	.	.	.	.	.	T	11.92	1.783415	0.31593	.	.	ENSG00000144026	ENST00000295208;ENST00000411425	T;T	0.07327	3.2;3.2	2.65	1.5	0.22942	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07279	0.0184	N	0.21194	0.64	0.26677	N	0.971611	B;P	0.37612	0.001;0.602	B;B	0.42653	0.004;0.394	T	0.32134	-0.9918	9	0.54805	T	0.06	.	5.9899	0.19454	0.0:0.1365:0.0:0.8635	.	307;126	Q96K75;Q658L7	ZN514_HUMAN;.	R	307	ENSP00000295208:Q307R;ENSP00000405509:Q307R	ENSP00000295208:Q307R	Q	-	2	0	ZNF514	95179037	0.000000	0.05858	1.000000	0.80357	0.951000	0.60555	-0.086000	0.11233	0.439000	0.26476	0.533000	0.62120	CAG	.	.		0.438	ZNF514-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252769.1	NM_032788	
FAM178B	51252	hgsc.bcm.edu	37	2	97586981	97586981	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:97586981T>C	ENST00000417561.3	-	16	1926	c.1927A>G	c.(1927-1929)Acc>Gcc	p.T643A	FAM178B_ENST00000327896.3_Missense_Mutation_p.T463A|FAM178B_ENST00000490605.2_Missense_Mutation_p.T495A			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	643										large_intestine(1)|ovary(1)	2						CAGCTCAGGGTGCAGCACAGT	0.657																																					p.T495A		Atlas-SNP	.											.	FAM178B	35	.	0			c.A1483G						.						60.0	64.0	63.0					2																	97586981		692	1591	2283	SO:0001583	missense	51252	exon12			TCAGGGTGCAGCA	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.1927A>G	chr2.hg19:g.97586981T>C	ENSP00000413245:p.Thr643Ala	94.0	0.0		59.0	4.0	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Missense_Mutation	SNP	ENST00000417561.3	hg19		.	.	.	.	.	.	.	.	.	.	T	0.011	-1.710213	0.00712	.	.	ENSG00000168754	ENST00000417561;ENST00000327896;ENST00000490605	T;T;T	0.39997	1.05;1.09;1.08	5.21	-4.31	0.03698	.	0.787278	0.10183	N	0.705656	T	0.09686	0.0238	N	0.01576	-0.805	0.09310	N	1	.	.	.	.	.	.	T	0.32508	-0.9904	8	0.02654	T	1	-1.9274	1.9878	0.03440	0.1416:0.2285:0.139:0.4909	.	.	.	.	A	643;463;495	ENSP00000413245:T643A;ENSP00000333553:T463A;ENSP00000429896:T495A	ENSP00000333553:T463A	T	-	1	0	FAM178B	96950708	0.000000	0.05858	0.008000	0.14137	0.038000	0.13279	-3.548000	0.00434	-0.351000	0.08249	-1.133000	0.01973	ACC	.	.		0.657	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490	
MAP4K4	9448	hgsc.bcm.edu	37	2	102490567	102490567	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:102490567A>G	ENST00000347699.4	+	23	2659	c.2659A>G	c.(2659-2661)Aga>Gga	p.R887G	MAP4K4_ENST00000425019.1_Missense_Mutation_p.R920G|MAP4K4_ENST00000413150.2_Missense_Mutation_p.R802G|MAP4K4_ENST00000350878.4_Missense_Mutation_p.R927G|MAP4K4_ENST00000302217.5_Missense_Mutation_p.R690G|MAP4K4_ENST00000456652.1_Missense_Mutation_p.R686G|MAP4K4_ENST00000350198.4_Missense_Mutation_p.R806G|MAP4K4_ENST00000324219.4_Missense_Mutation_p.R968G	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	887	Mediates interaction with RAP2A.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TGATGGGATGAGACCAGAAGC	0.458																																					p.R921G		Atlas-SNP	.											.	MAP4K4	111	.	0			c.A2761G						.						94.0	93.0	93.0					2																	102490567		1931	4126	6057	SO:0001583	missense	9448	exon24			GGGATGAGACCAG	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6866	protein-coding gene	gene with protein product	"""HPK/GCK-like kinase"", ""hepatocyte progenitor kinase-like/germinal center kinase-like kinase"""	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.2659A>G	chr2.hg19:g.102490567A>G	ENSP00000314363:p.Arg887Gly	158.0	0.0		111.0	6.0	NM_145686	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	hg19	CCDS56130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.35|15.35	2.806641|2.806641	0.50421|0.50421	.|.	.|.	ENSG00000071054|ENSG00000071054	ENST00000421882|ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699;ENST00000417294;ENST00000350878	.|T;T;T;T;T;T;T;T;T	.|0.75050	.|-0.81;-0.76;-0.76;-0.26;-0.77;-0.26;-0.77;-0.9;-0.78	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	.|0.066200	.|0.64402	.|D	.|0.000007	D|D	0.82365|0.82365	0.5021|0.5021	L|L	0.58810|0.58810	1.83|1.83	0.58432|0.58432	D|D	0.999992|0.999992	.|D;P;B;B;P;D;B;P;D;B	.|0.64830	.|0.967;0.717;0.047;0.069;0.814;0.99;0.073;0.814;0.994;0.443	.|P;P;B;B;P;P;B;P;D;B	.|0.68483	.|0.879;0.478;0.05;0.028;0.677;0.718;0.008;0.677;0.958;0.108	T|T	0.80527|0.80527	-0.1343|-0.1343	5|10	.|0.29301	.|T	.|0.29	.|.	15.1029|15.1029	0.72296|0.72296	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|927;883;686;690;805;887;920;806;859;968	.|B7Z388;B7Z3V5;E7EX83;C9J840;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.|.;.;.;.;.;M4K4_HUMAN;.;.;.;.	G|G	703|920;968;806;690;802;686;887;818;927	.|ENSP00000392830:R920G;ENSP00000313644:R968G;ENSP00000281111:R806G;ENSP00000303600:R690G;ENSP00000389752:R802G;ENSP00000387370:R686G;ENSP00000314363:R887G;ENSP00000409720:R818G;ENSP00000343658:R927G	.|ENSP00000303600:R690G	E|R	+|+	2|1	0|2	MAP4K4|MAP4K4	101856999|101856999	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	4.478000|4.478000	0.60230|0.60230	1.972000|1.972000	0.57404|0.57404	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.		0.458	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	
SH3RF3	344558	hgsc.bcm.edu	37	2	110015186	110015186	+	Silent	SNP	G	G	T	rs542535234		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:110015186G>T	ENST00000309415.6	+	4	1086	c.1086G>T	c.(1084-1086)gcG>gcT	p.A362A		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	362							zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						GCTCAGGGGCGGTCAGTGCCT	0.632																																					p.A362A		Atlas-SNP	.											SH3RF3,right_upper_lobe,carcinoma,0,1	SH3RF3	62	.	0			c.G1086T						.						40.0	47.0	45.0					2																	110015186		2203	4300	6503	SO:0001819	synonymous_variant	344558	exon4			AGGGGCGGTCAGT	AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"""RING-type (C3HC4) zinc fingers"""	24699	protein-coding gene	gene with protein product			"""SH3 multiple domains 4"""	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.1086G>T	chr2.hg19:g.110015186G>T		104.0	0.0		78.0	4.0	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Silent	SNP	ENST00000309415.6	hg19																																																																																				.	.		0.632	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289	
FBLN7	129804	hgsc.bcm.edu	37	2	112933383	112933383	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:112933383A>G	ENST00000331203.2	+	4	770	c.499A>G	c.(499-501)Act>Gct	p.T167A	FBLN7_ENST00000472377.1_3'UTR|FBLN7_ENST00000409667.3_Intron|FBLN7_ENST00000409903.1_Missense_Mutation_p.T167A|FBLN7_ENST00000409450.3_Missense_Mutation_p.T167A	NM_001128165.1|NM_153214.2	NP_001121637.1|NP_694946.2	Q53RD9	FBLN7_HUMAN	fibulin 7	167	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TCCAGGAAGGACTGGGAACCG	0.537																																					p.T167A		Atlas-SNP	.											.	FBLN7	49	.	0			c.A499G						.						129.0	109.0	115.0					2																	112933383		2203	4300	6503	SO:0001583	missense	129804	exon4			GGAAGGACTGGGA		CCDS2095.1, CCDS46391.1	2q13	2010-06-15			ENSG00000144152	ENSG00000144152		"""Fibulins"""	26740	protein-coding gene	gene with protein product		611551				17699513	Standard	NM_153214		Approved	FLJ37440, TM14	uc002tho.1	Q53RD9	OTTHUMG00000153267	ENST00000331203.2:c.499A>G	chr2.hg19:g.112933383A>G	ENSP00000331411:p.Thr167Ala	91.0	0.0		72.0	4.0	NM_153214	A0JNV1|A0JNV2|Q5H9P5|Q8N9G0	Missense_Mutation	SNP	ENST00000331203.2	hg19	CCDS2095.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.180743	0.38511	.	.	ENSG00000144152	ENST00000331203;ENST00000409903;ENST00000409450;ENST00000441565	D;D;D;D	0.94457	-3.43;-3.43;-3.43;-3.43	5.66	1.81	0.25067	EGF (1);Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.215378	0.47852	N	0.000202	D	0.92071	0.7487	M	0.71036	2.16	0.34385	D	0.69357	P;P;P	0.45957	0.459;0.566;0.869	B;B;P	0.48425	0.225;0.438;0.577	D	0.87482	0.2421	10	0.12103	T	0.63	-2.153	2.5345	0.04711	0.54:0.1335:0.07:0.2565	.	167;167;167	Q53RD9-2;Q53RD9;B8ZZC1	.;FBLN7_HUMAN;.	A	167;167;167;61	ENSP00000331411:T167A;ENSP00000386295:T167A;ENSP00000387000:T167A;ENSP00000388025:T61A	ENSP00000331411:T167A	T	+	1	0	FBLN7	112649854	1.000000	0.71417	0.510000	0.27712	0.921000	0.55340	2.912000	0.48782	0.063000	0.16370	0.533000	0.62120	ACT	.	.		0.537	FBLN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330505.1	NM_153214	
AMMECR1L	83607	hgsc.bcm.edu	37	2	128628438	128628438	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:128628438C>T	ENST00000272647.5	-	5	843	c.583G>A	c.(583-585)Gtc>Atc	p.V195I	AMMECR1L_ENST00000393001.1_Missense_Mutation_p.V195I	NM_001199140.1	NP_001186069.1	Q6DCA0	AMERL_HUMAN	AMMECR1-like	195	AMMECR1. {ECO:0000255|PROSITE- ProRule:PRU00467}.							p.V195L(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	9	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.07)		AGGAGGGAGACAGAGCAGAAA	0.522																																					p.V195I		Atlas-SNP	.											AMMECR1L,NS,carcinoma,0,1	AMMECR1L	22	.	1	Substitution - Missense(1)	lung(1)	c.G583A						.						64.0	59.0	60.0					2																	128628438		2203	4300	6503	SO:0001583	missense	83607	exon5			GGGAGACAGAGCA		CCDS2152.1	2q21	2012-11-15	2012-11-15		ENSG00000144233	ENSG00000144233			28658	protein-coding gene	gene with protein product			"""AMME chromosomal region gene 1-like"""				Standard	NM_001199140		Approved	MGC4268	uc002tpl.3	Q6DCA0	OTTHUMG00000131535	ENST00000272647.5:c.583G>A	chr2.hg19:g.128628438C>T	ENSP00000272647:p.Val195Ile	157.0	0.0		125.0	70.0	NM_031445	B4E276	Missense_Mutation	SNP	ENST00000272647.5	hg19	CCDS2152.1	.	.	.	.	.	.	.	.	.	.	C	36	5.707123	0.96821	.	.	ENSG00000144233	ENST00000272647;ENST00000393001	.	.	.	5.46	5.46	0.80206	AMMECR1 domain (2);	0.000000	0.64402	D	0.000002	T	0.75287	0.3829	L	0.54908	1.71	0.80722	D	1	P	0.51351	0.944	D	0.64237	0.923	T	0.72337	-0.4324	9	0.40728	T	0.16	-15.9275	19.6629	0.95879	0.0:1.0:0.0:0.0	.	195	Q6DCA0	AMERL_HUMAN	I	195	.	ENSP00000272647:V195I	V	-	1	0	AMMECR1L	128344908	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.445000	0.80570	2.726000	0.93360	0.655000	0.94253	GTC	.	.		0.522	AMMECR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254392.1	NM_031445	
THSD7B	80731	hgsc.bcm.edu	37	2	138400205	138400205	+	Splice_Site	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:138400205T>A	ENST00000409968.1	+	21	4123		c.e21+2		THSD7B_ENST00000272643.3_Splice_Site|THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000413152.2_Splice_Site			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B							integral component of membrane (GO:0016021)				NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		AAATTGGAGGTAGGTCATGTA	0.493																																					.		Atlas-SNP	.											.	THSD7B	506	.	0			c.3857+2T>A						.						62.0	64.0	64.0					2																	138400205		1894	4123	6017	SO:0001630	splice_region_variant	80731	exon20			TGGAGGTAGGTCA			2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.3945+2T>A	chr2.hg19:g.138400205T>A		70.0	0.0		52.0	4.0	NM_001080427		Splice_Site	SNP	ENST00000409968.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.90	3.502889	0.64298	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.413	0.67128	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	THSD7B	138116675	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.849000	0.62882	2.234000	0.73211	0.533000	0.62120	.	.	.		0.493	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9	Intron
UPP2	151531	hgsc.bcm.edu	37	2	158971674	158971674	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:158971674A>G	ENST00000005756.4	+	3	436	c.242A>G	c.(241-243)gAg>gGg	p.E81G	UPP2_ENST00000605860.1_Missense_Mutation_p.E138G|UPP2_ENST00000409859.4_Missense_Mutation_p.E138G|UPP2_ENST00000460456.1_Intron	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	81					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	ATGCACAAGGAGCTCGGGTTT	0.458																																					p.E138G		Atlas-SNP	.											.	UPP2	60	.	0			c.A413G						.						105.0	105.0	105.0					2																	158971674		2203	4300	6503	SO:0001583	missense	151531	exon5			ACAAGGAGCTCGG	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.242A>G	chr2.hg19:g.158971674A>G	ENSP00000005756:p.Glu81Gly	125.0	0.0		133.0	6.0	NM_001135098	B3KV87	Missense_Mutation	SNP	ENST00000005756.4	hg19	CCDS2207.1	.	.	.	.	.	.	.	.	.	.	A	15.99	2.995626	0.54147	.	.	ENSG00000007001	ENST00000409859;ENST00000005756	D;D	0.88741	-2.42;-2.42	5.7	4.55	0.56014	Nucleoside phosphorylase domain (1);	0.221802	0.45126	D	0.000383	D	0.93835	0.8028	M	0.87381	2.88	0.58432	D	0.999997	D	0.76494	0.999	D	0.65323	0.934	D	0.93291	0.6668	10	0.52906	T	0.07	.	10.5443	0.45052	0.9237:0.0:0.0763:0.0	.	81	O95045	UPP2_HUMAN	G	138;81	ENSP00000387230:E138G;ENSP00000005756:E81G	ENSP00000005756:E81G	E	+	2	0	UPP2	158679920	1.000000	0.71417	0.793000	0.32043	0.090000	0.18270	6.190000	0.72057	1.000000	0.39049	0.533000	0.62120	GAG	.	.		0.458	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355	
LRP2	4036	hgsc.bcm.edu	37	2	170058302	170058302	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:170058302T>C	ENST00000263816.3	-	44	8573	c.8288A>G	c.(8287-8289)tAc>tGc	p.Y2763C		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2763	LDL-receptor class A 17. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	ACAGTCATTGTAGTAATCACA	0.502																																					p.Y2763C		Atlas-SNP	.											.	LRP2	751	.	0			c.A8288G						.						157.0	133.0	141.0					2																	170058302		2203	4300	6503	SO:0001583	missense	4036	exon44			TCATTGTAGTAAT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.8288A>G	chr2.hg19:g.170058302T>C	ENSP00000263816:p.Tyr2763Cys	81.0	0.0		70.0	4.0	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	T	17.90	3.503190	0.64298	.	.	ENSG00000081479	ENST00000263816	D	0.95554	-3.74	5.7	5.7	0.88788	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.96800	0.8955	L	0.52905	1.665	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96450	0.9333	10	0.39692	T	0.17	.	15.9722	0.80027	0.0:0.0:0.0:1.0	.	2763	P98164	LRP2_HUMAN	C	2763	ENSP00000263816:Y2763C	ENSP00000263816:Y2763C	Y	-	2	0	LRP2	169766548	1.000000	0.71417	0.998000	0.56505	0.905000	0.53344	4.938000	0.63519	2.169000	0.68431	0.528000	0.53228	TAC	.	.		0.502	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
PDK1	5163	hgsc.bcm.edu	37	2	173423557	173423557	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:173423557C>T	ENST00000282077.3	+	2	500	c.318C>T	c.(316-318)tcC>tcT	p.S106S	PDK1_ENST00000410055.1_Silent_p.S106S|AC093818.1_ENST00000450443.1_RNA|Y_RNA_ENST00000362996.1_RNA|AC093818.1_ENST00000442417.1_RNA|AC093818.1_ENST00000444919.1_RNA|PDK1_ENST00000392571.2_Silent_p.S106S|PDK1_ENST00000543905.1_Silent_p.S30S|PDK1_ENST00000544863.1_5'UTR|AC093818.1_ENST00000436922.1_RNA			Q15118	PDK1_HUMAN	pyruvate dehydrogenase kinase, isozyme 1	106					cell proliferation (GO:0008283)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.12)			GGACACCATCCGTTCAATTGG	0.383									Autosomal Dominant Polycystic Kidney Disease																												p.S106S		Atlas-SNP	.											.	PDK1	39	.	0			c.C318T						.						95.0	92.0	93.0					2																	173423557		2203	4300	6503	SO:0001819	synonymous_variant	5163	exon2	Familial Cancer Database	ADPKD	ACCATCCGTTCAA	L42450	CCDS2250.1, CCDS63059.1	2q31.1	2008-05-23	2005-11-16		ENSG00000152256	ENSG00000152256			8809	protein-coding gene	gene with protein product		602524	"""pyruvate dehydrogenase kinase, isoenzyme 1"""			7499431	Standard	NR_103731		Approved		uc002uhs.3	Q15118	OTTHUMG00000132285	ENST00000282077.3:c.318C>T	chr2.hg19:g.173423557C>T		138.0	0.0		99.0	5.0	NM_002610	B2R6T1|B7Z937|D3DPD8|E9PD65|Q308M4	Silent	SNP	ENST00000282077.3	hg19	CCDS2250.1																																																																																			.	.		0.383	PDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255380.3	NM_002610	
HNRNPA3	220988	hgsc.bcm.edu	37	2	178083814	178083814	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:178083814A>G	ENST00000392524.2	+	9	1248	c.1011A>G	c.(1009-1011)ggA>ggG	p.G337G	HNRNPA3_ENST00000411529.2_Silent_p.G315G|HNRNPA3_ENST00000435711.1_Silent_p.G337G			P51991	ROA3_HUMAN	heterogeneous nuclear ribonucleoprotein A3	337	Gly-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|urinary_tract(1)	16						ATTATAGTGGACAACAGCAAT	0.388																																					p.G337G		Atlas-SNP	.											.	HNRNPA3	42	.	0			c.A1011G						.						85.0	92.0	90.0					2																	178083814		2203	4297	6500	SO:0001819	synonymous_variant	220988	exon9			TAGTGGACAACAG	AF517524	CCDS2273.1	2q31.2	2013-02-12		2008-04-18	ENSG00000170144	ENSG00000170144		"""RNA binding motif (RRM) containing"""	24941	protein-coding gene	gene with protein product		605372		HNRPA3		11886857, 15776420	Standard	XM_005246380		Approved		uc002ulc.1	P51991	OTTHUMG00000132529	ENST00000392524.2:c.1011A>G	chr2.hg19:g.178083814A>G		116.0	0.0		87.0	4.0	NM_194247	D3DPF4|Q53RW7|Q6URK5	Silent	SNP	ENST00000392524.2	hg19	CCDS2273.1																																																																																			.	.		0.388	HNRNPA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255729.3	NM_194247	
TTN	7273	hgsc.bcm.edu	37	2	179413062	179413062	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:179413062A>G	ENST00000591111.1	-	289	88592	c.88368T>C	c.(88366-88368)ggT>ggC	p.G29456G	TTN_ENST00000359218.5_Silent_p.G22157G|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Silent_p.G22032G|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Silent_p.G22224G|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Silent_p.G31097G|TTN_ENST00000342992.6_Silent_p.G28529G|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29456	Fibronectin type-III 114. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTCACCAACACCATACTCAT	0.463																																					p.G31097G		Atlas-SNP	.											.	TTN	18412	.	0			c.T93291C						.						211.0	211.0	211.0					2																	179413062		2059	4199	6258	SO:0001819	synonymous_variant	7273	exon339			ACCAACACCATAC	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.88368T>C	chr2.hg19:g.179413062A>G		86.0	0.0		56.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179419855	179419855	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:179419855A>G	ENST00000591111.1	-	281	83632	c.83408T>C	c.(83407-83409)cTa>cCa	p.L27803P	TTN_ENST00000359218.5_Missense_Mutation_p.L20504P|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L20379P|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L20571P|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L29444P|TTN_ENST00000342992.6_Missense_Mutation_p.L26876P|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27803	Ig-like 130.				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)			TGTATATTCTAGAGGCAAATC	0.363																																					p.L29444P		Atlas-SNP	.											.	TTN	18412	.	0			c.T88331C						.						74.0	71.0	72.0					2																	179419855		1824	4080	5904	SO:0001583	missense	7273	exon331			TATTCTAGAGGCA	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.83408T>C	chr2.hg19:g.179419855A>G	ENSP00000465570:p.Leu27803Pro	98.0	0.0		98.0	4.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.41	2.526121	0.44969	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63580	-0.05;0.18;0.18;0.15	5.66	5.66	0.87406	Fibronectin, type III (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.52597	0.1744	L	0.46157	1.445	0.53688	D	0.999973	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.10450	0.005;0.005;0.005;0.005	T	0.55503	-0.8131	9	0.87932	D	0	.	6.3004	0.21109	0.8067:0.0:0.1933:0.0	.	20379;20504;20571;27803	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	26876;20379;20571;20504;20376	ENSP00000343764:L26876P;ENSP00000434586:L20379P;ENSP00000340554:L20571P;ENSP00000352154:L20504P	ENSP00000340554:L20571P	L	-	2	0	TTN	179128101	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.012000	0.57131	2.279000	0.76181	0.533000	0.62120	CTA	.	.		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CCDC141	285025	hgsc.bcm.edu	37	2	179742806	179742806	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:179742806T>C	ENST00000409284.1	-	12	1901	c.1784A>G	c.(1783-1785)gAt>gGt	p.D595G	CCDC141_ENST00000420890.2_Missense_Mutation_p.D595G|CCDC141_ENST00000295723.5_Missense_Mutation_p.D20G			Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	595										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TTTAGCATCATCCTGCTCCTT	0.378																																					p.D595G		Atlas-SNP	.											.	CCDC141	362	.	0			c.A1784G						.						90.0	87.0	88.0					2																	179742806		2203	4300	6503	SO:0001583	missense	285025	exon12			GCATCATCCTGCT	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26821	protein-coding gene	gene with protein product	"""coiled-coil protein associated with myosin II and DISC1"""					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000409284.1:c.1784A>G	chr2.hg19:g.179742806T>C	ENSP00000386503:p.Asp595Gly	95.0	0.0		75.0	4.0	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000409284.1	hg19		.	.	.	.	.	.	.	.	.	.	t	9.057	0.993584	0.19043	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723;ENST00000443758;ENST00000446116;ENST00000409284	T;T;T;T	0.48522	0.81;1.44;1.46;1.44	5.23	2.5	0.30297	.	0.480260	0.18515	N	0.138929	T	0.27205	0.0667	N	0.17082	0.46	0.09310	N	1	B;B	0.11235	0.0;0.004	B;B	0.11329	0.0;0.006	T	0.16541	-1.0399	10	0.18276	T	0.48	-6.0665	8.2729	0.31855	0.0:0.1948:0.0:0.8052	.	595;20	B8ZZB3;Q6ZP82	.;CC141_HUMAN	G	595;39;20;595;530;595	ENSP00000395995:D595G;ENSP00000344627:D39G;ENSP00000295723:D20G;ENSP00000390190:D595G	ENSP00000295723:D20G	D	-	2	0	CCDC141	179451051	0.000000	0.05858	0.162000	0.22713	0.439000	0.31926	-0.319000	0.08039	0.825000	0.34637	0.473000	0.43528	GAT	.	.		0.378	CCDC141-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000335873.1	NM_173648	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187698746	187698746	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:187698746C>T	ENST00000295131.2	-	6	794	c.755G>A	c.(754-756)tGc>tAc	p.C252Y		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	252					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			ATATTCTATGCATTCGGTACA	0.358																																					p.C252Y		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.G755A						.						116.0	100.0	106.0					2																	187698746		2203	4300	6503	SO:0001583	missense	151112	exon6			TCTATGCATTCGG	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.755G>A	chr2.hg19:g.187698746C>T	ENSP00000295131:p.Cys252Tyr	122.0	0.0		96.0	4.0	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	hg19	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.367338	0.61513	.	.	ENSG00000163012	ENST00000295131	D	0.96073	-3.9	5.78	5.78	0.91487	Zinc finger, ZZ-type (4);	0.000000	0.64402	D	0.000012	D	0.98321	0.9443	M	0.93375	3.41	0.50632	D	0.999886	D	0.89917	1.0	D	0.79108	0.992	D	0.99191	1.0870	10	0.87932	D	0	-10.6671	16.9191	0.86159	0.0:1.0:0.0:0.0	.	252	Q8NEG5	ZSWM2_HUMAN	Y	252	ENSP00000295131:C252Y	ENSP00000295131:C252Y	C	-	2	0	ZSWIM2	187406991	0.997000	0.39634	0.309000	0.25155	0.710000	0.40934	5.004000	0.63966	2.722000	0.93159	0.467000	0.42956	TGC	.	.		0.358	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
ANKRD44	91526	hgsc.bcm.edu	37	2	197954757	197954757	+	Splice_Site	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:197954757C>A	ENST00000328737.2	-	11	1102		c.e11-1		ANKRD44_ENST00000409153.1_Splice_Site|ANKRD44_ENST00000450567.1_Splice_Site|ANKRD44_ENST00000539527.1_Splice_Site|ANKRD44_ENST00000282272.8_Splice_Site|ANKRD44_ENST00000477852.1_5'Flank|ANKRD44_ENST00000337207.5_Splice_Site			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44											NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GATTCCACACCTGAGGAGTAA	0.413																																					.		Atlas-SNP	.											.	ANKRD44	281	.	0			c.1101-1G>T						.						102.0	93.0	96.0					2																	197954757		2203	4300	6503	SO:0001630	splice_region_variant	91526	exon12			CCACACCTGAGGA	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.1026-1G>T	chr2.hg19:g.197954757C>A		95.0	0.0		105.0	5.0	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Splice_Site	SNP	ENST00000328737.2	hg19		.	.	.	.	.	.	.	.	.	.	C	25.0	4.590966	0.86851	.	.	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207;ENST00000422886;ENST00000409153;ENST00000539527	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1694	0.93570	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ANKRD44	197663002	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.434000	0.80377	2.765000	0.95021	0.655000	0.94253	.	.	.		0.413	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	Intron
ALS2	57679	hgsc.bcm.edu	37	2	202568849	202568849	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:202568849A>G	ENST00000264276.6	-	33	5303	c.4931T>C	c.(4930-4932)tTg>tCg	p.L1644S	ALS2_ENST00000457679.2_3'UTR	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	1644	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						ACTCACCTTCAAGGTGGTGAA	0.358																																					p.L1644S		Atlas-SNP	.											.	ALS2	172	.	0			c.T4931C						.						72.0	65.0	67.0					2																	202568849		1828	4079	5907	SO:0001583	missense	57679	exon33			ACCTTCAAGGTGG	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"""Rho guanine nucleotide exchange factors"""	443	protein-coding gene	gene with protein product	"""alsin"""	606352	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"""	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.4931T>C	chr2.hg19:g.202568849A>G	ENSP00000264276:p.Leu1644Ser	122.0	0.0		112.0	6.0	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Missense_Mutation	SNP	ENST00000264276.6	hg19	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.405316	0.83230	.	.	ENSG00000003393	ENST00000264276	T	0.49139	0.79	5.78	5.78	0.91487	Vacuolar sorting protein 9 (2);	0.142767	0.47852	D	0.000211	T	0.71904	0.3395	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76666	-0.2875	10	0.87932	D	0	.	16.1138	0.81283	1.0:0.0:0.0:0.0	.	1644	Q96Q42	ALS2_HUMAN	S	1644	ENSP00000264276:L1644S	ENSP00000264276:L1644S	L	-	2	0	ALS2	202277094	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	9.288000	0.96055	2.220000	0.72140	0.533000	0.62120	TTG	.	.		0.358	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919	
BMPR2	659	hgsc.bcm.edu	37	2	203420956	203420956	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:203420956C>A	ENST00000374580.4	+	12	3107	c.2568C>A	c.(2566-2568)acC>acA	p.T856T	BMPR2_ENST00000374574.2_Intron	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	856					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						GTGAGGACACCCGGCTGAATA	0.468																																					p.T856T		Atlas-SNP	.											.	BMPR2	142	.	0			c.C2568A						.						128.0	122.0	124.0					2																	203420956		2203	4300	6503	SO:0001819	synonymous_variant	659	exon12			GGACACCCGGCTG	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"""primary pulmonary hypertension 1"""	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.2568C>A	chr2.hg19:g.203420956C>A		85.0	0.0		90.0	5.0	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Silent	SNP	ENST00000374580.4	hg19	CCDS33361.1																																																																																			.	.		0.468	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204	
ZDBF2	57683	hgsc.bcm.edu	37	2	207170906	207170906	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:207170906A>G	ENST00000374423.3	+	5	2040	c.1654A>G	c.(1654-1656)Aga>Gga	p.R552G		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	552							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						AGTGGTTGACAGACCCCCAGT	0.438																																					p.R552G		Atlas-SNP	.											.	ZDBF2	531	.	0			c.A1654G						.						98.0	92.0	94.0					2																	207170906		1866	4113	5979	SO:0001583	missense	57683	exon5			GTTGACAGACCCC	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.1654A>G	chr2.hg19:g.207170906A>G	ENSP00000363545:p.Arg552Gly	84.0	0.0		63.0	5.0	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.300258	0.60195	.	.	ENSG00000204186	ENST00000374423	T	0.44083	0.93	4.09	-0.325	0.12702	.	1.722310	0.04110	N	0.314521	T	0.29817	0.0745	L	0.34521	1.04	0.09310	N	1	B	0.19817	0.039	B	0.19391	0.025	T	0.23619	-1.0183	10	0.56958	D	0.05	.	0.8148	0.01100	0.3866:0.2781:0.1415:0.1938	.	552	Q9HCK1	ZDBF2_HUMAN	G	552	ENSP00000363545:R552G	ENSP00000363545:R552G	R	+	1	2	ZDBF2	206879151	0.001000	0.12720	0.000000	0.03702	0.024000	0.10985	0.071000	0.14594	-0.324000	0.08589	-0.127000	0.14921	AGA	.	.		0.438	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
UNC80	285175	hgsc.bcm.edu	37	2	210843335	210843335	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:210843335T>C	ENST00000439458.1	+	58	8903	c.8823T>C	c.(8821-8823)tcT>tcC	p.S2941S	UNC80_ENST00000539183.1_Silent_p.S387S|UNC80_ENST00000272845.6_Silent_p.S2936S	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	2941					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						TGTCCCGCTCTAACACGGGCA	0.592																																					p.S2941S		Atlas-SNP	.											.	UNC80	280	.	0			c.T8823C						.						81.0	72.0	74.0					2																	210843335		692	1591	2283	SO:0001819	synonymous_variant	285175	exon58			CCGCTCTAACACG	AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.8823T>C	chr2.hg19:g.210843335T>C		107.0	0.0		85.0	4.0	NM_032504	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Silent	SNP	ENST00000439458.1	hg19	CCDS46504.1																																																																																			.	.		0.592	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
GPBAR1	151306	hgsc.bcm.edu	37	2	219127947	219127947	+	Missense_Mutation	SNP	A	A	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:219127947A>T	ENST00000522678.1	+	2	1368	c.500A>T	c.(499-501)tAc>tTc	p.Y167F	GPBAR1_ENST00000521462.1_Missense_Mutation_p.Y167F|GPBAR1_ENST00000519574.1_Missense_Mutation_p.Y167F|GPBAR1_ENST00000479077.1_Missense_Mutation_p.Y167F	NM_001077191.1	NP_001070659.1	Q8TDU6	GPBAR_HUMAN	G protein-coupled bile acid receptor 1	167					cell surface bile acid receptor signaling pathway (GO:0038184)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid receptor activity (GO:0038181)|G-protein coupled bile acid receptor activity (GO:0038182)			cervix(1)|kidney(1)|large_intestine(1)|ovary(1)	4		Renal(207;0.0474)		Epithelial(149;7.19e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCCTACCTGTACCTCGAAGTC	0.662																																					p.Y167F		Atlas-SNP	.											.	GPBAR1	22	.	0			c.A500T						.						50.0	54.0	52.0					2																	219127947		2074	4208	6282	SO:0001583	missense	151306	exon2			ACCTGTACCTCGA	AB086170	CCDS46515.1	2q35	2012-08-08			ENSG00000179921	ENSG00000179921			19680	protein-coding gene	gene with protein product		610147				12419312	Standard	NM_170699		Approved	BG37, GPCR, TGR5, M-BAR, GPCR19, GPR131, MGC40597	uc010zjw.1	Q8TDU6	OTTHUMG00000155203	ENST00000522678.1:c.500A>T	chr2.hg19:g.219127947A>T	ENSP00000430886:p.Tyr167Phe	110.0	0.0		81.0	5.0	NM_170699	B3KV35	Missense_Mutation	SNP	ENST00000522678.1	hg19	CCDS46515.1	.	.	.	.	.	.	.	.	.	.	A	18.92	3.726064	0.69074	.	.	ENSG00000179921	ENST00000479077;ENST00000522678;ENST00000519574;ENST00000521462	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	5.49	4.35	0.52113	GPCR, rhodopsin-like superfamily (1);	0.085753	0.48767	U	0.000179	T	0.45135	0.1327	M	0.66939	2.045	0.34397	D	0.694849	P	0.46784	0.884	P	0.50490	0.642	T	0.61710	-0.7007	10	0.54805	T	0.06	-10.0032	9.938	0.41563	0.9191:0.0:0.0809:0.0	.	167	Q8TDU6	GPBAR_HUMAN	F	167	ENSP00000430698:Y167F;ENSP00000430886:Y167F;ENSP00000430202:Y167F;ENSP00000428824:Y167F	ENSP00000430698:Y167F	Y	+	2	0	GPBAR1	218836191	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	4.566000	0.60843	2.082000	0.62665	0.459000	0.35465	TAC	.	.		0.662	GPBAR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338767.3	NM_001077191	
DNPEP	23549	hgsc.bcm.edu	37	2	220251502	220251502	+	Splice_Site	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:220251502T>C	ENST00000273075.4	-	4	440		c.e4-2		DNPEP_ENST00000373972.1_Splice_Site|DNPEP_ENST00000523282.1_Splice_Site|AC053503.4_ENST00000420563.1_RNA	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase						peptide metabolic process (GO:0006518)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CATGAAGTACTGAGGAGAAGG	0.587																																					.		Atlas-SNP	.											.	DNPEP	40	.	0			c.220-2A>G						.						39.0	42.0	41.0					2																	220251502		2066	4208	6274	SO:0001630	splice_region_variant	23549	exon5			AAGTACTGAGGAG		CCDS42823.1	2q36.1	2008-05-22			ENSG00000123992	ENSG00000123992			2981	protein-coding gene	gene with protein product		611367				9632644	Standard	NM_012100		Approved	DAP, ASPEP	uc002vle.2	Q9ULA0	OTTHUMG00000058919	ENST00000273075.4:c.220-2A>G	chr2.hg19:g.220251502T>C		68.0	0.0		63.0	4.0	NM_012100	Q9BW44|Q9NUV5	Splice_Site	SNP	ENST00000273075.4	hg19	CCDS42823.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.969727	0.53614	.	.	ENSG00000123992	ENST00000273075;ENST00000337010;ENST00000523282;ENST00000457935;ENST00000429013;ENST00000521459;ENST00000322176;ENST00000519905	.	.	.	3.59	3.59	0.41128	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.733	0.34512	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNPEP	219959746	1.000000	0.71417	0.998000	0.56505	0.773000	0.43773	7.617000	0.83032	1.641000	0.50575	0.402000	0.26972	.	.	.		0.587	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100	Intron
SPEG	10290	hgsc.bcm.edu	37	2	220333748	220333748	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:220333748C>A	ENST00000312358.7	+	12	3601	c.3469C>A	c.(3469-3471)Cgg>Agg	p.R1157R	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1157					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		AGAAGAGCCCCGGACAGCCGC	0.682																																					p.R1157R		Atlas-SNP	.											SPEG,NS,carcinoma,0,1	SPEG	272	.	0			c.C3469A						.						29.0	36.0	34.0					2																	220333748		1917	4120	6037	SO:0001819	synonymous_variant	10290	exon12			GAGCCCCGGACAG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.3469C>A	chr2.hg19:g.220333748C>A		114.0	0.0		47.0	3.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.		0.682	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
WDFY1	57590	hgsc.bcm.edu	37	2	224760297	224760297	+	Nonsense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:224760297C>A	ENST00000233055.4	-	7	751	c.649G>T	c.(649-651)Gga>Tga	p.G217*		NM_020830.3	NP_065881.1	Q8IWB7	WDFY1_HUMAN	WD repeat and FYVE domain containing 1	217						cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)	1-phosphatidylinositol binding (GO:0005545)|zinc ion binding (GO:0008270)	p.G217R(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)	18		all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;5.34e-10)|all cancers(144;1.67e-07)|Lung(261;0.00807)|LUSC - Lung squamous cell carcinoma(224;0.00843)		TCAGATGCTCCTGAGAAGAGT	0.552																																					p.G217X		Atlas-SNP	.											WDFY1,colon,carcinoma,0,1	WDFY1	46	.	1	Substitution - Missense(1)	large_intestine(1)	c.G649T						.						101.0	87.0	92.0					2																	224760297		2203	4300	6503	SO:0001587	stop_gained	57590	exon7			ATGCTCCTGAGAA	AB037856	CCDS33387.1	2q36.2	2013-01-09	2003-03-13		ENSG00000085449	ENSG00000085449		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20451	protein-coding gene	gene with protein product			"""WD40 and FYVE domain containing 1"""			11739631	Standard	NM_020830		Approved	KIAA1435, FENS-1, WDF1, ZFYVE17	uc002vnq.3	Q8IWB7	OTTHUMG00000153370	ENST00000233055.4:c.649G>T	chr2.hg19:g.224760297C>A	ENSP00000233055:p.Gly217*	100.0	0.0		69.0	3.0	NM_020830	Q53S17|Q9H9D5|Q9P2B3	Nonsense_Mutation	SNP	ENST00000233055.4	hg19	CCDS33387.1	.	.	.	.	.	.	.	.	.	.	C	37	6.256075	0.97417	.	.	ENSG00000085449	ENST00000233055;ENST00000429915	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-13.4219	19.575	0.95439	0.0:1.0:0.0:0.0	.	.	.	.	X	217;174	.	ENSP00000233055:G217X	G	-	1	0	WDFY1	224468541	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	7.314000	0.78988	2.630000	0.89119	0.491000	0.48974	GGA	.	.		0.552	WDFY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330908.1	NM_020830	
SPHKAP	80309	hgsc.bcm.edu	37	2	228881964	228881964	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:228881964G>T	ENST00000392056.3	-	7	3652	c.3606C>A	c.(3604-3606)atC>atA	p.I1202I	SPHKAP_ENST00000344657.5_Silent_p.I1202I	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1202						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TGTCTCTTTCGATGTCCCTCA	0.567																																					p.I1202I		Atlas-SNP	.											SPHKAP_ENST00000392056,NS,carcinoma,0,4	SPHKAP	750	.	0			c.C3606A						.						103.0	101.0	102.0					2																	228881964		2203	4300	6503	SO:0001819	synonymous_variant	80309	exon7			TCTTTCGATGTCC		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.3606C>A	chr2.hg19:g.228881964G>T		83.0	0.0		37.0	2.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	hg19	CCDS46537.1																																																																																			.	.		0.567	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
COL6A3	1293	hgsc.bcm.edu	37	2	238289710	238289710	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:238289710A>G	ENST00000295550.4	-	5	2197	c.1745T>C	c.(1744-1746)aTt>aCt	p.I582T	COL6A3_ENST00000353578.4_Missense_Mutation_p.I376T|COL6A3_ENST00000409809.1_Missense_Mutation_p.I376T|COL6A3_ENST00000392003.2_Missense_Mutation_p.I175T|COL6A3_ENST00000347401.3_Missense_Mutation_p.I381T|COL6A3_ENST00000346358.4_Missense_Mutation_p.I582T|COL6A3_ENST00000392004.3_Missense_Mutation_p.I376T|COL6A3_ENST00000472056.1_Missense_Mutation_p.I175T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	582	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)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CTTGTTCCCAATGGCAAAGGC	0.547																																					p.I582T		Atlas-SNP	.											.	COL6A3	608	.	0			c.T1745C						.						92.0	90.0	90.0					2																	238289710		2203	4300	6503	SO:0001583	missense	1293	exon5			TTCCCAATGGCAA	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.1745T>C	chr2.hg19:g.238289710A>G	ENSP00000295550:p.Ile582Thr	84.0	0.0		66.0	4.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	A	12.40	1.925465	0.34002	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762	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	5.81	5.81	0.92471	von Willebrand factor, type A (3);	0.821953	0.10433	N	0.675328	T	0.74711	0.3752	M	0.89968	3.075	0.09310	N	1	P;D;P;B;P;P	0.60160	0.505;0.987;0.482;0.268;0.876;0.549	B;P;B;B;P;B	0.62298	0.305;0.9;0.297;0.392;0.755;0.239	T	0.68213	-0.5468	10	0.87932	D	0	.	16.167	0.81768	1.0:0.0:0.0:0.0	.	582;175;175;376;376;582	E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;.;CO6A3_HUMAN	T	582;381;376;175;376;582;376;175;582	ENSP00000295550:I582T;ENSP00000315609:I381T;ENSP00000315873:I376T;ENSP00000418285:I175T;ENSP00000386844:I376T;ENSP00000295546:I582T;ENSP00000375861:I376T;ENSP00000375860:I175T;ENSP00000389539:I582T	ENSP00000295550:I582T	I	-	2	0	COL6A3	237954449	0.669000	0.27502	0.003000	0.11579	0.091000	0.18340	5.250000	0.65432	2.210000	0.71456	0.533000	0.62120	ATT	.	.		0.547	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
KLHL30	377007	hgsc.bcm.edu	37	2	239056574	239056574	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:239056574C>T	ENST00000409223.1	+	6	1357	c.1250C>T	c.(1249-1251)gCt>gTt	p.A417V	KLHL30_ENST00000305959.4_Missense_Mutation_p.A399V			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	417										lung(4)	4		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		AACTTCTCGGCTGCCGGCTGC	0.672																																					p.A417V		Atlas-SNP	.											.	KLHL30	79	.	0			c.C1250T						.						14.0	19.0	17.0					2																	239056574		1870	4091	5961	SO:0001583	missense	377007	exon6			TCTCGGCTGCCGG		CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427		"""Kelch-like"", ""BTB/POZ domain containing"""	24770	protein-coding gene	gene with protein product			"""kelch-like 30 (Drosophila)"""				Standard	NM_198582		Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.1250C>T	chr2.hg19:g.239056574C>T	ENSP00000386389:p.Ala417Val	95.0	0.0		76.0	4.0	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	hg19	CCDS46555.2	.	.	.	.	.	.	.	.	.	.	c	9.475	1.096539	0.20552	.	.	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.67865	-0.29;-0.29	3.89	3.01	0.34805	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.43188	0.1236	N	0.20881	0.62	0.39544	D	0.968868	B	0.14438	0.01	B	0.12837	0.008	T	0.31447	-0.9943	10	0.02654	T	1	.	7.611	0.28131	0.0:0.7907:0.0:0.2093	.	417	Q0D2K2	KLH30_HUMAN	V	417;399	ENSP00000386389:A417V;ENSP00000302386:A399V	ENSP00000302386:A399V	A	+	2	0	KLHL30	238721313	0.997000	0.39634	0.130000	0.21974	0.565000	0.35776	3.537000	0.53590	0.864000	0.35578	0.651000	0.88453	GCT	.	.		0.672	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
SNED1	25992	hgsc.bcm.edu	37	2	241979607	241979607	+	Splice_Site	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:241979607T>A	ENST00000310397.8	+	7	1159		c.e7+2		SNED1_ENST00000342631.6_Splice_Site|SNED1_ENST00000401884.1_Splice_Site|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000405547.3_Splice_Site	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1						cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GCGAGATGGGTGAGTGGCCTG	0.642																																					.		Atlas-SNP	.											.	SNED1	76	.	0			c.1159+2T>A						.						30.0	38.0	35.0					2																	241979607		2127	4234	6361	SO:0001630	splice_region_variant	25992	exon7			GATGGGTGAGTGG	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.1159+2T>A	chr2.hg19:g.241979607T>A		110.0	0.0		82.0	5.0	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Splice_Site	SNP	ENST00000310397.8	hg19	CCDS46562.1	.	.	.	.	.	.	.	.	.	.	T	8.512	0.866695	0.17250	.	.	ENSG00000162804	ENST00000401884;ENST00000405547;ENST00000310397;ENST00000342631;ENST00000401644;ENST00000431690;ENST00000420591	.	.	.	4.73	3.54	0.40534	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.1866	0.43002	0.0:0.0813:0.0:0.9187	.	.	.	.	.	-1	.	.	.	+	.	.	SNED1	241628280	1.000000	0.71417	0.504000	0.27639	0.040000	0.13550	4.521000	0.60532	0.619000	0.30197	0.482000	0.46254	.	.	.		0.642	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	Intron
HDLBP	3069	hgsc.bcm.edu	37	2	242186199	242186199	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr2:242186199G>T	ENST00000391975.1	-	16	2145	c.1918C>A	c.(1918-1920)Cgg>Agg	p.R640R	HDLBP_ENST00000476807.1_5'Flank|HDLBP_ENST00000310931.4_Silent_p.R640R|HDLBP_ENST00000427183.2_Silent_p.R607R|AC104841.1_ENST00000578965.1_RNA|HDLBP_ENST00000391976.2_Silent_p.R640R	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	640	KH 7. {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)	p.R640W(1)		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)		ATCCTGCTCCGGGCAGCTTCG	0.458																																					p.R640R		Atlas-SNP	.											HDLBP,NS,carcinoma,0,1	HDLBP	118	.	1	Substitution - Missense(1)	endometrium(1)	c.C1918A						.						131.0	135.0	134.0					2																	242186199		2203	4300	6503	SO:0001819	synonymous_variant	3069	exon16			TGCTCCGGGCAGC		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.1918C>A	chr2.hg19:g.242186199G>T		121.0	0.0		122.0	5.0	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Silent	SNP	ENST00000391975.1	hg19	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	G	0.112	-1.136950	0.01742	.	.	ENSG00000115677	ENST00000373292	.	.	.	6.16	1.38	0.22167	.	.	.	.	.	T	0.39835	0.1093	.	.	.	0.34007	D	0.650997	.	.	.	.	.	.	T	0.44559	-0.9320	4	.	.	.	-6.8468	4.7722	0.13162	0.2467:0.0:0.5192:0.2341	.	.	.	.	Q	448	.	.	P	-	2	0	HDLBP	241834872	1.000000	0.71417	0.000000	0.03702	0.004000	0.04260	3.222000	0.51223	-0.018000	0.14079	-0.188000	0.12872	CCG	.	.		0.458	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346	
CRBN	51185	hgsc.bcm.edu	37	3	3221342	3221342	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:3221342A>G	ENST00000231948.4	-	1	52	c.30T>C	c.(28-30)gcT>gcC	p.A10A	CRBN_ENST00000432408.2_Silent_p.A10A	NM_016302.3	NP_057386.2	Q96SW2	CRBN_HUMAN	cereblon	10					negative regulation of ion transmembrane transport (GO:0034766)|negative regulation of protein homooligomerization (GO:0032463)|positive regulation of protein homodimerization activity (GO:0090073)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP-dependent peptidase activity (GO:0004176)			endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	11				Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079)	Lenalidomide(DB00480)|Pomalidomide(DB08910)|Thalidomide(DB01041)	TGTTGTGCGCAGCGTCCTGCT	0.677											OREG0015364	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A10A		Atlas-SNP	.											.	CRBN	29	.	0			c.T30C						.						40.0	37.0	38.0					3																	3221342		2202	4300	6502	SO:0001819	synonymous_variant	51185	exon1			GTGCGCAGCGTCC	BC017419	CCDS2562.1, CCDS54547.1	3p26.3	2014-05-27			ENSG00000113851	ENSG00000113851			30185	protein-coding gene	gene with protein product		609262	"""mental retardation, non-syndromic, autosomal recessive, 2A"""	MRT2A		15557513	Standard	NM_016302		Approved	MRT2	uc003bpq.3	Q96SW2	OTTHUMG00000090261	ENST00000231948.4:c.30T>C	chr3.hg19:g.3221342A>G		234.0	0.0	609	161.0	8.0	NM_001173482	B2R6H4|C9IZA9|C9JAH6|Q6AI62|Q6NVZ0|Q9UHW4	Silent	SNP	ENST00000231948.4	hg19	CCDS2562.1	.	.	.	.	.	.	.	.	.	.	A	11.97	1.797374	0.31777	.	.	ENSG00000113851	ENST00000424814;ENST00000450014	.	.	.	2.87	0.479	0.16796	.	.	.	.	.	T	0.45418	0.1341	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24657	-1.0154	4	.	.	.	-1.3199	3.9654	0.09429	0.344:0.0:0.4575:0.1985	.	.	.	.	P	6	.	.	L	-	2	0	CRBN	3196342	1.000000	0.71417	0.961000	0.40146	0.888000	0.51559	1.650000	0.37292	0.083000	0.17047	0.455000	0.32223	CTG	.	.		0.677	CRBN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206579.3	NM_016302	
LRRN1	57633	hgsc.bcm.edu	37	3	3887042	3887042	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:3887042T>C	ENST00000319331.3	+	2	1478	c.717T>C	c.(715-717)gaT>gaC	p.D239D	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	239						integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		TGGGTCTGGATAGCCTTGAGA	0.393																																					p.D239D		Atlas-SNP	.											.	LRRN1	82	.	0			c.T717C						.						101.0	107.0	105.0					3																	3887042		2203	4300	6503	SO:0001819	synonymous_variant	57633	exon2			TCTGGATAGCCTT	AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"""Immunoglobulin superfamily / I-set domain containing"""	20980	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 3"""					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.717T>C	chr3.hg19:g.3887042T>C		79.0	0.0		66.0	4.0	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	hg19	CCDS33685.1																																																																																			.	.		0.393	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873	
RAF1	5894	hgsc.bcm.edu	37	3	12653516	12653516	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:12653516C>A	ENST00000251849.4	-	3	692	c.253G>T	c.(253-255)Gca>Tca	p.A85S	RAF1_ENST00000534997.1_5'Flank|RAF1_ENST00000542177.1_Intron|RAF1_ENST00000442415.2_Missense_Mutation_p.A85S	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	85	RBD. {ECO:0000255|PROSITE- ProRule:PRU00262}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|death-inducing signaling complex assembly (GO:0071550)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intermediate filament cytoskeleton organization (GO:0045104)|ion transmembrane transport (GO:0034220)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein complex assembly (GO:0031333)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of Rho protein signal transduction (GO:0035023)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		ESRP1/RAF1(4)|RAF1/DAZL(2)|SRGAP3/RAF1(6)	biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	32					Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)	ACCTTGAGTGCTTTCATAAGG	0.483			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.A85S		Atlas-SNP	.		Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	.	RAF1	66	.	0			c.G253T						.						171.0	158.0	163.0					3																	12653516		2203	4300	6503	SO:0001583	missense	5894	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	TGAGTGCTTTCAT	X03484	CCDS2612.1	3p25	2014-09-17	2014-06-26		ENSG00000132155	ENSG00000132155			9829	protein-coding gene	gene with protein product	"""C-Raf proto-oncogene, serine/threonine kinase"""	164760	"""v-raf-1 murine leukemia viral oncogene homolog 1"""			1611909	Standard	NM_002880		Approved	Raf-1, c-Raf, CRAF	uc003bxf.4	P04049	OTTHUMG00000129789	ENST00000251849.4:c.253G>T	chr3.hg19:g.12653516C>A	ENSP00000251849:p.Ala85Ser	90.0	0.0		86.0	4.0	NM_002880	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	hg19	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.635569	0.87760	.	.	ENSG00000132155	ENST00000251849;ENST00000442415	T;T	0.76839	-1.04;-1.05	5.7	5.7	0.88788	Raf-like Ras-binding (3);	0.000000	0.85682	D	0.000000	D	0.85075	0.5614	M	0.81942	2.565	0.80722	D	1	P	0.42296	0.775	P	0.48227	0.571	D	0.86103	0.1557	10	0.62326	D	0.03	.	19.8438	0.96701	0.0:1.0:0.0:0.0	.	85	P04049	RAF1_HUMAN	S	85	ENSP00000251849:A85S;ENSP00000401888:A85S	ENSP00000251849:A85S	A	-	1	0	RAF1	12628516	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	7.797000	0.85911	2.705000	0.92388	0.508000	0.49915	GCA	.	.		0.483	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880	
SATB1	6304	hgsc.bcm.edu	37	3	18458441	18458441	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:18458441G>A	ENST00000338745.6	-	3	2075	c.341C>T	c.(340-342)gCa>gTa	p.A114V	TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000417717.2_Missense_Mutation_p.A114V|SATB1_ENST00000454909.2_Missense_Mutation_p.A114V|SATB1_ENST00000475083.1_5'UTR	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	114	PDZ-like dimerization domain.				activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						AGACAGCAATGCCATTTCGAT	0.418																																					p.A114V		Atlas-SNP	.											.	SATB1	96	.	0			c.C341T						.						185.0	164.0	171.0					3																	18458441		2203	4300	6503	SO:0001583	missense	6304	exon3			AGCAATGCCATTT		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"""Homeoboxes / CUT class"""	10541	protein-coding gene	gene with protein product		602075	"""special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"""			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.341C>T	chr3.hg19:g.18458441G>A	ENSP00000341024:p.Ala114Val	114.0	0.0		96.0	4.0	NM_002971	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	hg19	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	G	19.06	3.753662	0.69648	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717;ENST00000440737;ENST00000452260;ENST00000415069;ENST00000457005;ENST00000414509	T;T;T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6	5.33	5.33	0.75918	.	0.104703	0.64402	D	0.000004	T	0.67998	0.2953	L	0.45581	1.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.65672	-0.6111	10	0.42905	T	0.14	-14.0945	19.3886	0.94570	0.0:0.0:1.0:0.0	.	114;114	Q01826-2;Q01826	.;SATB1_HUMAN	V	114	ENSP00000341024:A114V;ENSP00000399708:A114V;ENSP00000399518:A114V;ENSP00000402982:A114V;ENSP00000406727:A114V;ENSP00000390529:A114V;ENSP00000398072:A114V;ENSP00000408871:A114V	ENSP00000341024:A114V	A	-	2	0	SATB1	18433445	1.000000	0.71417	0.988000	0.46212	0.995000	0.86356	9.813000	0.99286	2.646000	0.89796	0.561000	0.74099	GCA	.	.		0.418	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010	
STT3B	201595	hgsc.bcm.edu	37	3	31574743	31574743	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:31574743T>C	ENST00000295770.2	+	1	462	c.253T>C	c.(253-255)Ttc>Ctc	p.F85L	STT3B_ENST00000453168.1_3'UTR	NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)	85					co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						GCTTGCCGGCTTCAGCTCGCG	0.706																																					p.F85L		Atlas-SNP	.											.	STT3B	52	.	0			c.T253C						.						11.0	11.0	11.0					3																	31574743		2127	4172	6299	SO:0001583	missense	201595	exon1			GCCGGCTTCAGCT	AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"""source of immunodominant MHC associated peptides"", ""dolichyl-diphosphooligosaccharide protein glycotransferase"""	608605	"""STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"""			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.253T>C	chr3.hg19:g.31574743T>C	ENSP00000295770:p.Phe85Leu	114.0	0.0		83.0	4.0	NM_178862	Q96JZ4|Q96KY7	Missense_Mutation	SNP	ENST00000295770.2	hg19	CCDS2650.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.972636	0.92919	.	.	ENSG00000163527	ENST00000295770	.	.	.	4.13	4.13	0.48395	.	0.053416	0.85682	D	0.000000	T	0.82006	0.4943	M	0.94142	3.5	0.80722	D	1	P	0.42584	0.784	P	0.51657	0.676	D	0.86183	0.1607	9	0.66056	D	0.02	0.6074	12.4573	0.55712	0.0:0.0:0.0:1.0	.	85	Q8TCJ2	STT3B_HUMAN	L	85	.	ENSP00000295770:F85L	F	+	1	0	STT3B	31549747	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	4.166000	0.58203	1.633000	0.50488	0.248000	0.18094	TTC	.	.		0.706	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862	
CLASP2	23122	hgsc.bcm.edu	37	3	33759302	33759302	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:33759302G>T	ENST00000468888.2	-	1	239	c.193C>A	c.(193-195)Cgg>Agg	p.R65R	CLASP2_ENST00000359576.5_Silent_p.R65R|CLASP2_ENST00000307312.7_5'UTR|CLASP2_ENST00000399362.4_Silent_p.R65R			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1117					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						TCGCTTACCCGGTAGTTGCTC	0.716																																					p.R65R		Atlas-SNP	.											.	CLASP2	138	.	0			c.C193A						.						8.0	12.0	11.0					3																	33759302		1907	4067	5974	SO:0001819	synonymous_variant	23122	exon1			TTACCCGGTAGTT	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.193C>A	chr3.hg19:g.33759302G>T		113.0	0.0		86.0	5.0	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	hg19																																																																																				.	.		0.716	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044	
TRANK1	9881	hgsc.bcm.edu	37	3	36880152	36880152	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:36880152A>G	ENST00000429976.2	-	18	5451	c.5204T>C	c.(5203-5205)cTg>cCg	p.L1735P	TRANK1_ENST00000301807.6_Missense_Mutation_p.L1185P|TRANK1_ENST00000428977.2_Missense_Mutation_p.L1185P	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1735							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						GTCATGGGCCAGGGCCAACTT	0.483																																					p.L1735P		Atlas-SNP	.											.	TRANK1	398	.	0			c.T5204C						.						79.0	75.0	76.0					3																	36880152		1933	4126	6059	SO:0001583	missense	9881	exon18			TGGGCCAGGGCCA	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.5204T>C	chr3.hg19:g.36880152A>G	ENSP00000416168:p.Leu1735Pro	117.0	0.0		136.0	7.0	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	hg19	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	A	16.48	3.136388	0.56936	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.34472	1.36;1.78;1.36	5.04	5.04	0.67666	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.33206	0.0855	N	0.24115	0.695	0.58432	D	0.999995	D	0.56521	0.976	P	0.47744	0.556	T	0.13335	-1.0513	9	0.52906	T	0.07	.	15.4909	0.75605	1.0:0.0:0.0:0.0	.	1735	O15050	TRNK1_HUMAN	P	1185;1735;1185	ENSP00000416826:L1185P;ENSP00000416168:L1735P;ENSP00000301807:L1185P	ENSP00000301807:L1185P	L	-	2	0	TRANK1	36855156	0.988000	0.35896	0.528000	0.27938	0.544000	0.35116	4.852000	0.62904	2.202000	0.70862	0.533000	0.62120	CTG	.	.		0.483	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
VILL	50853	hgsc.bcm.edu	37	3	38044780	38044780	+	Missense_Mutation	SNP	G	G	T	rs373953862		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:38044780G>T	ENST00000283713.6	+	15	2047	c.1781G>T	c.(1780-1782)cGg>cTg	p.R594L	VILL_ENST00000465644.1_Missense_Mutation_p.R312L|VILL_ENST00000383759.2_Missense_Mutation_p.R594L			O15195	VILL_HUMAN	villin-like	594					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		CTGGGAGGCCGGGCCCCCTAC	0.607											OREG0015475	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R594L		Atlas-SNP	.											.	VILL	61	.	0			c.G1781T						.						33.0	33.0	33.0					3																	38044780		2203	4300	6503	SO:0001583	missense	50853	exon14			GAGGCCGGGCCCC		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.1781G>T	chr3.hg19:g.38044780G>T	ENSP00000283713:p.Arg594Leu	58.0	0.0	875	74.0	4.0	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Missense_Mutation	SNP	ENST00000283713.6	hg19	CCDS2670.2	.	.	.	.	.	.	.	.	.	.	g	13.40	2.224929	0.39300	.	.	ENSG00000136059	ENST00000283713;ENST00000383759;ENST00000356246;ENST00000465644	T;T;T	0.21191	2.02;2.02;2.02	4.55	1.69	0.24217	.	0.240429	0.38959	N	0.001508	T	0.28732	0.0712	M	0.77103	2.36	0.30013	N	0.814963	P	0.38110	0.618	P	0.45506	0.483	T	0.23048	-1.0199	10	0.87932	D	0	-11.4828	4.879	0.13670	0.2874:0.3475:0.3651:0.0	.	594	O15195	VILL_HUMAN	L	594;594;580;312	ENSP00000283713:R594L;ENSP00000373266:R594L;ENSP00000422096:R312L	ENSP00000283713:R594L	R	+	2	0	VILL	38019784	0.964000	0.33143	0.994000	0.49952	0.035000	0.12851	1.397000	0.34543	0.099000	0.17552	-0.420000	0.06012	CGG	.	.		0.607	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
DLEC1	9940	hgsc.bcm.edu	37	3	38080908	38080908	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:38080908C>T	ENST00000308059.6	+	1	213	c.192C>T	c.(190-192)cgC>cgT	p.R64R	DLEC1_ENST00000346219.3_Silent_p.R64R|DLEC1_ENST00000452631.2_Silent_p.R64R					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CCCGGCCCCGCCGCCTCACGC	0.677																																					p.R64R		Atlas-SNP	.											.	DLEC1	278	.	0			c.C192T						.						35.0	43.0	40.0					3																	38080908		1996	4174	6170	SO:0001819	synonymous_variant	9940	exon1			GCCCCGCCGCCTC	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.192C>T	chr3.hg19:g.38080908C>T		176.0	0.0		138.0	46.0	NM_007337		Silent	SNP	ENST00000308059.6	hg19	CCDS2672.2																																																																																			.	.		0.677	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
XYLB	9942	hgsc.bcm.edu	37	3	38416703	38416703	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:38416703C>T	ENST00000207870.3	+	12	1047	c.957C>T	c.(955-957)caC>caT	p.H319H	XYLB_ENST00000542835.1_Silent_p.H182H	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	319					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		TGGAAGGCCACATCTTCTGCA	0.607																																					p.H319H		Atlas-SNP	.											.	XYLB	50	.	0			c.C957T						.						124.0	88.0	100.0					3																	38416703		2203	4300	6503	SO:0001819	synonymous_variant	9942	exon12			AGGCCACATCTTC	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"""xylulokinase (H. influenzae) homolog"""			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.957C>T	chr3.hg19:g.38416703C>T		134.0	0.0		88.0	4.0	NM_005108	B2RAW4|B4DDT2|B9EH64	Silent	SNP	ENST00000207870.3	hg19	CCDS2678.1																																																																																			.	.		0.607	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108	
ZNF662	389114	hgsc.bcm.edu	37	3	42956424	42956424	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:42956424C>A	ENST00000541208.1	+	5	1228	c.859C>A	c.(859-861)Cag>Aag	p.Q287K	ZNF662_ENST00000422021.1_Intron|ZNF662_ENST00000328199.6_Missense_Mutation_p.Q313K|KRBOX1_ENST00000426937.1_Intron|ZNF662_ENST00000440367.2_Missense_Mutation_p.Q287K			Q6ZS27	ZN662_HUMAN	zinc finger protein 662	287					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|large_intestine(6)|lung(5)|upper_aerodigestive_tract(1)	15				KIRC - Kidney renal clear cell carcinoma(284;0.217)		GGGCTTTAGTCAGAACACAAG	0.448																																					p.Q313K		Atlas-SNP	.											.	ZNF662	112	.	0			c.C937A						.						99.0	90.0	93.0					3																	42956424		2203	4300	6503	SO:0001583	missense	389114	exon4			TTTAGTCAGAACA	AK127779	CCDS2708.1, CCDS46807.1	3p22.1	2013-01-08			ENSG00000182983	ENSG00000182983		"""Zinc fingers, C2H2-type"", ""-"""	31930	protein-coding gene	gene with protein product							Standard	NM_207404		Approved	FLJ45880	uc003cmk.2	Q6ZS27	OTTHUMG00000133041	ENST00000541208.1:c.859C>A	chr3.hg19:g.42956424C>A	ENSP00000446208:p.Gln287Lys	87.0	0.0		91.0	4.0	NM_001134656	A1A4T9|F8W7S8|Q6ZNF8|Q6ZQW8	Missense_Mutation	SNP	ENST00000541208.1	hg19	CCDS2708.1	.	.	.	.	.	.	.	.	.	.	C	7.980	0.750912	0.15778	.	.	ENSG00000182983	ENST00000440367;ENST00000328199;ENST00000541208	T;T;T	0.07021	3.23;3.23;3.23	3.17	3.17	0.36434	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07413	0.0187	N	0.11927	0.2	0.22050	N	0.99939	D;D	0.54601	0.959;0.967	B;P	0.50570	0.434;0.644	T	0.33548	-0.9864	9	0.33940	T	0.23	.	8.4601	0.32923	0.0:0.7589:0.2411:0.0	.	313;287	F8W7S8;Q6ZS27	.;ZN662_HUMAN	K	287;313;287	ENSP00000405047:Q287K;ENSP00000329264:Q313K;ENSP00000446208:Q287K	ENSP00000329264:Q313K	Q	+	1	0	ZNF662	42931428	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	-0.353000	0.07691	1.797000	0.52628	0.555000	0.69702	CAG	.	.		0.448	ZNF662-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256646.4	NM_207404	
CDCP1	64866	hgsc.bcm.edu	37	3	45135024	45135024	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:45135024T>C	ENST00000296129.1	-	6	1506	c.1372A>G	c.(1372-1374)Agc>Ggc	p.S458G		NM_022842.3	NP_073753.3	Q9H5V8	CDCP1_HUMAN	CUB domain containing protein 1	458	CUB.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|skin(4)|urinary_tract(1)	29				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)		AGCACCAGGCTGAGCCTGTCC	0.597																																					p.S458G		Atlas-SNP	.											.	CDCP1	61	.	0			c.A1372G						.						93.0	84.0	87.0					3																	45135024		2203	4300	6503	SO:0001583	missense	64866	exon6			CCAGGCTGAGCCT	AF468010	CCDS2727.1, CCDS46812.1	3p21.3	2006-03-28			ENSG00000163814	ENSG00000163814		"""CD molecules"""	24357	protein-coding gene	gene with protein product		611735				11466621	Standard	NM_022842		Approved	CD318, SIMA135	uc003com.3	Q9H5V8	OTTHUMG00000133090	ENST00000296129.1:c.1372A>G	chr3.hg19:g.45135024T>C	ENSP00000296129:p.Ser458Gly	84.0	0.0		78.0	4.0	NM_022842	Q49UB4|Q6NT71|Q6U9Y2|Q8WU91|Q96QU7|Q9H676|Q9H8C2	Missense_Mutation	SNP	ENST00000296129.1	hg19	CCDS2727.1	.	.	.	.	.	.	.	.	.	.	T	14.23	2.472378	0.43942	.	.	ENSG00000163814	ENST00000296129	T	0.23754	1.89	5.85	4.67	0.58626	.	0.270974	0.44483	N	0.000441	T	0.21062	0.0507	L	0.38838	1.175	0.80722	D	1	B	0.12013	0.005	B	0.11329	0.006	T	0.02705	-1.1121	10	0.52906	T	0.07	.	10.5696	0.45192	0.0:0.0744:0.0:0.9256	.	458	Q9H5V8	CDCP1_HUMAN	G	458	ENSP00000296129:S458G	ENSP00000296129:S458G	S	-	1	0	CDCP1	45110028	0.994000	0.37717	0.974000	0.42286	0.772000	0.43724	2.542000	0.45744	1.000000	0.39049	0.459000	0.35465	AGC	.	.		0.597	CDCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256748.3	NM_022842	
ELP6	54859	hgsc.bcm.edu	37	3	47552681	47552681	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:47552681A>G	ENST00000296149.4	-	2	260	c.90T>C	c.(88-90)gaT>gaC	p.D30D	ELP6_ENST00000439305.1_5'UTR|ELP6_ENST00000446787.1_5'UTR|ELP6_ENST00000460502.1_5'Flank	NM_001031703.2	NP_001026873.2	Q0PNE2	ELP6_HUMAN	elongator acetyltransferase complex subunit 6	30					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Elongator holoenzyme complex (GO:0033588)											GGAAACTCCCATCTGTCTTGG	0.418																																					p.D30D		Atlas-SNP	.											.	.	.	.	0			c.T90C						.						106.0	100.0	102.0					3																	47552681		1874	4117	5991	SO:0001819	synonymous_variant	54859	exon2			ACTCCCATCTGTC	AK000218	CCDS43082.1	3p21.31	2012-08-14	2012-08-08	2012-08-08	ENSG00000163832	ENSG00000163832		"""Elongator acetyltransferase complex subunits"""	25976	protein-coding gene	gene with protein product		615020	"""transmembrane protein 103"", ""chromosome 3 open reading frame 75"""	TMEM103, C3orf75		22854966	Standard	XM_005265241		Approved	FLJ20211	uc003crk.3	Q0PNE2	OTTHUMG00000133521	ENST00000296149.4:c.90T>C	chr3.hg19:g.47552681A>G		96.0	0.0		98.0	4.0	NM_001031703	Q9BW57|Q9NXJ3	Silent	SNP	ENST00000296149.4	hg19	CCDS43082.1																																																																																			.	.		0.418	ELP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257493.1	NM_017713	
COL7A1	1294	hgsc.bcm.edu	37	3	48609831	48609831	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:48609831T>C	ENST00000328333.8	-	89	7067	c.6960A>G	c.(6958-6960)ggA>ggG	p.G2320G	COL7A1_ENST00000454817.1_Silent_p.G2288G	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2320	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)		CCACCAGGTCTCCAGCAAGGC	0.607																																					p.G2320G		Atlas-SNP	.											.	COL7A1	320	.	0			c.A6960G						.						84.0	89.0	87.0					3																	48609831		2203	4300	6503	SO:0001819	synonymous_variant	1294	exon89			CAGGTCTCCAGCA	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.6960A>G	chr3.hg19:g.48609831T>C		184.0	0.0		153.0	7.0	NM_000094	Q14054|Q16507	Silent	SNP	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.		0.607	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
P4HTM	54681	hgsc.bcm.edu	37	3	49043519	49043519	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:49043519A>G	ENST00000383729.4	+	8	1558	c.1187A>G	c.(1186-1188)gAc>gGc	p.D396G	P4HTM_ENST00000343546.4_Missense_Mutation_p.D457G|WDR6_ENST00000608424.1_5'Flank|WDR6_ENST00000415265.2_5'Flank|WDR6_ENST00000395474.3_5'Flank|WDR6_ENST00000448293.1_5'Flank	NM_177939.2	NP_808808.1	Q9NXG6	P4HTM_HUMAN	prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum)	396	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|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)			NS(1)|breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21					Vitamin C(DB00126)	GATGACGTGGACCTCCGTGAC	0.582																																					p.D457G		Atlas-SNP	.											.	P4HTM	71	.	0			c.A1370G						.						104.0	97.0	99.0					3																	49043519		2203	4300	6503	SO:0001583	missense	54681	exon8			ACGTGGACCTCCG		CCDS2781.2, CCDS43089.1	3p21.31	2009-01-14			ENSG00000178467	ENSG00000178467			28858	protein-coding gene	gene with protein product	"""Prolyl hydroxlase domain-containing 4"", ""hypoxia inducible factor prolyl 4 hydroxylase"""	614584				12163023, 17726031	Standard	XR_245139		Approved	P4H-TM, PHD4, PH4, HIFPH4, FLJ20262, EGLN4, PH-4	uc003cvh.3	Q9NXG6	OTTHUMG00000074057	ENST00000383729.4:c.1187A>G	chr3.hg19:g.49043519A>G	ENSP00000373235:p.Asp396Gly	112.0	0.0		91.0	4.0	NM_177938	Q6PAG6|Q8TCJ9|Q8WV55|Q96F22|Q9BW77	Missense_Mutation	SNP	ENST00000383729.4	hg19	CCDS43089.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.648164	0.87958	.	.	ENSG00000178467	ENST00000383729;ENST00000343546	T	0.79247	-1.25	5.85	5.85	0.93711	Oxoglutarate/iron-dependent oxygenase (2);Prolyl 4-hydroxylase, alpha subunit (1);	0.000000	0.85682	D	0.000000	D	0.83723	0.5316	L	0.48642	1.525	0.48632	D	0.999688	P;D	0.89917	0.659;1.0	P;D	0.87578	0.789;0.998	T	0.80360	-0.1415	10	0.20519	T	0.43	-35.4512	16.2303	0.82332	1.0:0.0:0.0:0.0	.	457;396	Q9NXG6-3;Q9NXG6	.;P4HTM_HUMAN	G	396;457	ENSP00000373235:D396G	ENSP00000341422:D457G	D	+	2	0	P4HTM	49018523	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	8.393000	0.90182	2.233000	0.73108	0.533000	0.62120	GAC	.	.		0.582	P4HTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157211.1	NM_177938	
LAMB2	3913	hgsc.bcm.edu	37	3	49159200	49159200	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:49159200T>C	ENST00000418109.1	-	31	5181	c.5017A>G	c.(5017-5019)Aaa>Gaa	p.K1673E	USP19_ENST00000398888.2_5'Flank|USP19_ENST00000453664.1_5'Flank|LAMB2_ENST00000305544.4_Missense_Mutation_p.K1673E|USP19_ENST00000434032.2_5'Flank|USP19_ENST00000398898.2_5'Flank|USP19_ENST00000417901.1_5'Flank|USP19_ENST00000398892.3_5'Flank|USP19_ENST00000488993.1_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1673	Domain I.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCTGCCCGTTTCAATTTCAGA	0.602																																					p.K1673E		Atlas-SNP	.											.	LAMB2	156	.	0			c.A5017G						.						75.0	76.0	75.0					3																	49159200		2203	4300	6503	SO:0001583	missense	3913	exon30			CCCGTTTCAATTT		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.5017A>G	chr3.hg19:g.49159200T>C	ENSP00000388325:p.Lys1673Glu	88.0	0.0		86.0	4.0	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	hg19	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.052051	0.75960	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.36520	1.25;1.25	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.59059	0.2166	M	0.69823	2.125	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.58381	-0.7646	10	0.38643	T	0.18	.	15.6945	0.77484	0.0:0.0:0.0:1.0	.	1673	P55268	LAMB2_HUMAN	E	1673	ENSP00000388325:K1673E;ENSP00000307156:K1673E	ENSP00000307156:K1673E	K	-	1	0	LAMB2	49134204	1.000000	0.71417	1.000000	0.80357	0.359000	0.29487	7.619000	0.83057	2.118000	0.64928	0.533000	0.62120	AAA	.	.		0.602	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	
MST1R	4486	hgsc.bcm.edu	37	3	49940121	49940121	+	Missense_Mutation	SNP	G	G	A	rs541331773		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:49940121G>A	ENST00000296474.3	-	1	949	c.922C>T	c.(922-924)Cgc>Tgc	p.R308C	CTD-2330K9.3_ENST00000419183.1_5'Flank|CTD-2330K9.2_ENST00000435478.1_RNA|MST1R_ENST00000344206.4_Missense_Mutation_p.R308C	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	308	Poly-Arg.|Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		GCCCCCCGGCGCCTGCGTTTT	0.662													G|||	1	0.000199681	0.0	0.0	5008	,	,		15347	0.0		0.0	False		,,,				2504	0.001				p.R308C		Atlas-SNP	.											.	MST1R	205	.	0			c.C922T						.						59.0	71.0	67.0					3																	49940121		2203	4300	6503	SO:0001583	missense	4486	exon1			CCCGGCGCCTGCG	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"""CD molecules"""	7381	protein-coding gene	gene with protein product		600168	"""PTK8 protein tyrosine kinase 8"""	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.922C>T	chr3.hg19:g.49940121G>A	ENSP00000296474:p.Arg308Cys	72.0	0.0		55.0	24.0	NM_001244937	B5A944|B5A945|B5A946|B5A947	Missense_Mutation	SNP	ENST00000296474.3	hg19	CCDS2807.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.753547	0.49362	.	.	ENSG00000164078	ENST00000296474;ENST00000344206	T;T	0.07021	3.23;3.23	4.7	3.75	0.43078	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.046283	0.85682	D	0.000000	T	0.25901	0.0631	M	0.80746	2.51	0.53005	D	0.999967	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.998;1.0;1.0;0.999	T	0.00909	-1.1518	10	0.87932	D	0	-17.5197	7.3058	0.26447	0.0:0.1414:0.4771:0.3815	.	308;308;308;308;308	Q04912-3;Q04912-4;Q04912-6;Q04912-5;Q04912	.;.;.;.;RON_HUMAN	C	308	ENSP00000296474:R308C;ENSP00000341325:R308C	ENSP00000296474:R308C	R	-	1	0	MST1R	49915125	0.792000	0.28813	0.693000	0.30195	0.185000	0.23345	1.383000	0.34385	2.151000	0.67156	0.561000	0.74099	CGC	.	.		0.662	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1		
IQCF5	389124	hgsc.bcm.edu	37	3	51908112	51908112	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:51908112T>C	ENST00000446461.1	-	2	136	c.84A>G	c.(82-84)cgA>cgG	p.R28R	RN7SL504P_ENST00000494496.2_RNA|IQCF5-AS1_ENST00000440723.1_RNA	NM_001145059.1	NP_001138531.1	A8MTL0	IQCF5_HUMAN	IQ motif containing F5	28	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.									kidney(1)	1						GCAGTGTGCGTCGCACCAGCA	0.572																																					p.R28R		Atlas-SNP	.											.	IQCF5	5	.	0			c.A84G						.						26.0	29.0	28.0					3																	51908112		692	1591	2283	SO:0001819	synonymous_variant	389124	exon2			TGTGCGTCGCACC		CCDS46838.1	3p21.1	2008-10-16			ENSG00000214681	ENSG00000214681			35159	protein-coding gene	gene with protein product							Standard	NM_001145059		Approved		uc011bdx.2	A8MTL0	OTTHUMG00000156913	ENST00000446461.1:c.84A>G	chr3.hg19:g.51908112T>C		96.0	0.0		91.0	5.0	NM_001145059		Silent	SNP	ENST00000446461.1	hg19	CCDS46838.1																																																																																			.	.		0.572	IQCF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346593.1	XM_371643	
STAB1	23166	hgsc.bcm.edu	37	3	52556640	52556640	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:52556640A>G	ENST00000321725.6	+	61	6756	c.6680A>G	c.(6679-6681)gAg>gGg	p.E2227G		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2227	Link. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		TCGGAGGCTGAGGCGGCATGC	0.617																																					p.E2227G		Atlas-SNP	.											.	STAB1	178	.	0			c.A6680G						.						65.0	69.0	68.0					3																	52556640		2203	4300	6503	SO:0001583	missense	23166	exon61			AGGCTGAGGCGGC	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.6680A>G	chr3.hg19:g.52556640A>G	ENSP00000312946:p.Glu2227Gly	116.0	0.0		88.0	4.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	A	14.56	2.570899	0.45798	.	.	ENSG00000010327	ENST00000321725	T	0.32753	1.44	5.75	4.61	0.57282	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.540280	0.21175	N	0.078918	T	0.33498	0.0865	M	0.71206	2.165	0.24342	N	0.994953	P;P	0.35872	0.525;0.525	B;B	0.37731	0.257;0.257	T	0.20505	-1.0273	10	0.28530	T	0.3	.	10.9201	0.47158	0.9264:0.0:0.0736:0.0	.	114;2227	B3KSK0;Q9NY15	.;STAB1_HUMAN	G	2227	ENSP00000312946:E2227G	ENSP00000312946:E2227G	E	+	2	0	STAB1	52531680	0.000000	0.05858	0.233000	0.24025	0.493000	0.33554	0.589000	0.23939	2.192000	0.70111	0.459000	0.35465	GAG	.	.		0.617	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
ADAMTS9	56999	hgsc.bcm.edu	37	3	64599079	64599079	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:64599079G>T	ENST00000498707.1	-	22	3638	c.3296C>A	c.(3295-3297)tCt>tAt	p.S1099Y	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.S1071Y	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1099	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		AGTCTGCATAGATGTTGGCTT	0.488																																					p.S1099Y		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.C3296A						.						108.0	105.0	106.0					3																	64599079		2203	4300	6503	SO:0001583	missense	56999	exon22			TGCATAGATGTTG	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13202	protein-coding gene	gene with protein product		605421	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"""			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.3296C>A	chr3.hg19:g.64599079G>T	ENSP00000418735:p.Ser1099Tyr	111.0	0.0		94.0	4.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	hg19	CCDS2903.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.6|24.6	4.549995|4.549995	0.86127|0.86127	.|.	.|.	ENSG00000163638|ENSG00000163638	ENST00000481060|ENST00000295903;ENST00000498707	.|T;T	.|0.61627	.|0.09;0.09	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	.|0.066684	.|0.64402	.|D	.|0.000006	T|T	0.76912|0.76912	0.4054|0.4054	M|M	0.84082|0.84082	2.675|2.675	0.80722|0.80722	D|D	1|1	.|B;D;B	.|0.76494	.|0.219;0.999;0.052	.|B;D;B	.|0.65323	.|0.158;0.934;0.082	T|T	0.71002|0.71002	-0.4718|-0.4718	5|10	.|0.18276	.|T	.|0.48	.|.	20.6282|20.6282	0.99521|0.99521	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1071;1099;1099	.|B7ZVX9;Q9P2N4-1;Q9P2N4	.|.;.;ATS9_HUMAN	I|Y	155|1071;1099	.|ENSP00000295903:S1071Y;ENSP00000418735:S1099Y	.|ENSP00000295903:S1071Y	L|S	-|-	1|2	2|0	ADAMTS9|ADAMTS9	64574119|64574119	1.000000|1.000000	0.71417|0.71417	0.726000|0.726000	0.30738|0.30738	0.766000|0.766000	0.43426|0.43426	7.536000|7.536000	0.82023|0.82023	2.871000|2.871000	0.98454|0.98454	0.655000|0.655000	0.94253|0.94253	CTA|TCT	.	.		0.488	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1		
EPHA3	2042	hgsc.bcm.edu	37	3	89390186	89390186	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:89390186G>T	ENST00000336596.2	+	4	1160	c.935G>T	c.(934-936)cGg>cTg	p.R312L	EPHA3_ENST00000494014.1_Missense_Mutation_p.R312L|EPHA3_ENST00000452448.2_Missense_Mutation_p.R312L	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	312	Cys-rich.				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)	p.R312L(2)		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)		AATTACTTCCGGGCAGACAAA	0.458										TSP Lung(6;0.00050)																											p.R312L		Atlas-SNP	.											EPHA3_ENST00000452448,colon,carcinoma,+1,4	EPHA3	501	.	2	Substitution - Missense(2)	lung(2)	c.G935T						.						157.0	156.0	156.0					3																	89390186		2203	4300	6503	SO:0001583	missense	2042	exon4			ACTTCCGGGCAGA	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.935G>T	chr3.hg19:g.89390186G>T	ENSP00000337451:p.Arg312Leu	74.0	0.0		94.0	4.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.914940	0.92178	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	D;D;D	0.96168	-3.93;-3.93;-3.93	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.98592	0.9529	H	0.95574	3.69	0.80722	D	1	D;D	0.65815	0.995;0.995	D;P	0.70227	0.968;0.886	D	0.98701	1.0700	9	.	.	.	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	312;312	P29320;P29320-2	EPHA3_HUMAN;.	L	312	ENSP00000337451:R312L;ENSP00000399926:R312L;ENSP00000419190:R312L	.	R	+	2	0	EPHA3	89472876	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	CGG	.	.		0.458	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
TBC1D23	55773	hgsc.bcm.edu	37	3	100002653	100002653	+	Silent	SNP	C	C	T	rs200870879		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:100002653C>T	ENST00000394144.4	+	4	481	c.474C>T	c.(472-474)ccC>ccT	p.P158P	TBC1D23_ENST00000486274.1_3'UTR|TBC1D23_ENST00000475134.1_Intron|TBC1D23_ENST00000344949.5_Silent_p.P158P	NM_001199198.2	NP_001186127.1	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23	158	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of interleukin-6 production (GO:0032755)|regulation of inflammatory response (GO:0050727)|regulation of tumor necrosis factor production (GO:0032680)		Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(10)|ovary(1)|prostate(2)|skin(2)	25						AGTACATTCCCAGGTAAAATA	0.368																																					p.P158P		Atlas-SNP	.											.	TBC1D23	133	.	0			c.C474T						.						69.0	67.0	68.0					3																	100002653		2203	4300	6503	SO:0001819	synonymous_variant	55773	exon4			CATTCCCAGGTAA	AK001908	CCDS2936.1, CCDS56265.1	3q12.2	2013-07-10			ENSG00000036054	ENSG00000036054			25622	protein-coding gene	gene with protein product						22312129	Standard	NM_001199198		Approved	FLJ11046	uc003dtt.4	Q9NUY8	OTTHUMG00000159067	ENST00000394144.4:c.474C>T	chr3.hg19:g.100002653C>T		108.0	0.0		83.0	4.0	NM_001199198	B9A6M5|Q8TCN8|Q8WUB7|Q96D90|Q9NV75	Silent	SNP	ENST00000394144.4	hg19	CCDS56265.1																																																																																			.	C|1.000;G|0.000		0.368	TBC1D23-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353150.1	NM_018309	
NXPE3	91775	hgsc.bcm.edu	37	3	101520615	101520615	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:101520615C>T	ENST00000491511.2	+	5	1586	c.630C>T	c.(628-630)ttC>ttT	p.F210F	NXPE3_ENST00000477909.1_Silent_p.F210F|NXPE3_ENST00000273347.5_Silent_p.F210F|NXPE3_ENST00000422132.1_Silent_p.F210F	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	210						extracellular region (GO:0005576)											GGGTCTATTTCAAGAGTCTCT	0.473																																					p.F210F		Atlas-SNP	.											.	.	.	.	0			c.C630T						.						68.0	70.0	70.0					3																	101520615		2203	4300	6503	SO:0001819	synonymous_variant	91775	exon5			CTATTTCAAGAGT	AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815			28238	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member C"""	FAM55C		12975309	Standard	NM_001134456		Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.630C>T	chr3.hg19:g.101520615C>T		87.0	0.0		78.0	4.0	NM_145037	A8K0X4|D3DN53|Q7Z2S8	Silent	SNP	ENST00000491511.2	hg19	CCDS2945.1																																																																																			.	.		0.473	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037	
PLCXD2	257068	hgsc.bcm.edu	37	3	111432809	111432809	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:111432809T>C	ENST00000477665.1	+	3	1024	c.700T>C	c.(700-702)Tgg>Cgg	p.W234R	PLCXD2_ENST00000393934.3_Missense_Mutation_p.W234R|PLCXD2_ENST00000472215.1_3'UTR	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	234					lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						TCCAGCGCCCTGGGCAAACAC	0.507																																					p.W234R		Atlas-SNP	.											PLCXD2,NS,carcinoma,0,1	PLCXD2	36	.	0			c.T700C						.						78.0	79.0	79.0					3																	111432809		2203	4300	6503	SO:0001583	missense	257068	exon3			GCGCCCTGGGCAA	AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.700T>C	chr3.hg19:g.111432809T>C	ENSP00000420686:p.Trp234Arg	93.0	1.0		53.0	3.0	NM_001185106	Q96N12	Missense_Mutation	SNP	ENST00000477665.1	hg19	CCDS54619.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.159586	0.78226	.	.	ENSG00000240891	ENST00000393934;ENST00000477665	.	.	.	5.39	5.39	0.77823	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	.	.	.	.	T	0.81118	0.4756	M	0.87381	2.88	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.997;0.998	D	0.84613	0.0679	8	0.87932	D	0	-9.1565	13.3815	0.60770	0.0:0.0:0.0:1.0	.	234;234	Q0VAA5;Q0VAA5-2	PLCX2_HUMAN;.	R	234	.	ENSP00000377511:W234R	W	+	1	0	PLCXD2	112915499	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.584000	0.82572	2.034000	0.60081	0.460000	0.39030	TGG	.	.		0.507	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268	
PHLDB2	90102	hgsc.bcm.edu	37	3	111658351	111658351	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:111658351A>G	ENST00000431670.2	+	7	2571	c.2160A>G	c.(2158-2160)aaA>aaG	p.K720K	PHLDB2_ENST00000393925.3_Silent_p.K720K|PHLDB2_ENST00000481953.1_Silent_p.K677K|PHLDB2_ENST00000393923.3_Silent_p.K704K|PHLDB2_ENST00000412622.1_Silent_p.K677K|PHLDB2_ENST00000495180.1_Silent_p.K306K	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	720						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						TTGAAAGCAAACACTTTGAAG	0.418																																					p.K720K		Atlas-SNP	.											.	PHLDB2	449	.	0			c.A2160G						.						125.0	118.0	120.0					3																	111658351		2203	4300	6503	SO:0001819	synonymous_variant	90102	exon7			AAGCAAACACTTT		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"""Pleckstrin homology (PH) domain containing"""	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.2160A>G	chr3.hg19:g.111658351A>G		85.0	0.0		64.0	4.0	NM_001134439	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Silent	SNP	ENST00000431670.2	hg19	CCDS46886.1																																																																																			.	.		0.418	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753	
BOC	91653	hgsc.bcm.edu	37	3	112989741	112989741	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:112989741T>C	ENST00000495514.1	+	6	1321	c.617T>C	c.(616-618)gTg>gCg	p.V206A	BOC_ENST00000355385.3_Missense_Mutation_p.V206A|BOC_ENST00000273395.4_Missense_Mutation_p.V206A			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	206	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TACAACCCAGTGACCCAGGAA	0.602																																					p.V206A		Atlas-SNP	.											.	BOC	139	.	0			c.T617C						.						147.0	144.0	145.0					3																	112989741		2203	4300	6503	SO:0001583	missense	91653	exon6			ACCCAGTGACCCA	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.617T>C	chr3.hg19:g.112989741T>C	ENSP00000418663:p.Val206Ala	130.0	0.0		89.0	4.0	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	hg19	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	T	31	5.088557	0.94100	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.12147	2.71;2.71;2.71	5.8	5.8	0.92144	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.061508	0.64402	D	0.000004	T	0.24547	0.0595	L	0.42487	1.325	0.58432	D	0.999999	P;P	0.47409	0.895;0.716	P;P	0.56648	0.779;0.803	T	0.01524	-1.1333	10	0.20519	T	0.43	.	16.1549	0.81657	0.0:0.0:0.0:1.0	.	206;206	Q9BWV1-3;Q9BWV1	.;BOC_HUMAN	A	206	ENSP00000418663:V206A;ENSP00000273395:V206A;ENSP00000347546:V206A	ENSP00000273395:V206A	V	+	2	0	BOC	114472431	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.698000	0.84413	2.209000	0.71365	0.533000	0.62120	GTG	.	.		0.602	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
CFAP44	55779	hgsc.bcm.edu	37	3	113119484	113119484	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:113119484T>C	ENST00000295868.2	-	12	1544	c.1382A>G	c.(1381-1383)gAc>gGc	p.D461G	WDR52_ENST00000393845.2_Missense_Mutation_p.D461G	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						GCATTCTGGGTCCTGGGTCTG	0.398																																					p.D461G		Atlas-SNP	.											.	WDR52	151	.	0			c.A1382G						.						51.0	56.0	54.0					3																	113119484		2203	4300	6503	SO:0001583	missense	55779	exon12			TCTGGGTCCTGGG																												ENST00000295868.2:c.1382A>G	chr3.hg19:g.113119484T>C	ENSP00000295868:p.Asp461Gly	129.0	0.0		89.0	4.0	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	hg19	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.481913	0.84747	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.65549	-0.16;0.87	5.98	5.98	0.97165	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.73938	0.3651	M	0.68317	2.08	0.80722	D	1	D	0.58970	0.984	P	0.60173	0.87	T	0.71417	-0.4599	9	0.27785	T	0.31	.	15.6593	0.77169	0.0:0.0:0.0:1.0	.	461	Q96MT7	WDR52_HUMAN	G	461	ENSP00000377428:D461G;ENSP00000295868:D461G	ENSP00000295868:D461G	D	-	2	0	WDR52	114602174	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.007000	0.76335	2.288000	0.76882	0.528000	0.53228	GAC	.	.		0.398	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		
C3orf30	152405	hgsc.bcm.edu	37	3	118870130	118870130	+	Silent	SNP	C	C	T	rs570667131		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:118870130C>T	ENST00000295622.1	+	3	1642	c.1602C>T	c.(1600-1602)tgC>tgT	p.C534C	RP11-484M3.5_ENST00000490594.1_Intron	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	534										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		TTATGCTGTGCCAGGTATAGA	0.373																																					p.C534C		Atlas-SNP	.											.	C3orf30	64	.	0			c.C1602T						.						165.0	177.0	173.0					3																	118870130		2203	4300	6503	SO:0001819	synonymous_variant	152405	exon3			GCTGTGCCAGGTA	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.1602C>T	chr3.hg19:g.118870130C>T		100.0	0.0		88.0	4.0	NM_152539	A1L4B7	Silent	SNP	ENST00000295622.1	hg19	CCDS2984.1	.	.	.	.	.	.	.	.	.	.	C	5.104	0.204832	0.09704	.	.	ENSG00000163424	ENST00000492792	.	.	.	5.01	-1.78	0.07957	.	.	.	.	.	T	0.19805	0.0476	.	.	.	0.29470	N	0.857114	.	.	.	.	.	.	T	0.29822	-0.9999	4	.	.	.	6.9124	1.057	0.01592	0.1438:0.2677:0.3112:0.2773	.	.	.	.	S	220	.	.	P	+	1	0	C3orf30	120352820	0.003000	0.15002	0.037000	0.18230	0.866000	0.49608	-0.420000	0.07062	-0.197000	0.10350	-0.218000	0.12543	CCA	.	.		0.373	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
ARHGAP31	57514	hgsc.bcm.edu	37	3	119109740	119109740	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:119109740C>T	ENST00000264245.4	+	7	1323	c.791C>T	c.(790-792)gCt>gTt	p.A264V		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	264					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						AACCATCCTGCTCGCAAGGAA	0.577																																					p.A264V	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											.	ARHGAP31	175	.	0			c.C791T						.						70.0	75.0	74.0					3																	119109740		1980	4167	6147	SO:0001583	missense	57514	exon7			ATCCTGCTCGCAA		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"""Rho GTPase activating proteins"""	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.791C>T	chr3.hg19:g.119109740C>T	ENSP00000264245:p.Ala264Val	118.0	0.0		94.0	4.0	NM_020754	Q9ULL6	Missense_Mutation	SNP	ENST00000264245.4	hg19	CCDS43135.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.100690	0.56183	.	.	ENSG00000031081	ENST00000264245;ENST00000543280	T	0.07216	3.21	5.8	5.8	0.92144	.	0.240214	0.34603	N	0.003838	T	0.05044	0.0135	N	0.02539	-0.55	0.42281	D	0.992091	B	0.11235	0.004	B	0.14023	0.01	T	0.51100	-0.8748	10	0.38643	T	0.18	.	19.1007	0.93272	0.0:1.0:0.0:0.0	.	264	Q2M1Z3	RHG31_HUMAN	V	264	ENSP00000264245:A264V	ENSP00000264245:A264V	A	+	2	0	ARHGAP31	120592430	1.000000	0.71417	0.702000	0.30337	0.933000	0.57130	4.989000	0.63870	2.760000	0.94817	0.478000	0.44815	GCT	.	.		0.577	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2		
GSK3B	2932	hgsc.bcm.edu	37	3	119642320	119642320	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:119642320A>G	ENST00000264235.8	-	4	1359	c.377T>C	c.(376-378)gTc>gCc	p.V126A	GSK3B_ENST00000316626.5_Missense_Mutation_p.V126A	NM_001146156.1|NM_002093.3	NP_001139628.1|NP_002084.2	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta	126	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|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 proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109)	beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|large_intestine(8)|lung(7)|prostate(2)	18				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	ATTAAGATAGACCTCATCTTT	0.338																																					p.V126A		Atlas-SNP	.											.	GSK3B	119	.	0			c.T377C						.						48.0	45.0	46.0					3																	119642320		2202	4300	6502	SO:0001583	missense	2932	exon4			AGATAGACCTCAT	BC012760	CCDS2996.1, CCDS54628.1	3q13.3	2008-02-15			ENSG00000082701	ENSG00000082701			4617	protein-coding gene	gene with protein product		605004				10486203	Standard	NM_002093		Approved		uc003edm.3	P49841	OTTHUMG00000133765	ENST00000264235.8:c.377T>C	chr3.hg19:g.119642320A>G	ENSP00000264235:p.Val126Ala	95.0	0.0		70.0	4.0	NM_002093	D3DN89|Q9BWH3|Q9UL47	Missense_Mutation	SNP	ENST00000264235.8	hg19	CCDS54628.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.123558	0.77436	.	.	ENSG00000082701	ENST00000264235;ENST00000316626	T;T	0.66280	-0.2;-0.2	4.28	4.28	0.50868	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	0.66694	0.2815	L	0.31371	0.925	0.80722	D	1	D;P	0.54207	0.965;0.956	D;P	0.63033	0.91;0.854	T	0.71144	-0.4678	10	0.87932	D	0	-5.4231	13.5977	0.62000	1.0:0.0:0.0:0.0	.	126;126	P49841;P49841-2	GSK3B_HUMAN;.	A	126	ENSP00000264235:V126A;ENSP00000324806:V126A	ENSP00000264235:V126A	V	-	2	0	GSK3B	121125010	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.761000	0.91691	1.804000	0.52760	0.460000	0.39030	GTC	.	.		0.338	GSK3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258240.2		
PARP14	54625	hgsc.bcm.edu	37	3	122437412	122437412	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:122437412T>C	ENST00000474629.2	+	14	4680	c.4414T>C	c.(4414-4416)Tat>Cat	p.Y1472H	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1472					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TGAAAAGGAGTATCAGGAGTT	0.388																																					p.Y1472H		Atlas-SNP	.											.	PARP14	242	.	0			c.T4414C						.						100.0	102.0	101.0					3																	122437412		2038	4200	6238	SO:0001583	missense	54625	exon14			AAGGAGTATCAGG	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4414T>C	chr3.hg19:g.122437412T>C	ENSP00000418194:p.Tyr1472His	93.0	0.0		86.0	4.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	hg19	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	T	8.965	0.971614	0.18736	.	.	ENSG00000173193	ENST00000474629;ENST00000398162;ENST00000310290;ENST00000398157	T	0.09630	2.96	5.23	2.75	0.32379	.	0.690200	0.13861	N	0.357641	T	0.16938	0.0407	M	0.70595	2.14	0.09310	N	1	D;P	0.59767	0.986;0.85	P;B	0.54100	0.742;0.37	T	0.16600	-1.0397	10	0.23891	T	0.37	.	1.4913	0.02457	0.3035:0.0819:0.1579:0.4567	.	1472;1472	Q460N5-4;Q460N5	.;PAR14_HUMAN	H	1472;1391;75;468	ENSP00000418194:Y1472H	ENSP00000310633:Y75H	Y	+	1	0	PARP14	123920102	0.000000	0.05858	0.066000	0.19879	0.064000	0.16182	-0.525000	0.06214	0.401000	0.25424	0.528000	0.53228	TAT	.	.		0.388	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
PARP14	54625	hgsc.bcm.edu	37	3	122439215	122439215	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:122439215T>C	ENST00000474629.2	+	15	5187	c.4921T>C	c.(4921-4923)Tca>Cca	p.S1641P	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1641	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TCAGACCTGCTCACACTTCAG	0.433																																					p.S1641P		Atlas-SNP	.											.	PARP14	242	.	0			c.T4921C						.						87.0	81.0	83.0					3																	122439215		1985	4160	6145	SO:0001583	missense	54625	exon15			ACCTGCTCACACT	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4921T>C	chr3.hg19:g.122439215T>C	ENSP00000418194:p.Ser1641Pro	103.0	0.0		95.0	4.0	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	hg19	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	T	7.840	0.721787	0.15372	.	.	ENSG00000173193	ENST00000474629;ENST00000398162;ENST00000310290;ENST00000398157	T	0.14640	2.49	5.06	-10.1	0.00402	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.934638	0.08919	N	0.874661	T	0.05593	0.0147	N	0.12637	0.245	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.003	T	0.41215	-0.9521	10	0.18710	T	0.47	.	11.276	0.49168	0.0:0.2472:0.5103:0.2424	.	1641;1641	Q460N5-4;Q460N5	.;PAR14_HUMAN	P	1641;1560;244;637	ENSP00000418194:S1641P	ENSP00000310633:S244P	S	+	1	0	PARP14	123921905	0.000000	0.05858	0.004000	0.12327	0.025000	0.11179	-5.482000	0.00119	-2.079000	0.00871	-1.333000	0.01266	TCA	.	.		0.433	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
KALRN	8997	hgsc.bcm.edu	37	3	124385357	124385357	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:124385357A>G	ENST00000291478.5	+	13	1476	c.1313A>G	c.(1312-1314)gAt>gGt	p.D438G	KALRN_ENST00000428018.2_Missense_Mutation_p.D406G|KALRN_ENST00000360013.3_Missense_Mutation_p.D2135G|KALRN_ENST00000459915.1_Missense_Mutation_p.D227G|KALRN_ENST00000393496.1_Missense_Mutation_p.D476G	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	2134					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						ATCGAGCTGGATGCAGGCATG	0.552																																					p.D2135G		Atlas-SNP	.											.	KALRN	556	.	0			c.A6404G						.						86.0	78.0	81.0					3																	124385357		2203	4300	6503	SO:0001583	missense	8997	exon46			AGCTGGATGCAGG	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000291478.5:c.1313A>G	chr3.hg19:g.124385357A>G	ENSP00000291478:p.Asp438Gly	121.0	0.0		95.0	5.0	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000291478.5	hg19	CCDS3028.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.3|22.3	4.274944|4.274944	0.80580|0.80580	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000360013;ENST00000393496;ENST00000291478;ENST00000428018;ENST00000459915|ENST00000354186	T;T;T;T;T|.	0.12361|.	2.69;2.69;2.69;2.69;2.69|.	5.15|5.15	5.15|5.15	0.70609|0.70609	Pleckstrin homology-type (1);Pleckstrin homology domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74473|0.74473	0.3721|0.3721	M|M	0.75447|0.75447	2.3|2.3	0.58432|0.58432	D|D	0.999997|0.999997	B;D;D;P|.	0.76494|.	0.054;0.999;0.999;0.598|.	B;D;D;B|.	0.70935|.	0.027;0.941;0.971;0.243|.	T|T	0.75575|0.75575	-0.3270|-0.3270	10|5	0.72032|.	D|.	0.01|.	.|.	15.1548|15.1548	0.72733|0.72733	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	227;438;476;2134|.	E7EUZ8;C9JQ37;O60229-5;O60229|.	.;.;.;KALRN_HUMAN|.	G|V	2135;476;438;406;227|2104	ENSP00000353109:D2135G;ENSP00000377134:D476G;ENSP00000291478:D438G;ENSP00000402419:D406G;ENSP00000420318:D227G|.	ENSP00000291478:D438G|.	D|M	+|+	2|1	0|0	KALRN|KALRN	125868047|125868047	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.829000|0.829000	0.46940|0.46940	9.139000|9.139000	0.94554|0.94554	2.170000|2.170000	0.68504|0.68504	0.460000|0.460000	0.39030|0.39030	GAT|ATG	.	.		0.552	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947	
MCM2	4171	hgsc.bcm.edu	37	3	127325501	127325501	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:127325501C>A	ENST00000265056.7	+	6	1186	c.942C>A	c.(940-942)agC>agA	p.S314R		NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	314					cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						TGGTGACCAGCTGCACTGGCG	0.607																																					p.S314R		Atlas-SNP	.											.	MCM2	79	.	0			c.C942A						.						77.0	71.0	73.0					3																	127325501		2203	4300	6503	SO:0001583	missense	4171	exon6			GACCAGCTGCACT	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"""mitotin"""	116945	"""minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)"", ""MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"""	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.942C>A	chr3.hg19:g.127325501C>A	ENSP00000265056:p.Ser314Arg	84.0	0.0		57.0	4.0	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Missense_Mutation	SNP	ENST00000265056.7	hg19	CCDS3043.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.367|4.367	0.067726|0.067726	0.08436|0.08436	.|.	.|.	ENSG00000073111|ENSG00000073111	ENST00000491422|ENST00000265056;ENST00000539922;ENST00000543142	.|T	.|0.02631	.|4.22	4.99|4.99	4.12|4.12	0.48240|0.48240	.|Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	.|0.078244	.|0.85682	.|D	.|0.000000	T|T	0.01940|0.01940	0.0061|0.0061	N|N	0.16098|0.16098	0.37|0.37	0.58432|0.58432	D|D	0.999991|0.999991	.|P;B;B	.|0.49559	.|0.925;0.001;0.003	.|P;B;B	.|0.44990	.|0.466;0.015;0.009	T|T	0.53258|0.53258	-0.8464|-0.8464	5|10	.|0.02654	.|T	.|1	-41.6488|-41.6488	7.9871|7.9871	0.30218|0.30218	0.0:0.7367:0.0:0.2633|0.0:0.7367:0.0:0.2633	.|.	.|295;184;314	.|F5H1E9;B4DSV5;P49736	.|.;.;MCM2_HUMAN	D|R	177|314;218;295	.|ENSP00000265056:S314R	.|ENSP00000265056:S314R	A|S	+|+	2|3	0|2	MCM2|MCM2	128808191|128808191	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	2.255000|2.255000	0.43222|0.43222	1.087000|1.087000	0.41251|0.41251	0.585000|0.585000	0.79938|0.79938	GCT|AGC	.	.		0.607	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1		
NME9	347736	hgsc.bcm.edu	37	3	138023727	138023727	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:138023727T>C	ENST00000333911.3	-	9	806	c.779A>G	c.(778-780)gAg>gGg	p.E260G	NME9_ENST00000317876.4_Missense_Mutation_p.E199G|NME9_ENST00000341790.5_Missense_Mutation_p.E197G|NME9_ENST00000383180.2_Missense_Mutation_p.E199G|NME9_ENST00000484930.1_Missense_Mutation_p.E197G|NME9_ENST00000536478.1_Missense_Mutation_p.E199G			Q86XW9	TXND6_HUMAN	NME/NM23 family member 9	260	NDK.				cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										TTCTGGCTGCTCCCTCCTGGC	0.577																																					p.E199G		Atlas-SNP	.											.	.	.	.	0			c.A596G						.						121.0	108.0	112.0					3																	138023727		2203	4300	6503	SO:0001583	missense	347736	exon10			GGCTGCTCCCTCC	AF196568	CCDS3099.1	3q22.3	2012-05-18	2012-05-18	2011-08-24	ENSG00000181322	ENSG00000181322			21343	protein-coding gene	gene with protein product			"""thioredoxin domain containing 6"", ""NME gene family member 9"", ""NME family member 9"""	TXNDC6		12569107, 19852809	Standard	NM_178130		Approved	TXL-2, NM23-H9	uc003ese.1	Q86XW9	OTTHUMG00000159823	ENST00000333911.3:c.779A>G	chr3.hg19:g.138023727T>C	ENSP00000335444:p.Glu260Gly	91.0	0.0		65.0	4.0	NM_178130	Q7Z4A8|Q8N1V7	Missense_Mutation	SNP	ENST00000333911.3	hg19		.	.	.	.	.	.	.	.	.	.	T	17.83	3.484498	0.63962	.	.	ENSG00000181322	ENST00000383180;ENST00000317876;ENST00000484930;ENST00000341790;ENST00000536478;ENST00000333911	T;T;T;T;T;T	0.49432	0.8;0.8;0.8;0.8;0.8;0.78	5.02	5.02	0.67125	.	0.052863	0.64402	D	0.000001	T	0.67924	0.2945	.	.	.	0.47949	D	0.999551	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.78314	0.933;0.991;0.963	T	0.72418	-0.4300	9	0.72032	D	0.01	-28.0486	12.7046	0.57054	0.0:0.0:0.0:1.0	.	197;260;199	Q86XW9-3;Q86XW9;Q86XW9-2	.;TXND6_HUMAN;.	G	199;199;197;197;199;260	ENSP00000372667:E199G;ENSP00000321929:E199G;ENSP00000419882:E197G;ENSP00000341084:E197G;ENSP00000440143:E199G;ENSP00000335444:E260G	ENSP00000321929:E199G	E	-	2	0	TXNDC6	139506417	1.000000	0.71417	1.000000	0.80357	0.451000	0.32288	5.841000	0.69409	1.881000	0.54492	0.482000	0.46254	GAG	.	.		0.577	NME9-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357583.1	NM_178130	
PIK3CB	5291	hgsc.bcm.edu	37	3	138376626	138376626	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:138376626C>T	ENST00000477593.1	-	21	2921	c.2848G>A	c.(2848-2850)Ggc>Agc	p.G950S	PIK3CB_ENST00000289153.2_Missense_Mutation_p.G950S|PIK3CB_ENST00000544716.1_Missense_Mutation_p.G401S			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	950	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|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)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	CTTTTAATGCCAAACTTAGAT	0.368																																					p.G950S		Atlas-SNP	.											.	PIK3CB	103	.	0			c.G2848A						.						92.0	93.0	93.0					3																	138376626		2203	4300	6503	SO:0001583	missense	5291	exon20			TAATGCCAAACTT		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"""phosphoinositide-3-kinase, catalytic, beta polypeptide"""	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.2848G>A	chr3.hg19:g.138376626C>T	ENSP00000418143:p.Gly950Ser	134.0	0.0		97.0	4.0	NM_006219	D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	hg19	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.005252	0.93287	.	.	ENSG00000051382	ENST00000477593;ENST00000544716;ENST00000289153	D;D;D	0.82433	-1.61;-1.61;-1.61	5.72	5.72	0.89469	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.103125	0.64402	D	0.000002	D	0.91178	0.7221	M	0.86268	2.805	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.976	D;D;D	0.77004	0.939;0.989;0.951	D	0.91478	0.5202	10	0.54805	T	0.06	-13.5388	13.128	0.59366	0.0:0.9271:0.0:0.0729	.	950;537;401	P42338;B4DZI3;Q68DL0	PK3CB_HUMAN;.;.	S	950;401;950	ENSP00000418143:G950S;ENSP00000438259:G401S;ENSP00000289153:G950S	ENSP00000289153:G950S	G	-	1	0	PIK3CB	139859316	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.088000	0.71371	2.684000	0.91462	0.650000	0.86243	GGC	.	.		0.368	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1		
ZBTB38	253461	hgsc.bcm.edu	37	3	141164366	141164366	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:141164366T>C	ENST00000514251.1	+	4	3415	c.3136T>C	c.(3136-3138)Tgc>Cgc	p.C1046R	ZBTB38_ENST00000321464.5_Missense_Mutation_p.C1047R|ZBTB38_ENST00000441582.2_Missense_Mutation_p.C1046R					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						CTGCGGACGGTGCTTTTCGGT	0.517																																					p.C1046R		Atlas-SNP	.											.	ZBTB38	92	.	0			c.T3136C						.						83.0	85.0	84.0					3																	141164366		2070	4200	6270	SO:0001583	missense	253461	exon8			GGACGGTGCTTTT	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.3136T>C	chr3.hg19:g.141164366T>C	ENSP00000426387:p.Cys1046Arg	103.0	0.0		107.0	6.0	NM_001080412		Missense_Mutation	SNP	ENST00000514251.1	hg19	CCDS43157.1	.	.	.	.	.	.	.	.	.	.	T	3.592	-0.083306	0.07141	.	.	ENSG00000177311	ENST00000514251;ENST00000441582;ENST00000321464	T;T;T	0.07216	3.21;3.21;3.21	5.76	-3.08	0.05347	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.293174	0.35555	N	0.003129	T	0.02047	0.0064	N	0.03071	-0.42	0.39004	D	0.959415	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.46569	-0.9182	9	.	.	.	-11.9993	1.957	0.03378	0.1022:0.2343:0.2105:0.453	.	1047;1046	B4DYR8;Q8NAP3	.;ZBT38_HUMAN	R	1046;1046;1047	ENSP00000426387:C1046R;ENSP00000406955:C1046R;ENSP00000372635:C1047R	.	C	+	1	0	ZBTB38	142647056	0.997000	0.39634	0.037000	0.18230	0.440000	0.31957	0.772000	0.26647	-0.403000	0.07622	0.533000	0.62120	TGC	.	.		0.517	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
GK5	256356	hgsc.bcm.edu	37	3	141884509	141884509	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:141884509C>A	ENST00000392993.2	-	16	1696	c.1545G>T	c.(1543-1545)tgG>tgT	p.W515C		NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	515					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						CTGCTTTGGCCCAGTTTTCCA	0.388																																					p.W515C		Atlas-SNP	.											.	GK5	45	.	0			c.G1545T						.						222.0	202.0	209.0					3																	141884509		2203	4300	6503	SO:0001583	missense	256356	exon16			TTTGGCCCAGTTT	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.1545G>T	chr3.hg19:g.141884509C>A	ENSP00000418001:p.Trp515Cys	651.0	1.0		514.0	246.0	NM_001039547	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Missense_Mutation	SNP	ENST00000392993.2	hg19	CCDS33871.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.421896	0.83559	.	.	ENSG00000175066	ENST00000392993	D	0.91124	-2.79	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	D	0.97052	0.9037	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97577	1.0108	10	0.87932	D	0	-10.5498	19.2235	0.93808	0.0:1.0:0.0:0.0	.	515	Q6ZS86	GLPK5_HUMAN	C	515	ENSP00000418001:W515C	ENSP00000418001:W515C	W	-	3	0	GK5	143367199	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	6.578000	0.74032	2.838000	0.97847	0.591000	0.81541	TGG	.	.		0.388	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	NM_001039547	
MED12L	116931	hgsc.bcm.edu	37	3	150911407	150911407	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:150911407A>G	ENST00000474524.1	+	14	2137	c.2099A>G	c.(2098-2100)gAc>gGc	p.D700G	MED12L_ENST00000422248.2_Missense_Mutation_p.D700G|MED12L_ENST00000309237.4_Missense_Mutation_p.D735G|MED12L_ENST00000273432.4_Missense_Mutation_p.D560G	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	700						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TCTAATTATGACCTCCTTCGC	0.368																																					p.D700G		Atlas-SNP	.											.	MED12L	271	.	0			c.A2099G						.						142.0	142.0	142.0					3																	150911407		2203	4300	6503	SO:0001583	missense	116931	exon14			ATTATGACCTCCT	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.2099A>G	chr3.hg19:g.150911407A>G	ENSP00000417235:p.Asp700Gly	133.0	0.0		121.0	5.0	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.81|13.81	2.348768|2.348768	0.41599|0.41599	.|.	.|.	ENSG00000144893|ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432|ENST00000480026	T;T;T;T|.	0.33438|.	1.41;1.41;1.41;1.41|.	5.18|5.18	3.88|3.88	0.44766|0.44766	Mediator complex, subunit Med12, LCEWAV-domain (1);|.	0.216134|.	0.47455|.	N|.	0.000224|.	T|.	0.61664|.	0.2365|.	L|L	0.58669|0.58669	1.825|1.825	0.42457|0.42457	D|D	0.992776|0.992776	B;B;B;B|.	0.18741|.	0.03;0.001;0.003;0.001|.	B;B;B;B|.	0.21708|.	0.036;0.006;0.004;0.0|.	T|.	0.58640|.	-0.7601|.	10|.	0.72032|.	D|.	0.01|.	-9.8062|-9.8062	10.561|10.561	0.45146|0.45146	0.9159:0.0:0.0841:0.0|0.9159:0.0:0.0841:0.0	.|.	560;700;700;735|.	F8WAE6;Q86YW9;Q86YW9-2;Q86YW9-3|.	.;MD12L_HUMAN;.;.|.	G|W	700;735;700;560|49	ENSP00000403308:D700G;ENSP00000310760:D735G;ENSP00000417235:D700G;ENSP00000273432:D560G|.	ENSP00000273432:D560G|.	D|X	+|+	2|3	0|0	MED12L|MED12L	152394097|152394097	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.926000|0.926000	0.56050|0.56050	4.683000|4.683000	0.61679|0.61679	0.780000|0.780000	0.33566|0.33566	0.496000|0.496000	0.49642|0.49642	GAC|TGA	.	.		0.368	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
OTOL1	131149	hgsc.bcm.edu	37	3	161221321	161221321	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:161221321G>T	ENST00000327928.4	+	4	1025	c.1025G>T	c.(1024-1026)cGg>cTg	p.R342L		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	342	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						AGAGTGCCCCGGTCGGCTTTC	0.522																																					p.R342L		Atlas-SNP	.											.	OTOL1	63	.	0			c.G1025T						.						39.0	38.0	38.0					3																	161221321		1872	4099	5971	SO:0001583	missense	131149	exon4			TGCCCCGGTCGGC		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"""C1q and tumor necrosis factor related protein 15"""		"""otolin 1 homolog (zebrafish)"""			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.1025G>T	chr3.hg19:g.161221321G>T	ENSP00000330808:p.Arg342Leu	164.0	0.0		106.0	5.0	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	hg19	CCDS46948.1	.	.	.	.	.	.	.	.	.	.	G	5.140	0.211399	0.09757	.	.	ENSG00000182447	ENST00000327928	D	0.86297	-2.1	5.23	-2.2	0.06994	Tumour necrosis factor-like (2);Complement C1q protein (2);	0.298148	0.35407	N	0.003223	D	0.83552	0.5279	M	0.79123	2.44	0.09310	N	0.999994	P	0.49862	0.929	B	0.41440	0.357	T	0.77032	-0.2738	10	0.25106	T	0.35	.	11.4066	0.49902	0.5857:0.0:0.4143:0.0	.	342	A6NHN0	OTOL1_HUMAN	L	342	ENSP00000330808:R342L	ENSP00000330808:R342L	R	+	2	0	OTOL1	162704015	0.062000	0.20869	0.000000	0.03702	0.001000	0.01503	0.639000	0.24690	-0.955000	0.03636	-1.031000	0.02408	CGG	.	.		0.522	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440	
SLITRK3	22865	hgsc.bcm.edu	37	3	164907028	164907028	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:164907028G>T	ENST00000475390.1	-	2	2034	c.1591C>A	c.(1591-1593)Cgg>Agg	p.R531R	SLITRK3_ENST00000241274.3_Silent_p.R531R			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	531					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						AGGTTGAGCCGGGCCAGGGAT	0.507										HNSCC(40;0.11)																											p.R531R		Atlas-SNP	.											SLITRK3,right_upper_lobe,carcinoma,0,1	SLITRK3	263	.	0			c.C1591A						.						56.0	59.0	58.0					3																	164907028		2203	4300	6503	SO:0001819	synonymous_variant	22865	exon2			TGAGCCGGGCCAG	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1591C>A	chr3.hg19:g.164907028G>T		88.0	0.0		60.0	3.0	NM_014926	Q1RMY6	Silent	SNP	ENST00000475390.1	hg19	CCDS3197.1																																																																																			.	.		0.507	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926	
TBL1XR1	79718	hgsc.bcm.edu	37	3	176744244	176744244	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:176744244T>C	ENST00000430069.1	-	15	1694	c.1435A>G	c.(1435-1437)Agc>Ggc	p.S479G	TBL1XR1_ENST00000457928.2_Missense_Mutation_p.S479G			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	479					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			CCCCTATAGCTGTGAACTAGA	0.338																																					p.S479G		Atlas-SNP	.											.	TBL1XR1	87	.	0			c.A1435G						.						92.0	80.0	84.0					3																	176744244		1841	4093	5934	SO:0001583	missense	79718	exon15			TATAGCTGTGAAC	AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"""WD repeat domain containing"""	29529	protein-coding gene	gene with protein product		608628	"""transducin (beta)-like 1X-linked receptor 1"""			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.1435A>G	chr3.hg19:g.176744244T>C	ENSP00000405574:p.Ser479Gly	96.0	0.0		99.0	4.0	NM_024665	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Missense_Mutation	SNP	ENST00000430069.1	hg19	CCDS46961.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.994341	0.74703	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000536758	D;D	0.81739	-1.53;-1.53	6.17	6.17	0.99709	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	D	0.84197	0.5419	M	0.84511	2.7	0.80722	D	1	P	0.42010	0.768	B	0.41088	0.347	D	0.86669	0.1909	10	0.72032	D	0.01	-6.0741	16.0034	0.80327	0.0:0.0:0.0:1.0	.	479	Q9BZK7	TBL1R_HUMAN	G	479;479;341	ENSP00000405574:S479G;ENSP00000413251:S479G	ENSP00000405574:S479G	S	-	1	0	TBL1XR1	178226938	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	AGC	.	.		0.338	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3	NM_024665	
ZMAT3	64393	hgsc.bcm.edu	37	3	178745434	178745434	+	Splice_Site	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:178745434G>T	ENST00000311417.2	-	4	1298	c.557C>A	c.(556-558)tCg>tAg	p.S186*	ZMAT3_ENST00000432729.1_Splice_Site_p.S186*	NM_022470.3	NP_071915.1			zinc finger, matrin-type 3											breast(1)|endometrium(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(1)|skin(1)	14	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			CAATACCTACGAGAATGAGTT	0.463																																					p.S186X		Atlas-SNP	.											.	ZMAT3	42	.	0			c.C557A						.						61.0	64.0	63.0					3																	178745434		2203	4300	6503	SO:0001630	splice_region_variant	64393	exon4			ACCTACGAGAATG	AK122768	CCDS3224.1, CCDS46962.1	3q26.32	2012-10-05	2010-09-15		ENSG00000172667	ENSG00000172667		"""Zinc fingers, matrin-type"""	29983	protein-coding gene	gene with protein product		606452				9400996, 11689294	Standard	NM_022470		Approved	WIG1, MGC10613, FLJ12296, WIG-1, PAG608	uc003fjg.3	Q9HA38	OTTHUMG00000157290	ENST00000311417.2:c.557+1C>A	chr3.hg19:g.178745434G>T		104.0	0.0		81.0	4.0	NM_022470		Nonsense_Mutation	SNP	ENST00000311417.2	hg19	CCDS3224.1	.	.	.	.	.	.	.	.	.	.	G	42	9.424593	0.99167	.	.	ENSG00000172667	ENST00000311417;ENST00000432729	.	.	.	5.6	4.54	0.55810	.	0.471891	0.24454	N	0.038381	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-28.5812	11.8513	0.52413	0.15:0.0:0.85:0.0	.	.	.	.	X	186	.	.	S	-	2	0	ZMAT3	180228128	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.682000	0.54656	2.635000	0.89317	0.650000	0.86243	TCG	.	.		0.463	ZMAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348336.2	NM_152240	Nonsense_Mutation
EPHB3	2049	hgsc.bcm.edu	37	3	184290572	184290572	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:184290572T>C	ENST00000330394.2	+	3	916	c.464T>C	c.(463-465)gTg>gCg	p.V155A	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	155	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			AACCCCTACGTGAAAGTGGAC	0.602																																					p.V155A		Atlas-SNP	.											.	EPHB3	114	.	0			c.T464C						.						75.0	74.0	74.0					3																	184290572		2203	4300	6503	SO:0001583	missense	2049	exon3			CCTACGTGAAAGT	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.464T>C	chr3.hg19:g.184290572T>C	ENSP00000332118:p.Val155Ala	91.0	0.0		60.0	4.0	NM_004443	Q7Z740	Missense_Mutation	SNP	ENST00000330394.2	hg19	CCDS3268.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.520275	0.64747	.	.	ENSG00000182580	ENST00000330394	T	0.03496	3.91	5.48	5.48	0.80851	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.147656	0.48286	D	0.000200	T	0.07638	0.0192	L	0.59912	1.85	0.58432	D	0.999995	P	0.36990	0.577	B	0.40825	0.341	T	0.15954	-1.0419	10	0.44086	T	0.13	.	14.7622	0.69614	0.0:0.0:0.0:1.0	.	155	P54753	EPHB3_HUMAN	A	155	ENSP00000332118:V155A	ENSP00000332118:V155A	V	+	2	0	EPHB3	185773266	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	8.040000	0.89188	2.074000	0.62210	0.459000	0.35465	GTG	.	.		0.602	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
SLC51A	200931	hgsc.bcm.edu	37	3	195955119	195955119	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:195955119T>C	ENST00000296327.5	+	5	705	c.496T>C	c.(496-498)Tgc>Cgc	p.C166R		NM_152672.5	NP_689885.4	Q86UW1	OSTA_HUMAN	solute carrier family 51, alpha subunit	166	Poly-Cys.				bile acid and bile salt transport (GO:0015721)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)									Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)	ctgctgcccctgctgtccacg	0.677																																					p.C166R		Atlas-SNP	.											.	.	.	.	0			c.T496C						.						66.0	66.0	66.0					3																	195955119		2203	4300	6503	SO:0001583	missense	200931	exon5			TGCCCCTGCTGTC		CCDS3314.1	3q29	2013-05-22			ENSG00000163959	ENSG00000163959		"""Solute carriers"""	29955	protein-coding gene	gene with protein product	"""organic solute transporter, alpha subunit"""	612084				12719432, 20538072	Standard	NM_152672		Approved	OSTalpha	uc003fwd.3	Q86UW1	OTTHUMG00000155684	ENST00000296327.5:c.496T>C	chr3.hg19:g.195955119T>C	ENSP00000296327:p.Cys166Arg	82.0	0.0		59.0	4.0	NM_152672	Q6ZMC7	Missense_Mutation	SNP	ENST00000296327.5	hg19	CCDS3314.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.665807	0.47677	.	.	ENSG00000163959	ENST00000296327	T	0.42131	0.98	5.5	5.5	0.81552	.	0.000000	0.53938	D	0.000046	T	0.67468	0.2896	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72567	-0.4254	10	0.72032	D	0.01	-14.1685	14.9457	0.71029	0.0:0.0:0.0:1.0	.	166	Q86UW1	OSTA_HUMAN	R	166	ENSP00000296327:C166R	ENSP00000296327:C166R	C	+	1	0	AC069257.9	197439516	1.000000	0.71417	1.000000	0.80357	0.103000	0.19146	4.997000	0.63921	2.308000	0.77769	0.533000	0.62120	TGC	.	.		0.677	SLC51A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341253.1	NM_152672	
FBXO45	200933	hgsc.bcm.edu	37	3	196304623	196304623	+	Silent	SNP	A	A	T	rs374910244		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr3:196304623A>T	ENST00000311630.6	+	2	915	c.618A>T	c.(616-618)ctA>ctT	p.L206L	FBXO45_ENST00000440469.1_Silent_p.L27L	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	206	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				anterior commissure morphogenesis (GO:0021960)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|corticospinal tract morphogenesis (GO:0021957)|neuron migration (GO:0001764)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|synapse assembly involved in innervation (GO:0060386)	cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	7	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		ATAATCTACTACATAATGGAG	0.478																																					p.L206L		Atlas-SNP	.											.	FBXO45	18	.	0			c.A618T						.						58.0	58.0	58.0					3																	196304623		1947	4155	6102	SO:0001819	synonymous_variant	200933	exon2			TCTACTACATAAT	AK025697	CCDS46985.1	3q29	2008-02-05			ENSG00000174013	ENSG00000174013		"""F-boxes /  ""other"""""	29148	protein-coding gene	gene with protein product		609112					Standard	NM_001105573		Approved	Fbx45	uc010iai.3	P0C2W1	OTTHUMG00000155571	ENST00000311630.6:c.618A>T	chr3.hg19:g.196304623A>T		94.0	0.0		49.0	4.0	NM_001105573	A6NF90|D3DXB5	Silent	SNP	ENST00000311630.6	hg19	CCDS46985.1																																																																																			.	.		0.478	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2		
ZNF141	7700	hgsc.bcm.edu	37	4	367349	367349	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:367349G>T	ENST00000240499.7	+	4	1272	c.1123G>T	c.(1123-1125)Gcc>Tcc	p.A375S	ZNF141_ENST00000505939.1_Intron|ZNF141_ENST00000512994.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	375					anatomical structure morphogenesis (GO:0009653)|limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(3)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	18						ATGTGGCAAAGCCTTTGGACG	0.423																																					p.A375S		Atlas-SNP	.											.	ZNF141	48	.	0			c.G1123T						.						44.0	47.0	46.0					4																	367349		2203	4299	6502	SO:0001583	missense	7700	exon4			GGCAAAGCCTTTG	L15309	CCDS33931.1	4p16.3	2013-01-08	2006-06-13			ENSG00000131127		"""Zinc fingers, C2H2-type"", ""-"""	12926	protein-coding gene	gene with protein product		194648	"""zinc finger protein 141 (clone pHZ-44)"""	D4S90		8268908	Standard	NM_003441		Approved	pHZ-44	uc003gaa.2	Q15928		ENST00000240499.7:c.1123G>T	chr4.hg19:g.367349G>T	ENSP00000240499:p.Ala375Ser	122.0	0.0		91.0	4.0	NM_003441	Q6DK07	Missense_Mutation	SNP	ENST00000240499.7	hg19	CCDS33931.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.513547	0.64522	.	.	ENSG00000131127	ENST00000240499	T	0.18338	2.22	1.24	1.24	0.21308	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10723	0.0262	N	0.16790	0.44	0.24477	N	0.994366	P	0.42337	0.776	P	0.44811	0.461	T	0.18366	-1.0339	8	.	.	.	.	3.6174	0.08082	0.2802:0.0:0.7198:0.0	.	375	Q15928	ZN141_HUMAN	S	375	ENSP00000240499:A375S	.	A	+	1	0	ZNF141	357349	0.000000	0.05858	0.192000	0.23308	0.899000	0.52679	0.077000	0.14738	0.591000	0.29711	0.313000	0.20887	GCC	.	.		0.423	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441	
ZFYVE28	57732	hgsc.bcm.edu	37	4	2306996	2306996	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:2306996G>A	ENST00000290974.2	-	8	1410	c.1071C>T	c.(1069-1071)tcC>tcT	p.S357S	ZFYVE28_ENST00000511071.1_Silent_p.S327S|ZFYVE28_ENST00000515312.1_Silent_p.S287S|RP11-478C1.7_ENST00000510632.1_RNA	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	357					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						AAAGCAAAGAGGACATCTCGT	0.672																																					p.S357S		Atlas-SNP	.											.	ZFYVE28	79	.	0			c.C1071T						.						46.0	46.0	46.0					4																	2306996		2203	4299	6502	SO:0001819	synonymous_variant	57732	exon8			CAAAGAGGACATC	AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"""Zinc fingers, FYVE domain containing"""	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.1071C>T	chr4.hg19:g.2306996G>A		109.0	0.0		94.0	4.0	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Silent	SNP	ENST00000290974.2	hg19	CCDS33942.1																																																																																			.	.		0.672	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371	
ADRA2C	152	hgsc.bcm.edu	37	4	3768868	3768868	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:3768868T>C	ENST00000330055.5	+	1	744	c.535T>C	c.(535-537)Tcg>Ccg	p.S179P	ADRA2C_ENST00000509482.1_Missense_Mutation_p.S179P	NM_000683.3	NP_000674.2	P18825	ADA2C_HUMAN	adrenoceptor alpha 2C	179					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|energy reserve metabolic process (GO:0006112)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|negative regulation of uterine smooth muscle contraction (GO:0070473)|platelet activation (GO:0030168)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of vasoconstriction (GO:0045907)|regulation of insulin secretion (GO:0050796)|regulation of sensory perception of pain (GO:0051930)|small molecule metabolic process (GO:0044281)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Fenoldopam(DB00800)|Iloperidone(DB04946)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Tizanidine(DB00697)|Tolazoline(DB00797)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GTGGCTCATCTCGGCCGTCAT	0.677																																					p.S179P	Esophageal Squamous(12;454 628 4517 14479)	Atlas-SNP	.											.	ADRA2C	24	.	0			c.T535C						.						30.0	30.0	30.0					4																	3768868		2201	4295	6496	SO:0001583	missense	152	exon1			CTCATCTCGGCCG	AY455666	CCDS47004.1	4p16.3	2013-10-22	2012-05-09		ENSG00000184160	ENSG00000184160		"""GPCR / Class A : Adrenoceptors : alpha"""	283	protein-coding gene	gene with protein product		104250	"""adrenergic, alpha-2C-, receptor"""	ADRA2L2, ADRA2RL2		1849485	Standard	NM_000683		Approved	ADRARL2	uc003ghm.3	P18825	OTTHUMG00000159830	ENST00000330055.5:c.535T>C	chr4.hg19:g.3768868T>C	ENSP00000386069:p.Ser179Pro	157.0	0.0		91.0	5.0	NM_000683	P35369|Q9HB49	Missense_Mutation	SNP	ENST00000330055.5	hg19	CCDS47004.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.618455	0.66787	.	.	ENSG00000184160	ENST00000509482;ENST00000330055	T;T	0.46063	0.88;0.88	3.37	3.37	0.38596	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.61299	0.2336	M	0.74389	2.26	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.985;0.99	T	0.65307	-0.6200	9	0.72032	D	0.01	.	11.1249	0.48312	0.0:0.0:0.0:1.0	.	179;179	D6RGL0;P18825	.;ADA2C_HUMAN	P	179	ENSP00000426268:S179P;ENSP00000386069:S179P	ENSP00000386069:S179P	S	+	1	0	ADRA2C	3738666	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.806000	0.38892	1.394000	0.46624	0.459000	0.35465	TCG	.	.		0.677	ADRA2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357607.1	NM_000683	
SLC34A2	10568	hgsc.bcm.edu	37	4	25678341	25678341	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:25678341G>T	ENST00000382051.3	+	13	2093	c.2043G>T	c.(2041-2043)tcG>tcT	p.S681S	SLC34A2_ENST00000503434.1_Silent_p.S680S|SLC34A2_ENST00000504570.1_Silent_p.S680S	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	681					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)	p.S681S(1)	SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				TCCCTGCCTCGGACTCAAAGA	0.582			T	ROS1	NSCLC																																p.S681S		Atlas-SNP	.		Dom	yes		4	4p15.2	10568	"""solute carrier family 34 (sodium phosphate), member 2"""		E	SLC34A2,NS,carcinoma,0,2	SLC34A2	93	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2043T						.						56.0	57.0	57.0					4																	25678341		2203	4300	6503	SO:0001819	synonymous_variant	10568	exon13			TGCCTCGGACTCA	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"""Solute carriers"""	11020	protein-coding gene	gene with protein product		604217	"""solute carrier family 34 (sodium phosphate), member 2"""			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.2043G>T	chr4.hg19:g.25678341G>T		99.0	1.0		66.0	3.0	NM_006424	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Silent	SNP	ENST00000382051.3	hg19	CCDS3435.1																																																																																			.	.		0.582	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424	
PGM2	55276	hgsc.bcm.edu	37	4	37847313	37847313	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:37847313G>T	ENST00000381967.4	+	8	1069	c.969G>T	c.(967-969)ccG>ccT	p.P323P	PGM2_ENST00000537241.1_Silent_p.P163P|PGM2_ENST00000544359.1_Silent_p.P184P	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	323					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						CTAACGACCCGGATGCTGATA	0.333																																					p.P323P		Atlas-SNP	.											.	PGM2	45	.	0			c.G969T						.						104.0	108.0	107.0					4																	37847313		2203	4300	6503	SO:0001819	synonymous_variant	55276	exon8			CGACCCGGATGCT	BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"""phosphopentomutase"""	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.969G>T	chr4.hg19:g.37847313G>T		128.0	0.0		98.0	4.0	NM_018290	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Silent	SNP	ENST00000381967.4	hg19	CCDS3443.1																																																																																			.	.		0.333	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290	
TBC1D1	23216	hgsc.bcm.edu	37	4	38055861	38055861	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:38055861G>T	ENST00000261439.4	+	12	2307	c.1952G>T	c.(1951-1953)gGg>gTg	p.G651V	TBC1D1_ENST00000508802.1_Missense_Mutation_p.G745V	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	651					membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						GATTCTGGTGGGACTCCTGTG	0.473																																					p.G745V		Atlas-SNP	.											.	TBC1D1	94	.	0			c.G2234T						.						111.0	122.0	118.0					4																	38055861		2203	4300	6503	SO:0001583	missense	23216	exon14			CTGGTGGGACTCC	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.1952G>T	chr4.hg19:g.38055861G>T	ENSP00000261439:p.Gly651Val	92.0	0.0		70.0	4.0	NM_001253912	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	hg19	CCDS33972.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	10.64|10.64|10.64	1.408372|1.408372|1.408372	0.25378|0.25378|0.25378	.|.|.	.|.|.	ENSG00000065882|ENSG00000065882|ENSG00000065882	ENST00000508802;ENST00000261439;ENST00000446803;ENST00000421339|ENST00000513936;ENST00000443855|ENST00000510573	T;T;T;T|.|.	0.56611|.|.	3.49;0.45;0.45;0.45|.|.	5.55|5.55|5.55	2.46|2.46|2.46	0.29980|0.29980|0.29980	.|.|.	0.436222|0.436222|.	0.21738|0.21738|.	N|N|.	0.069863|0.069863|.	T|.|T	0.55081|.|0.55081	0.1898|.|0.1898	L|L|L	0.49778|0.49778|0.49778	1.585|1.585|1.585	0.80722|0.80722|0.80722	D|D|D	1|1|1	P;P;B;P|.|.	0.40660|.|.	0.726;0.59;0.314;0.726|.|.	P;B;B;P|.|.	0.50970|.|.	0.655;0.424;0.174;0.655|.|.	T|.|T	0.48103|.|0.48103	-0.9064|.|-0.9064	10|.|5	0.87932|0.54805|.	D|T|.	0|0.06|.	-12.8101|-12.8101|-12.8101	6.9507|6.9507|6.9507	0.24544|0.24544|0.24544	0.4656:0.0:0.5343:0.0|0.4656:0.0:0.5343:0.0|0.4656:0.0:0.5343:0.0	.|.|.	651;745;383;651|.|.	B9A6J6;E9PGH8;Q6PJJ8;Q86TI0|.|.	.;.;.;TBCD1_HUMAN|.|.	V|X|C	745;651;522;119|176;197|338	ENSP00000423651:G745V;ENSP00000261439:G651V;ENSP00000396877:G522V;ENSP00000410167:G119V|.|.	ENSP00000261439:G651V|ENSP00000397640:G197X|.	G|G|W	+|+|+	2|1|3	0|0|0	TBC1D1|TBC1D1|TBC1D1	37732256|37732256|37732256	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.831000|0.831000|0.831000	0.32960|0.32960|0.32960	0.241000|0.241000|0.241000	0.25554|0.25554|0.25554	2.314000|2.314000|2.314000	0.43743|0.43743|0.43743	0.720000|0.720000|0.720000	0.32209|0.32209|0.32209	-0.136000|-0.136000|-0.136000	0.14681|0.14681|0.14681	GGG|GGA|TGG	.	.		0.473	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
TLR10	81793	hgsc.bcm.edu	37	4	38776477	38776477	+	Silent	SNP	C	C	A	rs578031272		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:38776477C>A	ENST00000308973.4	-	4	1340	c.735G>T	c.(733-735)tcG>tcT	p.S245S	TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000361424.2_Silent_p.S245S|TLR10_ENST00000506111.1_Silent_p.S245S|TLR10_ENST00000508334.1_Silent_p.S245S	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	245					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						GCAATAGAACCGATGTCTTAG	0.323																																					p.S245S		Atlas-SNP	.											.	TLR10	87	.	0			c.G735T						.						63.0	62.0	62.0					4																	38776477		2203	4300	6503	SO:0001819	synonymous_variant	81793	exon2			TAGAACCGATGTC	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.735G>T	chr4.hg19:g.38776477C>A		130.0	0.0		109.0	5.0	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	hg19	CCDS3445.1																																																																																			.	.		0.323	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
UGDH	7358	hgsc.bcm.edu	37	4	39511398	39511398	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:39511398A>G	ENST00000316423.6	-	6	1135	c.793T>C	c.(793-795)Ttt>Ctt	p.F265L	UGDH_ENST00000501493.2_Missense_Mutation_p.F198L|UGDH_ENST00000515398.1_5'Flank|UGDH_ENST00000507089.1_Missense_Mutation_p.F168L|UGDH_ENST00000506179.1_Missense_Mutation_p.F265L	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	265	Substrate binding.				cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)			breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						GCTTTTAGAAACTTGTTTCCA	0.388																																					p.F265L		Atlas-SNP	.											.	UGDH	52	.	0			c.T793C						.						132.0	131.0	132.0					4																	39511398		2203	4300	6503	SO:0001583	missense	7358	exon6			TTAGAAACTTGTT	AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"""UDP-glucose dehydrogenase"""			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.793T>C	chr4.hg19:g.39511398A>G	ENSP00000319501:p.Phe265Leu	90.0	0.0		77.0	4.0	NM_003359	B3KUU2|B4DN25|O60589	Missense_Mutation	SNP	ENST00000316423.6	hg19	CCDS3455.1	.	.	.	.	.	.	.	.	.	.	A	29.7	5.027330	0.93518	.	.	ENSG00000109814	ENST00000316423;ENST00000501493;ENST00000506179;ENST00000507089	D;T;D;D	0.84873	-1.91;-1.29;-1.91;-1.89	5.51	5.51	0.81932	UDP-glucose/GDP-mannose dehydrogenase, dimerisation (1);NAD(P)-binding domain (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.000000	0.85682	D	0.000000	D	0.95642	0.8583	H	0.99011	4.4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.951	D	0.97443	1.0023	10	0.87932	D	0	-9.485	15.1102	0.72349	1.0:0.0:0.0:0.0	.	198;265	B3KUU2;O60701	.;UGDH_HUMAN	L	265;198;265;168	ENSP00000319501:F265L;ENSP00000422909:F198L;ENSP00000421757:F265L;ENSP00000426560:F168L	ENSP00000319501:F265L	F	-	1	0	UGDH	39187793	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.569000	0.90744	2.213000	0.71641	0.528000	0.53228	TTT	.	.		0.388	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359	
PDS5A	23244	hgsc.bcm.edu	37	4	39850470	39850470	+	Splice_Site	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:39850470C>T	ENST00000303538.8	-	28	3879		c.e28+1			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						AAGAAAATTACCTTTTCAGGT	0.368																																					.		Atlas-SNP	.											.	PDS5A	114	.	0			c.3339+1G>A						.						77.0	75.0	76.0					4																	39850470		1830	4087	5917	SO:0001630	splice_region_variant	23244	exon29			AAATTACCTTTTC	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.3339+1G>A	chr4.hg19:g.39850470C>T		80.0	0.0		65.0	4.0	NM_001100399		Splice_Site	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364380	0.82463	.	.	ENSG00000121892	ENST00000303538	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3219	0.94245	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PDS5A	39526865	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.298000	0.78815	2.538000	0.85594	0.655000	0.94253	.	.	.		0.368	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200	Intron
NSUN7	79730	hgsc.bcm.edu	37	4	40800850	40800850	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:40800850A>G	ENST00000381782.2	+	10	1824	c.1329A>G	c.(1327-1329)ccA>ccG	p.P443P	NSUN7_ENST00000316607.5_Silent_p.P443P	NM_024677.4	NP_078953	Q8NE18	NSUN7_HUMAN	NOP2/Sun domain family, member 7	443							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|cervix(1)|large_intestine(1)|lung(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						CAGTTTTTCCAGAAGAAAATG	0.338																																					p.P443P		Atlas-SNP	.											.	NSUN7	70	.	0			c.A1329G						.						96.0	100.0	98.0					4																	40800850		2202	4299	6501	SO:0001819	synonymous_variant	79730	exon10			TTTTCCAGAAGAA	BC036568	CCDS3461.2	4p14	2013-10-11	2009-11-23		ENSG00000179299	ENSG00000179299		"""NOP2/Sun domain containing"""	25857	protein-coding gene	gene with protein product			"""NOL1/NOP2/Sun domain family, member 7"""			17442852	Standard	NM_024677		Approved	FLJ14001	uc003gvj.4	Q8NE18	OTTHUMG00000128597	ENST00000381782.2:c.1329A>G	chr4.hg19:g.40800850A>G		109.0	0.0		94.0	4.0	NM_024677	C9JI19|Q8N9K8|Q9H815	Silent	SNP	ENST00000381782.2	hg19	CCDS3461.2																																																																																			.	.		0.338	NSUN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250454.2	NM_024677	
GABRB1	2560	hgsc.bcm.edu	37	4	47427703	47427703	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:47427703G>T	ENST00000295454.3	+	9	1385	c.1093G>T	c.(1093-1095)Ggt>Tgt	p.G365C	GABRB1_ENST00000538619.1_Missense_Mutation_p.G295C	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	365					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CGACGCCCACGGTAACATTCT	0.522																																					p.G365C		Atlas-SNP	.											.	GABRB1	107	.	0			c.G1093T						.						78.0	74.0	76.0					4																	47427703		2203	4300	6503	SO:0001583	missense	2560	exon9			GCCCACGGTAACA		CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4081	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 1"""	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.1093G>T	chr4.hg19:g.47427703G>T	ENSP00000295454:p.Gly365Cys	85.0	0.0		96.0	4.0	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Missense_Mutation	SNP	ENST00000295454.3	hg19	CCDS3474.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.685643	0.88639	.	.	ENSG00000163288	ENST00000295454;ENST00000538619	D;D	0.85556	-2.0;-2.0	5.48	5.48	0.80851	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.915575	0.09463	N	0.798742	D	0.93390	0.7892	M	0.79258	2.445	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.78314	0.931;0.991	D	0.90947	0.4802	10	0.87932	D	0	-23.5004	19.5559	0.95347	0.0:0.0:1.0:0.0	.	295;365	F5GXV5;P18505	.;GBRB1_HUMAN	C	365;295	ENSP00000295454:G365C;ENSP00000440330:G295C	ENSP00000295454:G365C	G	+	1	0	GABRB1	47122460	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.519000	0.98025	2.861000	0.98227	0.650000	0.86243	GGT	.	.		0.522	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1		
CORIN	10699	hgsc.bcm.edu	37	4	47628491	47628491	+	Missense_Mutation	SNP	C	C	A	rs373955478		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:47628491C>A	ENST00000273857.4	-	17	2245	c.2246G>T	c.(2245-2247)cGg>cTg	p.R749L	CORIN_ENST00000508498.1_Missense_Mutation_p.R610L|CORIN_ENST00000515827.1_5'UTR|CORIN_ENST00000502252.1_Missense_Mutation_p.R682L|CORIN_ENST00000505909.1_Missense_Mutation_p.R712L	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	749	SRCR.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						TGTCAGCCACCGCGGCTCTTT	0.418																																					p.R749L		Atlas-SNP	.											.	CORIN	154	.	0			c.G2246T						.						179.0	170.0	173.0					4																	47628491		2203	4300	6503	SO:0001583	missense	10699	exon17			AGCCACCGCGGCT	AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"""Serine peptidases / Transmembrane"""	19012	protein-coding gene	gene with protein product		605236	"""corin, serine protease"""			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.2246G>T	chr4.hg19:g.47628491C>A	ENSP00000273857:p.Arg749Leu	156.0	0.0		122.0	5.0	NM_006587	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Missense_Mutation	SNP	ENST00000273857.4	hg19	CCDS3477.1	.	.	.	.	.	.	.	.	.	.	C	2.407	-0.336151	0.05278	.	.	ENSG00000145244	ENST00000273857;ENST00000508498;ENST00000502252;ENST00000505909	T;T;T;T	0.59772	0.24;0.24;0.24;0.78	5.26	-7.29	0.01451	Speract/scavenger receptor-related (2);	0.847295	0.10512	N	0.665971	T	0.27765	0.0683	N	0.12182	0.205	0.19775	N	0.999954	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.40515	-0.9559	10	0.06891	T	0.86	.	9.922	0.41470	0.0:0.1303:0.5796:0.29	.	682;749	B4E1Y7;Q9Y5Q5	.;CORIN_HUMAN	L	749;610;682;712	ENSP00000273857:R749L;ENSP00000425597:R610L;ENSP00000424212:R682L;ENSP00000425401:R712L	ENSP00000273857:R749L	R	-	2	0	CORIN	47323248	0.000000	0.05858	0.023000	0.16930	0.004000	0.04260	-0.340000	0.07821	-1.267000	0.02443	-1.910000	0.00522	CGG	.	.		0.418	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2		
SGCB	6443	hgsc.bcm.edu	37	4	52890227	52890227	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:52890227A>G	ENST00000381431.5	-	6	1075	c.853T>C	c.(853-855)Tac>Cac	p.Y285H	SGCB_ENST00000535450.1_Missense_Mutation_p.Y215H	NM_000232.4	NP_000223.1	Q16585	SGCB_HUMAN	sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)	285	Cys-rich.				cardiac muscle cell development (GO:0055013)|muscle fiber development (GO:0048747)|muscle organ development (GO:0007517)|vascular smooth muscle cell development (GO:0097084)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(6)|prostate(1)	17			GBM - Glioblastoma multiforme(4;7.63e-12)|LUSC - Lung squamous cell carcinoma(32;0.00204)			CAGAGCTTGTAGCGTACCCAG	0.527																																					p.Y285H		Atlas-SNP	.											.	SGCB	35	.	0			c.T853C						.						120.0	102.0	108.0					4																	52890227		2203	4300	6503	SO:0001583	missense	6443	exon6			GCTTGTAGCGTAC	U29586	CCDS3488.1	4q12	2014-09-17	2002-08-29		ENSG00000163069	ENSG00000163069			10806	protein-coding gene	gene with protein product		600900	"""sarcoglycan, beta (43kD dystrophin-associated glycoprotein)"""	LGMD2E		8968749	Standard	NM_000232		Approved	SGC, A3b	uc003gzj.2	Q16585	OTTHUMG00000128697	ENST00000381431.5:c.853T>C	chr4.hg19:g.52890227A>G	ENSP00000370839:p.Tyr285His	183.0	0.0		133.0	17.0	NM_000232	B7Z635|O00661	Missense_Mutation	SNP	ENST00000381431.5	hg19	CCDS3488.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.982405	0.74474	.	.	ENSG00000163069	ENST00000381431;ENST00000535450	D;D	0.96885	-4.16;-4.16	5.3	5.3	0.74995	.	0.055782	0.64402	D	0.000001	D	0.97433	0.9160	M	0.73217	2.22	0.53688	D	0.999974	D;D	0.56287	0.975;0.975	P;P	0.62298	0.9;0.845	D	0.98100	1.0414	10	0.87932	D	0	-31.5733	14.7196	0.69297	1.0:0.0:0.0:0.0	.	215;285	B7Z635;Q16585	.;SGCB_HUMAN	H	285;215	ENSP00000370839:Y285H;ENSP00000441199:Y215H	ENSP00000370839:Y285H	Y	-	1	0	SGCB	52584984	1.000000	0.71417	0.993000	0.49108	0.235000	0.25334	9.134000	0.94467	2.129000	0.65627	0.482000	0.46254	TAC	.	.		0.527	SGCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250596.2		
KIAA1211	57482	hgsc.bcm.edu	37	4	57181298	57181298	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:57181298G>T	ENST00000504228.1	+	6	1735	c.1630G>T	c.(1630-1632)Gga>Tga	p.G544*	KIAA1211_ENST00000264229.6_Nonsense_Mutation_p.G544*|KIAA1211_ENST00000541073.1_Nonsense_Mutation_p.G537*			Q6ZU35	K1211_HUMAN	KIAA1211	544										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)					GGTGTCCTCCGGAGGGAAGCA	0.647																																					p.G544X		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G1630T						.						15.0	21.0	19.0					4																	57181298		2035	4174	6209	SO:0001587	stop_gained	57482	exon8			TCCTCCGGAGGGA	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.1630G>T	chr4.hg19:g.57181298G>T	ENSP00000423366:p.Gly544*	152.0	0.0		91.0	4.0	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Nonsense_Mutation	SNP	ENST00000504228.1	hg19	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	G	39	7.345149	0.98224	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	.	.	.	4.86	4.86	0.63082	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-27.0663	17.9911	0.89169	0.0:0.0:1.0:0.0	.	.	.	.	X	544;544;537;454	.	ENSP00000264229:G544X	G	+	1	0	KIAA1211	56876055	1.000000	0.71417	0.070000	0.20053	0.886000	0.51366	7.489000	0.81451	2.229000	0.72834	0.561000	0.74099	GGA	.	.		0.647	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
SLC4A4	8671	hgsc.bcm.edu	37	4	72412214	72412214	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:72412214C>A	ENST00000264485.5	+	19	2707	c.2590C>A	c.(2590-2592)Cct>Act	p.P864T	SLC4A4_ENST00000351898.6_Intron|SLC4A4_ENST00000340595.3_Missense_Mutation_p.P820T|SLC4A4_ENST00000425175.1_Missense_Mutation_p.P864T	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	864					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	GACTTCTGCACCTGGAGAACA	0.473																																					p.P864T		Atlas-SNP	.											.	SLC4A4	269	.	0			c.C2590A						.						110.0	88.0	96.0					4																	72412214		2203	4300	6503	SO:0001583	missense	8671	exon19			TCTGCACCTGGAG	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"""Solute carriers"""	11030	protein-coding gene	gene with protein product		603345	"""solute carrier family 4, sodium bicarbonate cotransporter, member 4"""	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.2590C>A	chr4.hg19:g.72412214C>A	ENSP00000264485:p.Pro864Thr	67.0	0.0		80.0	4.0	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	hg19	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.993049	0.93167	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000340595	D;D;D	0.88354	-2.37;-2.37;-2.37	5.76	5.76	0.90799	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94938	0.8363	M	0.80616	2.505	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.77557	0.99;0.972;0.99	D	0.94949	0.8098	10	0.87932	D	0	.	19.976	0.97309	0.0:1.0:0.0:0.0	.	864;820;864	A5JJ20;Q9Y6R1-2;Q9Y6R1	.;.;S4A4_HUMAN	T	864;864;820	ENSP00000264485:P864T;ENSP00000393557:P864T;ENSP00000344272:P820T	ENSP00000264485:P864T	P	+	1	0	SLC4A4	72631078	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.818000	0.86416	2.713000	0.92767	0.655000	0.94253	CCT	.	.		0.473	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	
ALB	213	hgsc.bcm.edu	37	4	74275126	74275126	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:74275126T>C	ENST00000503124.1	+	3	294	c.87T>C	c.(85-87)ctT>ctC	p.L29L	ALB_ENST00000509063.1_Silent_p.L179L|ALB_ENST00000415165.2_Intron|ALB_ENST00000401494.3_Silent_p.L64L|ALB_ENST00000295897.4_Silent_p.L179L|ALB_ENST00000505649.1_3'UTR			Q8TES7	FBF1_HUMAN	albumin	0					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)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CGGAACTCCTTTTCTTTGCTA	0.353																																					p.L179L		Atlas-SNP	.											.	ALB	132	.	0			c.T537C						.						72.0	76.0	75.0					4																	74275126		2203	4299	6502	SO:0001819	synonymous_variant	213	exon5			ACTCCTTTTCTTT	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.87T>C	chr4.hg19:g.74275126T>C		388.0	0.0		293.0	172.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000503124.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.14	2.447201	0.43429	.	.	ENSG00000163631	ENST00000511370	.	.	.	5.55	-3.31	0.04988	.	.	.	.	.	T	0.41696	0.1170	.	.	.	0.46149	D	0.998893	.	.	.	.	.	.	T	0.33624	-0.9861	4	.	.	.	-11.4619	3.7631	0.08611	0.1125:0.1341:0.462:0.2914	.	.	.	.	L	24	.	.	F	+	1	0	ALB	74493990	0.001000	0.12720	0.195000	0.23364	0.710000	0.40934	-0.314000	0.08092	-0.676000	0.05238	0.482000	0.46254	TTT	.	.		0.353	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	
ALB	213	hgsc.bcm.edu	37	4	74275205	74275205	+	Splice_Site	SNP	G	G	A	rs75828235		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:74275205G>A	ENST00000503124.1	+	3	372		c.e3+1		ALB_ENST00000509063.1_Splice_Site|ALB_ENST00000415165.2_Intron|ALB_ENST00000401494.3_Splice_Site|ALB_ENST00000295897.4_Splice_Site|ALB_ENST00000505649.1_Splice_Site			Q8TES7	FBF1_HUMAN	albumin						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)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GTTGCCAAAGGTATTATGCAA	0.388																																					.		Atlas-SNP	.											.	ALB	132	.	0			c.615+1G>A						.						71.0	74.0	73.0					4																	74275205		2203	4299	6502	SO:0001630	splice_region_variant	213	exon5			CCAAAGGTATTAT	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.165+1G>A	chr4.hg19:g.74275205G>A		198.0	0.0		144.0	41.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Splice_Site	SNP	ENST00000503124.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.04	1.521991	0.27211	.	.	ENSG00000163631	ENST00000295897;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202;ENST00000511370	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9449	0.89036	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ALB	74494069	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	5.592000	0.67543	2.894000	0.99253	0.591000	0.81541	.	.	.		0.388	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	Intron
FRAS1	80144	hgsc.bcm.edu	37	4	79418004	79418004	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:79418004C>T	ENST00000264895.6	+	60	9444	c.9004C>T	c.(9004-9006)Cca>Tca	p.P3002S		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2998	Calx-beta 4.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CATGTTTGAGCCAGAGGAACA	0.448																																					p.P3002S		Atlas-SNP	.											.	FRAS1	779	.	0			c.C9004T						.						184.0	178.0	180.0					4																	79418004		1941	4157	6098	SO:0001583	missense	80144	exon60			TTTGAGCCAGAGG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.9004C>T	chr4.hg19:g.79418004C>T	ENSP00000264895:p.Pro3002Ser	120.0	0.0		91.0	4.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.14|17.14	3.312455|3.312455	0.60414|0.60414	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000512123|ENST00000264895	.|T	.|0.28666	.|1.6	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.47303|0.47303	0.1438|0.1438	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.965;0.999	.|P;D	.|0.71656	.|0.791;0.974	T|T	0.28332|0.28332	-1.0047|-1.0047	5|10	.|0.40728	.|T	.|0.16	.|.	19.4366|19.4366	0.94798|0.94798	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|3001;3002	.|Q86XX4-2;E9PHH6	.|.;.	V|S	1230|3002	.|ENSP00000264895:P3002S	.|ENSP00000264895:P3002S	A|P	+|+	2|1	0|0	FRAS1|FRAS1	79637028|79637028	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.757000|0.757000	0.42996|0.42996	5.796000|5.796000	0.69080|0.69080	2.580000|2.580000	0.87095|0.87095	0.650000|0.650000	0.86243|0.86243	GCC|CCA	.	.		0.448	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
BMP3	651	hgsc.bcm.edu	37	4	81967507	81967507	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:81967507A>G	ENST00000282701.2	+	2	1252	c.932A>G	c.(931-933)aAg>aGg	p.K311R		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	311					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						CAGTATAAAAAGGATGAGGTG	0.512																																					p.K311R		Atlas-SNP	.											.	BMP3	59	.	0			c.A932G						.						44.0	50.0	48.0					4																	81967507		2203	4299	6502	SO:0001583	missense	651	exon2			ATAAAAAGGATGA	M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"""Bone morphogenetic proteins"""	1070	protein-coding gene	gene with protein product	"""osteogenin"""	112263	"""bone morphogenetic protein 3 (osteogenic)"""				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.932A>G	chr4.hg19:g.81967507A>G	ENSP00000282701:p.Lys311Arg	155.0	0.0		92.0	4.0	NM_001201	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	hg19	CCDS3588.1	.	.	.	.	.	.	.	.	.	.	A	4.253	0.045891	0.08196	.	.	ENSG00000152785	ENST00000282701	T	0.74632	-0.86	5.16	2.67	0.31697	.	0.352028	0.35555	N	0.003139	T	0.54886	0.1886	N	0.24115	0.695	0.20074	N	0.999935	B	0.06786	0.001	B	0.01281	0.0	T	0.39121	-0.9629	10	0.33940	T	0.23	.	5.4368	0.16486	0.6584:0.0:0.0735:0.2681	.	311	P12645	BMP3_HUMAN	R	311	ENSP00000282701:K311R	ENSP00000282701:K311R	K	+	2	0	BMP3	82186531	1.000000	0.71417	0.830000	0.32933	0.011000	0.07611	2.110000	0.41873	0.359000	0.24239	-1.229000	0.01577	AAG	.	.		0.512	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1		
SCD5	79966	hgsc.bcm.edu	37	4	83601881	83601881	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:83601881G>T	ENST00000319540.4	-	3	867	c.548C>A	c.(547-549)cCt>cAt	p.P183H	SCD5_ENST00000273908.4_Missense_Mutation_p.P183H	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	183					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				CCGGACCACAGGATCAGCAAG	0.512																																					p.P183H		Atlas-SNP	.											SCD5_ENST00000273908,NS,malignant_melanoma,-1,2	SCD5	58	.	0			c.C548A						.						92.0	87.0	89.0					4																	83601881		2203	4300	6503	SO:0001583	missense	79966	exon3			ACCACAGGATCAG	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"""Fatty acid desaturases"""	21088	protein-coding gene	gene with protein product		608370	"""stearoyl-CoA desaturase 4"""	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.548C>A	chr4.hg19:g.83601881G>T	ENSP00000316329:p.Pro183His	70.0	0.0		51.0	3.0	NM_024906	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	hg19	CCDS34024.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.316324	0.60524	.	.	ENSG00000145284	ENST00000319540;ENST00000273908	T;T	0.15256	2.44;2.44	5.44	4.59	0.56863	Fatty acid desaturase, type 1 (1);	0.329489	0.31301	N	0.007883	T	0.45994	0.1370	M	0.91818	3.245	0.27273	N	0.958306	D;D	0.89917	1.0;1.0	D;D	0.72982	0.973;0.979	T	0.50101	-0.8867	10	0.87932	D	0	-10.1797	8.5047	0.33179	0.0776:0.0:0.7698:0.1526	.	183;183	Q86SK9-2;Q86SK9	.;SCD5_HUMAN	H	183	ENSP00000316329:P183H;ENSP00000273908:P183H	ENSP00000273908:P183H	P	-	2	0	SCD5	83820905	0.939000	0.31865	0.981000	0.43875	0.933000	0.57130	2.169000	0.42434	1.506000	0.48736	0.591000	0.81541	CCT	.	.		0.512	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906	
SCD5	79966	hgsc.bcm.edu	37	4	83601977	83601977	+	Missense_Mutation	SNP	A	A	G	rs138660783	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:83601977A>G	ENST00000319540.4	-	3	771	c.452T>C	c.(451-453)tTc>tCc	p.F151S	SCD5_ENST00000273908.4_Missense_Mutation_p.F151S	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	151					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				GGAGAAGAAGAAGCCCCGGCG	0.542																																					p.F151S		Atlas-SNP	.											.	SCD5	58	.	0			c.T452C						.						104.0	111.0	109.0					4																	83601977		2203	4300	6503	SO:0001583	missense	79966	exon3			AAGAAGAAGCCCC	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"""Fatty acid desaturases"""	21088	protein-coding gene	gene with protein product		608370	"""stearoyl-CoA desaturase 4"""	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.452T>C	chr4.hg19:g.83601977A>G	ENSP00000316329:p.Phe151Ser	118.0	0.0		81.0	4.0	NM_024906	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	hg19	CCDS34024.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.861183	0.91433	.	.	ENSG00000145284	ENST00000319540;ENST00000273908	T;T	0.15487	2.42;2.42	5.27	5.27	0.74061	Fatty acid desaturase, type 1 (1);	0.049186	0.85682	D	0.000000	T	0.57110	0.2031	H	0.96996	3.92	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	T	0.73170	-0.4067	10	0.87932	D	0	-12.9515	15.3641	0.74507	1.0:0.0:0.0:0.0	.	151;151	Q86SK9-2;Q86SK9	.;SCD5_HUMAN	S	151	ENSP00000316329:F151S;ENSP00000273908:F151S	ENSP00000273908:F151S	F	-	2	0	SCD5	83821001	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.241000	0.78201	2.220000	0.72140	0.383000	0.25322	TTC	.	A|0.999;C|0.001		0.542	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906	
AGPAT9	84803	hgsc.bcm.edu	37	4	84519219	84519219	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:84519219G>T	ENST00000395226.2	+	11	1230	c.1012G>T	c.(1012-1014)Ggt>Tgt	p.G338C	AGPAT9_ENST00000264409.4_Missense_Mutation_p.G338C	NM_001256421.1	NP_001243350.1	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	338					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|regulation of TOR signaling (GO:0032006)|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)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(3)	13		Hepatocellular(203;0.114)				CCCTCAGTTCGGTGATGCATT	0.448																																					p.G338C		Atlas-SNP	.											.	AGPAT9	41	.	0			c.G1012T						.						124.0	116.0	119.0					4																	84519219		2203	4300	6503	SO:0001583	missense	84803	exon11			CAGTTCGGTGATG	AK055749	CCDS3606.1	4q21.23	2014-02-13	2008-01-29		ENSG00000138678	ENSG00000138678	2.3.1.15	"""1-acylglycerol-3-phosphate O-acyltransferases"""	28157	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, theta"""	610958	"""1-acylglycerol-3-phosphate O-acyltransferase 9 (lysophosphatidic acid acyltransferase, theta)"""			12975309	Standard	NM_001256421		Approved	MGC11324, LPAAT-theta, MAG1, HMFN0839	uc003how.4	Q53EU6	OTTHUMG00000130431	ENST00000395226.2:c.1012G>T	chr4.hg19:g.84519219G>T	ENSP00000378651:p.Gly338Cys	44.0	0.0		45.0	4.0	NM_001256421	Q68CJ4|Q6GPI6|Q96NA3	Missense_Mutation	SNP	ENST00000395226.2	hg19	CCDS3606.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.295114	0.81025	.	.	ENSG00000138678	ENST00000395226;ENST00000264409	T;T	0.48522	0.81;0.81	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.76644	0.4016	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79708	-0.1690	10	0.48119	T	0.1	-16.6768	19.6718	0.95914	0.0:0.0:1.0:0.0	.	338	Q53EU6	GPAT3_HUMAN	C	338	ENSP00000378651:G338C;ENSP00000264409:G338C	ENSP00000264409:G338C	G	+	1	0	AGPAT9	84738243	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	9.764000	0.98949	2.639000	0.89480	0.557000	0.71058	GGT	.	.		0.448	AGPAT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252821.3	NM_032717	
AFF1	4299	hgsc.bcm.edu	37	4	87967360	87967360	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:87967360G>T	ENST00000307808.6	+	2	480	c.60G>T	c.(58-60)aaG>aaT	p.K20N	AFF1_ENST00000395146.4_Missense_Mutation_p.K27N|AFF1_ENST00000544085.1_Intron	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	20					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TTAGAGAGAAGGAAAGACGCA	0.398																																					p.K27N		Atlas-SNP	.											.	AFF1	102	.	0			c.G81T						.						107.0	106.0	107.0					4																	87967360		2203	4300	6503	SO:0001583	missense	4299	exon3			AGAGAAGGAAAGA	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2"", ""pre-B-cell monocytic leukemia partner 1"""	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.60G>T	chr4.hg19:g.87967360G>T	ENSP00000305689:p.Lys20Asn	148.0	0.0		99.0	4.0	NM_001166693	B4DTU1|E9PBM3	Missense_Mutation	SNP	ENST00000307808.6	hg19	CCDS3616.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.702663	0.68501	.	.	ENSG00000172493	ENST00000395146;ENST00000395142;ENST00000507468;ENST00000503477;ENST00000307808	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	5.73	3.02	0.34903	.	0.068104	0.64402	D	0.000015	T	0.76198	0.3954	M	0.67953	2.075	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.997;0.994;0.994;1.0	D;D;D;D;D	0.79784	0.993;0.967;0.918;0.918;0.993	T	0.74090	-0.3777	10	0.62326	D	0.03	-29.5459	7.7224	0.28740	0.4644:0.0:0.5356:0.0	.	27;27;20;20;27	E9PBM3;B4DXZ8;Q14C88;P51825;B4DTU1	.;.;.;AFF1_HUMAN;.	N	27;27;27;27;20	ENSP00000378578:K27N;ENSP00000427593:K27N;ENSP00000424483:K27N;ENSP00000305689:K20N	ENSP00000305689:K20N	K	+	3	2	AFF1	88186384	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.800000	0.27042	0.407000	0.25591	0.655000	0.94253	AAG	.	.		0.398	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935	
PDHA2	5161	hgsc.bcm.edu	37	4	96762199	96762199	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:96762199C>A	ENST00000295266.4	+	1	961	c.898C>A	c.(898-900)Cgt>Agt	p.R300S		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	300					glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)	p.R300C(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(23)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	46		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)		AGTCAGTTATCGTACACGAGA	0.433																																					p.R300S		Atlas-SNP	.											PDHA2,caecum,carcinoma,0,2	PDHA2	118	.	1	Substitution - Missense(1)	large_intestine(1)	c.C898A						.						103.0	100.0	101.0					4																	96762199		2203	4300	6503	SO:0001583	missense	5161	exon1			AGTTATCGTACAC		CCDS3644.1	4q22-q23	2009-11-09			ENSG00000163114	ENSG00000163114	1.2.4.1		8807	protein-coding gene	gene with protein product		179061		PDHAL			Standard	NM_005390		Approved		uc003htr.4	P29803	OTTHUMG00000130990	ENST00000295266.4:c.898C>A	chr4.hg19:g.96762199C>A	ENSP00000295266:p.Arg300Ser	110.0	0.0		71.0	37.0	NM_005390	B2R9Q3|Q0VDI5|Q4VC02|Q6NXQ1	Missense_Mutation	SNP	ENST00000295266.4	hg19	CCDS3644.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.969579	0.53614	.	.	ENSG00000163114	ENST00000295266	D	0.97870	-4.58	4.91	4.07	0.47477	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.99168	0.9712	H	0.98682	4.3	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98674	1.0689	10	0.87932	D	0	-10.2397	11.2932	0.49263	0.0:0.9113:0.0:0.0887	.	300	P29803	ODPAT_HUMAN	S	300	ENSP00000295266:R300S	ENSP00000295266:R300S	R	+	1	0	PDHA2	96981222	1.000000	0.71417	0.053000	0.19242	0.437000	0.31866	5.205000	0.65186	1.456000	0.47831	0.467000	0.42956	CGT	.	.		0.433	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1		
KIAA1109	84162	hgsc.bcm.edu	37	4	123265683	123265683	+	Missense_Mutation	SNP	A	A	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:123265683A>T	ENST00000264501.4	+	74	13073	c.12700A>T	c.(12700-12702)Agc>Tgc	p.S4234C	KIAA1109_ENST00000388738.3_Missense_Mutation_p.S4234C			Q2LD37	K1109_HUMAN	KIAA1109	4234					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CAAGTCTGCAAGCAAAATGGA	0.323																																					p.S4234C		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A12700T						.						131.0	124.0	126.0					4																	123265683		1849	4099	5948	SO:0001583	missense	84162	exon72			TCTGCAAGCAAAA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.12700A>T	chr4.hg19:g.123265683A>T	ENSP00000264501:p.Ser4234Cys	157.0	0.0		87.0	4.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	17.81|17.81|17.81	3.481623|3.481623|3.481623	0.63849|0.63849|0.63849	.|.|.	.|.|.	ENSG00000138688|ENSG00000138688|ENSG00000138688	ENST00000442707|ENST00000306802|ENST00000264501;ENST00000388738;ENST00000438707	.|.|T;T;T	.|.|0.34859	.|.|2.32;2.32;1.34	5.52|5.52|5.52	5.52|5.52|5.52	0.82312|0.82312|0.82312	.|.|.	.|.|0.167446	.|.|0.53938	.|.|D	.|.|0.000051	T|T|T	0.38268|0.38268|0.38268	0.1034|0.1034|0.1034	L|L|L	0.46157|0.46157|0.46157	1.445|1.445|1.445	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|P;P	.|.|0.42123	.|.|0.771;0.661	.|.|B;B	.|.|0.42653	.|.|0.394;0.299	T|T|T	0.26815|0.26815|0.26815	-1.0092|-1.0092|-1.0092	5|5|10	.|.|0.59425	.|.|D	.|.|0.04	.|.|.	15.6544|15.6544|15.6544	0.77121|0.77121|0.77121	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	.|.|4233;4234	.|.|Q2LD37-4;Q2LD37	.|.|.;K1109_HUMAN	M|H|C	179|609|4234;4234;903	.|.|ENSP00000264501:S4234C;ENSP00000373390:S4234C;ENSP00000410874:S903C	.|.|ENSP00000264501:S4234C	K|Q|S	+|+|+	2|3|1	0|2|0	KIAA1109|KIAA1109|KIAA1109	123485133|123485133|123485133	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.957000|0.957000|0.957000	0.61999|0.61999|0.61999	4.347000|4.347000|4.347000	0.59373|0.59373|0.59373	2.094000|2.094000|2.094000	0.63399|0.63399|0.63399	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	AAG|CAA|AGC	.	.		0.323	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
PLK4	10733	hgsc.bcm.edu	37	4	128803010	128803010	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:128803010G>T	ENST00000270861.5	+	2	329	c.55G>T	c.(55-57)Ggt>Tgt	p.G19C	PLK4_ENST00000513090.1_Missense_Mutation_p.G19C|PLK4_ENST00000511942.1_3'UTR|PLK4_ENST00000507249.1_Missense_Mutation_p.G19C|PLK4_ENST00000514379.1_5'UTR|PLK4_ENST00000515069.1_Missense_Mutation_p.G19C	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	19	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						AAATCTGCTTGGTAAAGGATC	0.368																																					p.G19C	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.G55T						.						95.0	94.0	94.0					4																	128803010		2203	4300	6503	SO:0001583	missense	10733	exon2			CTGCTTGGTAAAG	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"""serine/threonine kinase 18"", ""polo-like kinase 4 (Drosophila)"""	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.55G>T	chr4.hg19:g.128803010G>T	ENSP00000270861:p.Gly19Cys	181.0	0.0		98.0	4.0	NM_001190799	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	hg19	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.472526	0.84640	.	.	ENSG00000142731	ENST00000270861;ENST00000515069;ENST00000513090;ENST00000507249	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	3.97	3.97	0.46021	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	0.87497	0.6192	H	0.98769	4.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93053	0.6467	10	0.87932	D	0	-7.6902	16.6235	0.84936	0.0:0.0:1.0:0.0	.	19;19	O00444-2;O00444	.;PLK4_HUMAN	C	19	ENSP00000270861:G19C;ENSP00000421774:G19C;ENSP00000427554:G19C;ENSP00000423412:G19C	ENSP00000270861:G19C	G	+	1	0	PLK4	129022460	1.000000	0.71417	0.996000	0.52242	0.962000	0.63368	8.776000	0.91776	2.211000	0.71520	0.561000	0.74099	GGT	.	.		0.368	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3		
TENM3	55714	hgsc.bcm.edu	37	4	183676072	183676072	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:183676072G>T	ENST00000511685.1	+	22	4675	c.4552G>T	c.(4552-4554)Gat>Tat	p.D1518Y	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Missense_Mutation_p.D1518Y			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1518					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTCTCCAACTGATCAAGAACT	0.378																																					p.D1518Y		Atlas-SNP	.											.	.	.	.	0			c.G4552T						.						78.0	78.0	78.0					4																	183676072		1909	4121	6030	SO:0001583	missense	55714	exon21			CCAACTGATCAAG	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.4552G>T	chr4.hg19:g.183676072G>T	ENSP00000424226:p.Asp1518Tyr	73.0	0.0		53.0	4.0	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.669295	0.47677	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	T;T	0.17854	2.25;2.25	5.25	5.25	0.73442	.	.	.	.	.	T	0.18923	0.0454	L	0.36672	1.1	0.52501	D	0.999955	P	0.47350	0.894	B	0.41813	0.367	T	0.01140	-1.1439	9	0.72032	D	0.01	.	19.0324	0.92963	0.0:0.0:1.0:0.0	.	1518	Q9P273	TEN3_HUMAN	Y	1518	ENSP00000424226:D1518Y;ENSP00000385276:D1518Y	ENSP00000385276:D1518Y	D	+	1	0	ODZ3	183913066	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	7.492000	0.81482	2.737000	0.93849	0.563000	0.77884	GAT	.	.		0.378	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
CENPU	79682	hgsc.bcm.edu	37	4	185646185	185646185	+	Silent	SNP	A	A	G	rs374160243		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:185646185A>G	ENST00000281453.5	-	4	316	c.246T>C	c.(244-246)gcT>gcC	p.A82A	MLF1IP_ENST00000541971.1_Silent_p.A82A	NM_024629.3	NP_078905.2														endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		CTTCTTCATCAGCATATATAG	0.373																																					p.A82A		Atlas-SNP	.											.	MLF1IP	33	.	0			c.T246C						.	A		0,4406		0,0,2203	142.0	135.0	137.0		246	-5.4	0.3	4		137	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MLF1IP	NM_024629.3		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		82/419	185646185	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	79682	exon4			TTCATCAGCATAT																												ENST00000281453.5:c.246T>C	chr4.hg19:g.185646185A>G		111.0	0.0		83.0	5.0	NM_024629		Silent	SNP	ENST00000281453.5	hg19	CCDS3838.1																																																																																			.	.		0.373	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2		
CCT5	22948	hgsc.bcm.edu	37	5	10254914	10254914	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:10254914G>A	ENST00000280326.4	+	3	715	c.295G>A	c.(295-297)Gat>Aat	p.D99N	CCT5_ENST00000503026.1_Missense_Mutation_p.D78N|CCT5_ENST00000515676.1_Missense_Mutation_p.D61N|CCT5_ENST00000506600.1_Intron|CCT5_ENST00000515390.1_Intron	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	99					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)	p.D99Y(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						CAAGTCTCAGGATGATGAAAT	0.428																																					p.D99N		Atlas-SNP	.											CCT5,NS,carcinoma,0,1	CCT5	49	.	1	Substitution - Missense(1)	lung(1)	c.G295A						.						141.0	122.0	129.0					5																	10254914		2203	4300	6503	SO:0001583	missense	22948	exon3			TCTCAGGATGATG	D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"""Heat Shock Proteins / Chaperonins"""	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.295G>A	chr5.hg19:g.10254914G>A	ENSP00000280326:p.Asp99Asn	169.0	1.0		94.0	4.0	NM_012073	A8JZY8|A8K2X8|B4DYD8	Missense_Mutation	SNP	ENST00000280326.4	hg19	CCDS3877.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.777527|5.777527	0.96929|0.96929	.|.	.|.	ENSG00000150753|ENSG00000150753	ENST00000440011|ENST00000280326;ENST00000503026;ENST00000515676	.|T;T;T	.|0.15256	.|2.44;2.44;2.44	5.64|5.64	5.64|5.64	0.86602|0.86602	.|Chaperonin TCP-1, conserved site (1);	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.59348	.|0.2187	H|H	0.96916|0.96916	3.905|3.905	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|1.0;1.0;1.0	.|T	.|0.73914	.|-0.3832	.|10	.|0.87932	.|D	.|0	.|-28.1245	18.761|18.761	0.91851|0.91851	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|97;99;99	.|Q9BU08;A8K2X8;P48643	.|.;.;TCPE_HUMAN	.|N	-1|99;78;61	.|ENSP00000280326:D99N;ENSP00000423318:D78N;ENSP00000427297:D61N	.|ENSP00000280326:D99N	.|D	+|+	.|1	.|0	CCT5|CCT5	10307914|10307914	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	9.288000|9.288000	0.96055|0.96055	2.656000|2.656000	0.90262|0.90262	0.644000|0.644000	0.83932|0.83932	.|GAT	.	.		0.428	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2		
RAI14	26064	hgsc.bcm.edu	37	5	34796132	34796132	+	Splice_Site	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:34796132G>T	ENST00000265109.3	+	4	543	c.256G>T	c.(256-258)Gga>Tga	p.G86*	RAI14_ENST00000512629.1_Splice_Site_p.G86*|RAI14_ENST00000397449.1_Splice_Site_p.G79*|RAI14_ENST00000506376.1_Splice_Site_p.G78*|RAI14_ENST00000503673.1_Splice_Site_p.G86*|RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000428746.2_Splice_Site_p.G86*|RAI14_ENST00000515799.1_Splice_Site_p.G89*	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	86						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					AGATACTACCGGTATGTGGTT	0.428																																					p.G89X		Atlas-SNP	.											.	RAI14	100	.	0			c.G265T						.						196.0	174.0	182.0					5																	34796132		2203	4300	6503	SO:0001630	splice_region_variant	26064	exon6			ACTACCGGTATGT	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.256+1G>T	chr5.hg19:g.34796132G>T		187.0	0.0		119.0	5.0	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Nonsense_Mutation	SNP	ENST00000265109.3	hg19	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.791353	0.90367	.	.	ENSG00000039560	ENST00000265109;ENST00000514527;ENST00000513974;ENST00000512629;ENST00000428746;ENST00000514873;ENST00000503673;ENST00000504052;ENST00000512305;ENST00000514036;ENST00000515799;ENST00000508315;ENST00000512625;ENST00000506376;ENST00000397449	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.9939	17.5802	0.87965	0.0:0.0:1.0:0.0	.	.	.	.	X	86;86;86;86;86;86;86;86;86;86;89;86;86;78;79	.	ENSP00000265109:G86X	G	+	1	0	RAI14	34831889	1.000000	0.71417	0.982000	0.44146	0.935000	0.57460	6.310000	0.72830	2.894000	0.99253	0.655000	0.94253	GGA	.	.		0.428	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	Nonsense_Mutation
NADK2	133686	hgsc.bcm.edu	37	5	36226594	36226594	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:36226594G>A	ENST00000381937.4	-	3	460	c.461C>T	c.(460-462)gCt>gTt	p.A154V	NADK2_ENST00000397338.1_5'UTR|NADK2_ENST00000506945.1_5'UTR|NADK2_ENST00000514504.1_Missense_Mutation_p.A154V|NADK2_ENST00000282512.3_5'UTR	NM_001085411.1	NP_001078880.1	Q4G0N4	NAKD2_HUMAN	NAD kinase 2, mitochondrial	154					NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|NAD+ kinase activity (GO:0003951)|protein homodimerization activity (GO:0042803)										AGCTATGACAGCATCTGCCCA	0.373																																					p.A154V		Atlas-SNP	.											.	NADKD1	47	.	0			c.C461T						.						144.0	137.0	139.0					5																	36226594		1915	4135	6050	SO:0001583	missense	133686	exon3			ATGACAGCATCTG	BC062567	CCDS3917.1, CCDS47197.1, CCDS75235.1	5p13.2	2013-04-30	2013-04-30	2013-04-30	ENSG00000152620	ENSG00000152620			26404	protein-coding gene	gene with protein product	"""mitochondrial NAD kinase"""	615787	"""chromosome 5 open reading frame 33"", ""NAD kinase domain containing 1"""	C5orf33, NADKD1		23616928	Standard	NM_001085411		Approved	FLJ30596, MNADK	uc003jkf.4	Q4G0N4	OTTHUMG00000131105	ENST00000381937.4:c.461C>T	chr5.hg19:g.36226594G>A	ENSP00000371362:p.Ala154Val	113.0	0.0		71.0	4.0	NM_001085411	B5MC93|Q6UTX5|Q96NM0	Missense_Mutation	SNP	ENST00000381937.4	hg19	CCDS47197.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247985	0.59103	.	.	ENSG00000152620	ENST00000381937;ENST00000514504	T;T	0.40225	1.04;1.04	5.87	5.87	0.94306	ATP-NAD kinase, PpnK-type, alpha/beta (1);ATP-NAD kinase, PpnK-type (1);	.	.	.	.	T	0.39145	0.1067	N	0.02674	-0.535	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	T	0.48007	-0.9072	9	0.13853	T	0.58	.	18.9723	0.92719	0.0:0.0:1.0:0.0	.	154	Q4G0N4	NAKD1_HUMAN	V	154	ENSP00000371362:A154V;ENSP00000421029:A154V	ENSP00000371362:A154V	A	-	2	0	NADKD1	36262351	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.683000	0.91236	2.767000	0.95098	0.591000	0.81541	GCT	.	.		0.373	NADK2-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367541.1	NM_153013	
LIFR	3977	hgsc.bcm.edu	37	5	38481738	38481738	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:38481738A>G	ENST00000263409.4	-	20	3415	c.3253T>C	c.(3253-3255)Tgg>Cgg	p.W1085R	LIFR_ENST00000453190.2_Missense_Mutation_p.W1085R	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	1085					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					GTAAAGGACCACCCTCCTCCA	0.408			T	PLAG1	salivary adenoma																																p.W1085R	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.T3253C						.						123.0	128.0	126.0					5																	38481738		2203	4300	6503	SO:0001583	missense	3977	exon20			AGGACCACCCTCC	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.3253T>C	chr5.hg19:g.38481738A>G	ENSP00000263409:p.Trp1085Arg	144.0	0.0		96.0	4.0	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	hg19	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.054177	0.75960	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.72725	-0.68;-0.68	5.94	5.94	0.96194	.	0.255835	0.38005	N	0.001855	D	0.82664	0.5086	M	0.62723	1.935	0.53688	D	0.99997	D	0.89917	1.0	D	0.87578	0.998	D	0.84307	0.0508	10	0.87932	D	0	-10.4001	16.3908	0.83537	1.0:0.0:0.0:0.0	.	1085	P42702	LIFR_HUMAN	R	1085	ENSP00000263409:W1085R;ENSP00000398368:W1085R	ENSP00000263409:W1085R	W	-	1	0	LIFR	38517495	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.125000	0.71627	2.269000	0.75478	0.455000	0.32223	TGG	.	.		0.408	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
RICTOR	253260	hgsc.bcm.edu	37	5	38952348	38952348	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:38952348G>T	ENST00000357387.3	-	30	3107	c.3077C>A	c.(3076-3078)tCg>tAg	p.S1026*	RICTOR_ENST00000503698.1_5'Flank|RICTOR_ENST00000296782.5_Nonsense_Mutation_p.S1026*	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					GGTTGACTCCGAGTTCAAACT	0.413																																					p.S1026X		Atlas-SNP	.											.	RICTOR	182	.	0			c.C3077A						.						113.0	108.0	110.0					5																	38952348		2203	4300	6503	SO:0001587	stop_gained	253260	exon30			GACTCCGAGTTCA		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"""rapamycin-insensitive companion of mTOR"", ""pianissimo"""	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.3077C>A	chr5.hg19:g.38952348G>T	ENSP00000349959:p.Ser1026*	174.0	0.0		91.0	4.0	NM_152756		Nonsense_Mutation	SNP	ENST00000357387.3	hg19	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	G	41	8.702961	0.98920	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.4694	19.4443	0.94840	0.0:0.0:1.0:0.0	.	.	.	.	X	1026	.	ENSP00000296782:S1026X	S	-	2	0	RICTOR	38988105	1.000000	0.71417	0.995000	0.50966	0.975000	0.68041	9.434000	0.97515	2.590000	0.87494	0.460000	0.39030	TCG	.	.		0.413	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756	
DAB2	1601	hgsc.bcm.edu	37	5	39390554	39390554	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:39390554C>A	ENST00000320816.6	-	5	921	c.454G>T	c.(454-456)Ggg>Tgg	p.G152W	DAB2_ENST00000545653.1_Missense_Mutation_p.G152W|DAB2_ENST00000339788.6_Missense_Mutation_p.G152W|DAB2_ENST00000512525.1_5'UTR|DAB2_ENST00000509337.1_Missense_Mutation_p.G152W	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	152	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)	p.G152R(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			ACCTGTTGCCCGGTTTTTATG	0.443																																					p.G152W		Atlas-SNP	.											DAB2,NS,carcinoma,0,1	DAB2	124	.	1	Substitution - Missense(1)	endometrium(1)	c.G454T						.						90.0	88.0	89.0					5																	39390554		2203	4300	6503	SO:0001583	missense	1601	exon5			GTTGCCCGGTTTT	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"""disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)"", ""disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"""			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.454G>T	chr5.hg19:g.39390554C>A	ENSP00000313391:p.Gly152Trp	91.0	0.0		58.0	4.0	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	hg19	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.885439	0.91814	.	.	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	5.6	5.6	0.85130	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.045830	0.85682	D	0.000000	T	0.72011	0.3408	L	0.29908	0.895	0.53688	D	0.99997	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.983	T	0.74321	-0.3703	10	0.87932	D	0	-7.8572	19.9823	0.97331	0.0:1.0:0.0:0.0	.	152;152	P98082;P98082-3	DAB2_HUMAN;.	W	152	ENSP00000313391:G152W;ENSP00000345508:G152W;ENSP00000439919:G152W;ENSP00000426245:G152W	ENSP00000313391:G152W	G	-	1	0	DAB2	39426311	1.000000	0.71417	0.995000	0.50966	0.965000	0.64279	5.545000	0.67237	2.788000	0.95919	0.650000	0.86243	GGG	.	.		0.443	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343	
CARD6	84674	hgsc.bcm.edu	37	5	40853234	40853234	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:40853234G>A	ENST00000254691.5	+	3	1999	c.1800G>A	c.(1798-1800)ctG>ctA	p.L600L	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	600					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						AGAGGATACTGAACTTGAAGC	0.483																																					p.L600L		Atlas-SNP	.											.	CARD6	141	.	0			c.G1800A						.						118.0	119.0	118.0					5																	40853234		2203	4300	6503	SO:0001819	synonymous_variant	84674	exon3			GATACTGAACTTG	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.1800G>A	chr5.hg19:g.40853234G>A		193.0	0.0		93.0	4.0	NM_032587	Q52LR2	Silent	SNP	ENST00000254691.5	hg19	CCDS3935.1																																																																																			.	.		0.483	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3		
C6	729	hgsc.bcm.edu	37	5	41186295	41186295	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:41186295T>C	ENST00000263413.3	-	6	867	c.603A>G	c.(601-603)gcA>gcG	p.A201A	C6_ENST00000475349.1_Intron|C6_ENST00000337836.5_Silent_p.A201A	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	201	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TGGGCTCTCCTGCCAGAAAAT	0.373																																					p.A201A		Atlas-SNP	.											.	C6	197	.	0			c.A603G						.						68.0	67.0	68.0					5																	41186295		2203	4300	6503	SO:0001819	synonymous_variant	729	exon6			CTCTCCTGCCAGA	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.603A>G	chr5.hg19:g.41186295T>C		174.0	0.0		97.0	4.0	NM_001115131		Silent	SNP	ENST00000263413.3	hg19	CCDS3936.1																																																																																			.	.		0.373	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1		
C5orf34	375444	hgsc.bcm.edu	37	5	43490731	43490731	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:43490731A>G	ENST00000306862.2	-	11	2055		c.e11+1		RP11-159F24.3_ENST00000505645.1_RNA	NM_198566.2	NP_940968	Q96MH7	CE034_HUMAN	chromosome 5 open reading frame 34											breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|stomach(2)	21	Lung NSC(6;2.07e-05)					AAAGAAAAATACCAATTTTCT	0.338																																					.		Atlas-SNP	.											.	C5orf34	47	.	0			c.1679+2T>C						.						58.0	57.0	57.0					5																	43490731		2203	4299	6502	SO:0001630	splice_region_variant	375444	exon12			AAAAATACCAATT	AK056925	CCDS3946.1	5p12	2012-02-23			ENSG00000172244	ENSG00000172244			24738	protein-coding gene	gene with protein product						12477932	Standard	XM_006714473		Approved	FLJ32363	uc003jnz.2	Q96MH7	OTTHUMG00000131151	ENST00000306862.2:c.1679+1T>C	chr5.hg19:g.43490731A>G		128.0	0.0		82.0	4.0	NM_198566		Splice_Site	SNP	ENST00000306862.2	hg19	CCDS3946.1	.	.	.	.	.	.	.	.	.	.	A	16.95	3.262381	0.59431	.	.	ENSG00000172244	ENST00000306862	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1728	0.59609	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C5orf34	43526488	1.000000	0.71417	0.996000	0.52242	0.703000	0.40648	4.739000	0.62080	2.190000	0.69967	0.528000	0.53228	.	.	.		0.338	C5orf34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253843.1	NM_198566	Intron
MRPS30	10884	hgsc.bcm.edu	37	5	44815068	44815068	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:44815068A>G	ENST00000507110.1	+	5	1122	c.1084A>G	c.(1084-1086)Aca>Gca	p.T362A		NM_016640.3	NP_057724.2	Q9NP92	RT30_HUMAN	mitochondrial ribosomal protein S30	362					apoptotic process (GO:0006915)|translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.T362A(2)		central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(11)|prostate(1)	20	Lung NSC(6;8.08e-07)					GGCTGTGATCACAGATGGAAA	0.378																																					p.T362A		Atlas-SNP	.											MRPS30_ENST00000507110,NS,carcinoma,0,2	MRPS30	90	.	2	Substitution - Missense(2)	endometrium(2)	c.A1084G						.						162.0	166.0	164.0					5																	44815068		2203	4300	6503	SO:0001583	missense	10884	exon5			GTGATCACAGATG	AF146192	CCDS3951.1	5q11	2012-09-13		2001-11-09	ENSG00000112996	ENSG00000112996		"""Mitochondrial ribosomal proteins / small subunits"""	8769	protein-coding gene	gene with protein product		611991		PDCD9		10640817, 11279123	Standard	NM_016640		Approved	PAP	uc003joh.3	Q9NP92	OTTHUMG00000096967	ENST00000507110.1:c.1084A>G	chr5.hg19:g.44815068A>G	ENSP00000424328:p.Thr362Ala	144.0	0.0		75.0	3.0	NM_016640	Q96I91|Q96Q19|Q9H0P8|Q9NSF9|Q9NZ76	Missense_Mutation	SNP	ENST00000507110.1	hg19	CCDS3951.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.323158	0.81580	.	.	ENSG00000112996	ENST00000507110	T	0.30448	1.53	5.86	5.86	0.93980	.	0.047675	0.85682	D	0.000000	T	0.54951	0.1890	M	0.81341	2.54	0.58432	D	0.999999	D	0.63046	0.992	D	0.66716	0.946	T	0.60301	-0.7290	10	0.72032	D	0.01	-23.2635	11.3486	0.49575	0.8646:0.0:0.0:0.1354	.	362	Q9NP92	RT30_HUMAN	A	362	ENSP00000424328:T362A	ENSP00000424328:T362A	T	+	1	0	MRPS30	44850825	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.139000	0.77314	2.237000	0.73441	0.528000	0.53228	ACA	.	.		0.378	MRPS30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214033.2	NM_016640	
GPX8	493869	hgsc.bcm.edu	37	5	54456944	54456944	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:54456944T>C	ENST00000503787.1	+	2	402	c.327T>C	c.(325-327)aaT>aaC	p.N109N	GPX8_ENST00000515370.1_Silent_p.N58N|CDC20B_ENST00000331730.3_Intron|CDC20B_ENST00000296733.1_Intron|GPX8_ENST00000506123.1_3'UTR|CDC20B_ENST00000381375.2_Intron|CDC20B_ENST00000334206.5_Intron|GPX8_ENST00000296734.6_Intron|CDC20B_ENST00000322374.6_Intron	NM_001008397.2	NP_001008398.2	Q8TED1	GPX8_HUMAN	glutathione peroxidase 8 (putative)	109					response to oxidative stress (GO:0006979)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	glutathione peroxidase activity (GO:0004602)|peroxidase activity (GO:0004601)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)	11					Glutathione(DB00143)	TTCCCTGCAATCAGTTTGGAG	0.463																																					p.N109N		Atlas-SNP	.											.	GPX8	20	.	0			c.T327C						.						86.0	83.0	84.0					5																	54456944		2203	4300	6503	SO:0001819	synonymous_variant	493869	exon2			CTGCAATCAGTTT	BC029424	CCDS34156.1	5q11.2	2008-09-29				ENSG00000164294			33100	protein-coding gene	gene with protein product							Standard	NM_001008397		Approved	UNQ847, EPLA847	uc003jpq.2	Q8TED1		ENST00000503787.1:c.327T>C	chr5.hg19:g.54456944T>C		143.0	0.0		77.0	4.0	NM_001008397		Silent	SNP	ENST00000503787.1	hg19	CCDS34156.1																																																																																			.	.		0.463	GPX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369717.1	NM_001008397	
IL6ST	3572	hgsc.bcm.edu	37	5	55237449	55237449	+	Missense_Mutation	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:55237449T>A	ENST00000381298.2	-	17	2530	c.2218A>T	c.(2218-2220)Agc>Tgc	p.S740C	IL6ST_ENST00000381294.3_Missense_Mutation_p.S679C|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000336909.5_Missense_Mutation_p.S740C|IL6ST_ENST00000502326.3_Missense_Mutation_p.S740C|CTD-2031P19.5_ENST00000576302.1_RNA	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	740	Ser-rich.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				CTAGAAATGCTTGGCCTAGAA	0.428			O		hepatocellular ca																																p.S740C		Atlas-SNP	.		Dom	yes		5	5q11	3572	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""		E	.	IL6ST	75	.	0			c.A2218T						.						180.0	179.0	180.0					5																	55237449		2203	4300	6503	SO:0001583	missense	3572	exon17			AAATGCTTGGCCT	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6021	protein-coding gene	gene with protein product	"""gp130, oncostatin M receptor"""	600694	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.2218A>T	chr5.hg19:g.55237449T>A	ENSP00000370698:p.Ser740Cys	155.0	0.0		97.0	4.0	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	hg19	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.398179	0.83120	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.44482	1.2;1.2;0.92	5.4	5.4	0.78164	.	0.161133	0.64402	D	0.000002	T	0.55768	0.1941	L	0.36672	1.1	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.59295	-0.7481	10	0.87932	D	0	.	15.7345	0.77831	0.0:0.0:0.0:1.0	.	740;679;740	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	C	740;740;679	ENSP00000370698:S740C;ENSP00000338799:S740C;ENSP00000370694:S679C	ENSP00000338799:S740C	S	-	1	0	IL6ST	55273206	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.299000	0.78831	2.170000	0.68504	0.455000	0.32223	AGC	.	.		0.428	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184	
PLK2	10769	hgsc.bcm.edu	37	5	57753099	57753099	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:57753099G>T	ENST00000274289.3	-	7	1217	c.917C>A	c.(916-918)cCt>cAt	p.P306H	PLK2_ENST00000502671.1_5'UTR	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	306	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		GTGCTTGGCAGGAGCCAGCAA	0.438																																					p.P306H		Atlas-SNP	.											.	PLK2	71	.	0			c.C917A						.						86.0	81.0	83.0					5																	57753099		2203	4300	6503	SO:0001583	missense	10769	exon7			TTGGCAGGAGCCA		CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"""serum-inducible kinase"""	607023	"""polo-like kinase 2 (Drosophila)"""				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.917C>A	chr5.hg19:g.57753099G>T	ENSP00000274289:p.Pro306His	46.0	0.0		20.0	4.0	NM_006622	O60679|Q96CV7|Q9UE61	Missense_Mutation	SNP	ENST00000274289.3	hg19	CCDS3974.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.419916	0.42918	.	.	ENSG00000145632	ENST00000274289;ENST00000537944;ENST00000442330	T	0.65178	-0.14	5.27	5.27	0.74061	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.168065	0.56097	D	0.000040	T	0.59473	0.2196	L	0.39020	1.185	0.45662	D	0.998584	B	0.24186	0.099	B	0.32762	0.152	T	0.57676	-0.7770	10	0.49607	T	0.09	-15.0317	18.9292	0.92558	0.0:0.0:1.0:0.0	.	306	Q9NYY3	PLK2_HUMAN	H	306;306;292	ENSP00000274289:P306H	ENSP00000274289:P306H	P	-	2	0	PLK2	57788856	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	5.947000	0.70242	2.461000	0.83175	0.655000	0.94253	CCT	.	.		0.438	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622	
MAP1B	4131	hgsc.bcm.edu	37	5	71489755	71489755	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:71489755T>C	ENST00000296755.7	+	5	871	c.573T>C	c.(571-573)ccT>ccC	p.P191P		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	191					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.P191P(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		TGTTCTGTCCTGAAGAAGGGG	0.423																																					p.P191P	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											MAP1B,NS,carcinoma,0,1	MAP1B	243	.	1	Substitution - coding silent(1)	lung(1)	c.T573C						.						81.0	78.0	79.0					5																	71489755		2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			CTGTCCTGAAGAA	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.573T>C	chr5.hg19:g.71489755T>C		98.0	0.0		37.0	2.0	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	hg19	CCDS4012.1																																																																																			.	.		0.423	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
MAP1B	4131	hgsc.bcm.edu	37	5	71493402	71493402	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:71493402A>G	ENST00000296755.7	+	5	4518	c.4220A>G	c.(4219-4221)gAg>gGg	p.E1407G		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1407					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		ATTGGATCCGAGTCTGCTTAT	0.493																																					p.E1407G	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.A4220G						.						46.0	48.0	48.0					5																	71493402		2202	4300	6502	SO:0001583	missense	4131	exon5			GATCCGAGTCTGC	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.4220A>G	chr5.hg19:g.71493402A>G	ENSP00000296755:p.Glu1407Gly	121.0	0.0		70.0	4.0	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	A	14.40	2.522854	0.44866	.	.	ENSG00000131711	ENST00000296755	T	0.04275	3.66	5.55	5.55	0.83447	.	0.082420	0.51477	D	0.000082	T	0.04724	0.0128	N	0.24115	0.695	0.49130	D	0.999753	P;P	0.39665	0.682;0.546	B;B	0.34590	0.186;0.186	T	0.44636	-0.9315	10	0.87932	D	0	-17.0322	15.6992	0.77528	1.0:0.0:0.0:0.0	.	1281;1407	A2BDK6;P46821	.;MAP1B_HUMAN	G	1407	ENSP00000296755:E1407G	ENSP00000296755:E1407G	E	+	2	0	MAP1B	71529158	1.000000	0.71417	0.984000	0.44739	0.566000	0.35808	3.881000	0.56152	2.122000	0.65172	0.459000	0.35465	GAG	.	.		0.493	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73189069	73189069	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:73189069A>G	ENST00000426542.2	+	27	3634	c.3614A>G	c.(3613-3615)aAg>aGg	p.K1205R	ARHGEF28_ENST00000512883.1_Missense_Mutation_p.K169R|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.K1205R|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.K1205R|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.K892R|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.K1205R|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.K1205R|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.K1205R			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1205					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)										GATGAAGACAAGAGGAAAGCT	0.458																																					p.K1205R		Atlas-SNP	.											.	.	.	.	0			c.A3614G						.						78.0	75.0	76.0					5																	73189069		1947	4124	6071	SO:0001583	missense	64283	exon28			AAGACAAGAGGAA		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.3614A>G	chr5.hg19:g.73189069A>G	ENSP00000412175:p.Lys1205Arg	152.0	0.0		97.0	4.0	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	A	3.469	-0.108308	0.06924	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.30714	3.17;3.18;3.17;2.86;3.18;3.17;3.0;1.52	4.87	0.227	0.15359	.	.	.	.	.	T	0.12518	0.0304	N	0.04335	-0.225	0.18873	N	0.999981	B;B;B;B;B	0.09022	0.001;0.001;0.0;0.002;0.0	B;B;B;B;B	0.11329	0.004;0.005;0.004;0.006;0.003	T	0.35895	-0.9770	9	0.12430	T	0.62	.	9.1023	0.36676	0.4434:0.0:0.5566:0.0	.	892;1205;1205;169;1205	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	R	1205;1205;1205;1205;1205;1205;892;169	ENSP00000296794:K1205R;ENSP00000441913:K1205R;ENSP00000441436:K1205R;ENSP00000287898:K1205R;ENSP00000411459:K1205R;ENSP00000412175:K1205R;ENSP00000296799:K892R;ENSP00000421081:K169R	ENSP00000287898:K1205R	K	+	2	0	RP11-428C6.1	73224825	1.000000	0.71417	0.999000	0.59377	0.926000	0.56050	1.135000	0.31454	0.211000	0.20683	-0.177000	0.13119	AAG	.	.		0.458	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
HMGCR	3156	hgsc.bcm.edu	37	5	74638583	74638583	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:74638583A>G	ENST00000287936.4	+	2	309	c.153A>G	c.(151-153)ccA>ccG	p.P51P	HMGCR_ENST00000343975.5_Silent_p.P51P|HMGCR_ENST00000511206.1_Silent_p.P51P	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	51					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)	ATGAATGTCCAAAGTTTGAAG	0.373																																					p.P51P		Atlas-SNP	.											.	HMGCR	53	.	0			c.A153G						.						101.0	93.0	95.0					5																	74638583		2203	4300	6503	SO:0001819	synonymous_variant	3156	exon2			ATGTCCAAAGTTT		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.153A>G	chr5.hg19:g.74638583A>G		159.0	0.0		91.0	5.0	NM_001130996	B7Z3Y9|Q8N190	Silent	SNP	ENST00000287936.4	hg19	CCDS4027.1																																																																																			.	.		0.373	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2		
JMY	133746	hgsc.bcm.edu	37	5	78587025	78587025	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:78587025T>C	ENST00000396137.4	+	4	1892	c.1430T>C	c.(1429-1431)aTg>aCg	p.M477T		NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	477					'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		GCTGAACGGATGGAAAAACTC	0.393																																					p.M477T		Atlas-SNP	.											.	JMY	82	.	0			c.T1430C						.						72.0	71.0	71.0					5																	78587025		1874	4096	5970	SO:0001583	missense	133746	exon4			AACGGATGGAAAA	AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.1430T>C	chr5.hg19:g.78587025T>C	ENSP00000379441:p.Met477Thr	119.0	0.0		77.0	4.0	NM_152405	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	hg19	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	T	19.35	3.811531	0.70797	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.08807	3.05	5.31	5.31	0.75309	.	0.081869	0.85682	D	0.000000	T	0.14570	0.0352	M	0.66939	2.045	0.53688	D	0.999973	P	0.47910	0.902	B	0.43301	0.415	T	0.01027	-1.1476	10	0.87932	D	0	.	15.2486	0.73526	0.0:0.0:0.0:1.0	.	477	Q8N9B5	JMY_HUMAN	T	477	ENSP00000379441:M477T	ENSP00000282259:M477T	M	+	2	0	JMY	78622781	1.000000	0.71417	0.993000	0.49108	0.824000	0.46624	7.226000	0.78060	1.999000	0.58509	0.454000	0.30748	ATG	.	.		0.393	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405	
HOMER1	9456	hgsc.bcm.edu	37	5	78692728	78692728	+	Splice_Site	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:78692728T>C	ENST00000334082.6	-	8	2238		c.e8-2		HOMER1_ENST00000535690.1_Splice_Site|HOMER1_ENST00000508576.1_Intron|HOMER1_ENST00000282260.6_Splice_Site	NM_004272.3	NP_004263.1	Q86YM7	HOME1_HUMAN	homer homolog 1 (Drosophila)						behavioral response to cocaine (GO:0048148)|chemical homeostasis within a tissue (GO:0048875)|circadian rhythm (GO:0007623)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of signal transduction (GO:0009967)|protein localization to synapse (GO:0035418)|regulation of calcium ion import (GO:0090279)|regulation of cation channel activity (GO:2001257)|regulation of store-operated calcium entry (GO:2001256)|response to calcium ion (GO:0051592)|response to nicotine (GO:0035094)|skeletal muscle contraction (GO:0003009)|skeletal muscle fiber development (GO:0048741)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell junction (GO:0030054)|costamere (GO:0043034)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|signaling adaptor activity (GO:0035591)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|skin(1)	14		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)		TTCTATTTCCTAGAAAAGACA	0.338																																					.		Atlas-SNP	.											.	HOMER1	37	.	0			c.406-2A>G						.						98.0	86.0	89.0					5																	78692728		1822	4077	5899	SO:0001630	splice_region_variant	9456	exon6			ATTTCCTAGAAAA	BC015502	CCDS43335.1, CCDS64188.1, CCDS64189.1	5q14.2	2008-02-05			ENSG00000152413	ENSG00000152413			17512	protein-coding gene	gene with protein product		604798				9808459, 9808458	Standard	NM_004272		Approved	Ves-1, SYN47, HOMER-1B	uc003kfy.4	Q86YM7	OTTHUMG00000134278	ENST00000334082.6:c.796-2A>G	chr5.hg19:g.78692728T>C		240.0	0.0		123.0	5.0	NM_001277077	B2R688|O96003|Q86YM5	Splice_Site	SNP	ENST00000334082.6	hg19	CCDS43335.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.806032	0.70682	.	.	ENSG00000152413	ENST00000334082;ENST00000282260;ENST00000535690	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1139	0.72384	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	HOMER1	78728484	1.000000	0.71417	0.998000	0.56505	0.884000	0.51177	7.063000	0.76714	2.267000	0.75376	0.533000	0.62120	.	.	.		0.338	HOMER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258856.1	NM_004272	Intron
SPZ1	84654	hgsc.bcm.edu	37	5	79616053	79616053	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:79616053T>C	ENST00000296739.4	+	1	264	c.19T>C	c.(19-21)Tca>Cca	p.S7P		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	7					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		CTCTGCTAAGTCAGCTGAGAT	0.473																																					p.S7P		Atlas-SNP	.											.	SPZ1	60	.	0			c.T19C						.						197.0	197.0	197.0					5																	79616053		1960	4163	6123	SO:0001583	missense	84654	exon1			GCTAAGTCAGCTG		CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 148"""					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.19T>C	chr5.hg19:g.79616053T>C	ENSP00000369611:p.Ser7Pro	144.0	0.0		82.0	4.0	NM_032567	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	hg19	CCDS43336.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.865170	0.51482	.	.	ENSG00000164299	ENST00000511881;ENST00000296739	T;T	0.52983	0.64;1.26	4.19	-1.18	0.09617	.	1.029180	0.07769	N	0.951371	T	0.36386	0.0965	L	0.42245	1.32	0.09310	N	1	B	0.17667	0.023	B	0.19391	0.025	T	0.39961	-0.9588	10	0.66056	D	0.02	-3.7233	4.0791	0.09917	0.0:0.2015:0.3598:0.4387	.	7	Q9BXG8	SPZ1_HUMAN	P	7	ENSP00000426530:S7P;ENSP00000369611:S7P	ENSP00000369611:S7P	S	+	1	0	SPZ1	79651809	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	0.014000	0.13333	-0.176000	0.10707	0.379000	0.24179	TCA	.	.		0.473	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567	
GPR98	84059	hgsc.bcm.edu	37	5	89971070	89971070	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:89971070G>A	ENST00000405460.2	+	24	5217	c.5121G>A	c.(5119-5121)caG>caA	p.Q1707Q	GPR98_ENST00000450321.2_3'UTR	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1707					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GCTTGCTGCAGTTCTCCACAG	0.483																																					p.Q1707Q		Atlas-SNP	.											.	GPR98	605	.	0			c.G5121A						.						47.0	49.0	48.0					5																	89971070		2067	4215	6282	SO:0001819	synonymous_variant	84059	exon24			GCTGCAGTTCTCC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.5121G>A	chr5.hg19:g.89971070G>A		84.0	0.0		53.0	41.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	hg19	CCDS47246.1																																																																																			.	.		0.483	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
MCTP1	79772	hgsc.bcm.edu	37	5	94245051	94245051	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:94245051T>C	ENST00000515393.1	-	10	1556	c.1557A>G	c.(1555-1557)gaA>gaG	p.E519E	MCTP1_ENST00000312216.8_Silent_p.E298E|MCTP1_ENST00000505078.1_Silent_p.E35E|MCTP1_ENST00000505208.1_Silent_p.E298E|MCTP1_ENST00000429576.2_Silent_p.E252E	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	519	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		AATCAAATTGTTCCCTCCACT	0.368																																					p.E519E		Atlas-SNP	.											.	MCTP1	110	.	0			c.A1557G						.						80.0	78.0	79.0					5																	94245051		2203	4300	6503	SO:0001819	synonymous_variant	79772	exon10			AAATTGTTCCCTC		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.1557A>G	chr5.hg19:g.94245051T>C		175.0	0.0		105.0	6.0	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Silent	SNP	ENST00000515393.1	hg19	CCDS34203.1	.	.	.	.	.	.	.	.	.	.	T	9.049	0.991491	0.18966	.	.	ENSG00000175471	ENST00000503301	.	.	.	5.68	3.35	0.38373	.	.	.	.	.	T	0.55768	0.1941	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50634	-0.8805	4	.	.	.	-20.4283	6.8803	0.24168	0.0:0.3275:0.0:0.6725	.	.	.	.	A	282	.	.	T	-	1	0	MCTP1	94270807	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.993000	0.29680	1.003000	0.39130	0.477000	0.44152	ACA	.	.		0.368	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717	
CHD1	1105	hgsc.bcm.edu	37	5	98204197	98204197	+	Splice_Site	SNP	A	A	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:98204197A>T	ENST00000284049.3	-	30	4398		c.e30+1		CHD1_ENST00000511067.1_Splice_Site	NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1						chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TCTAAGGCTTACAATGCTGAA	0.343																																					.		Atlas-SNP	.											.	CHD1	137	.	0			c.4248+2T>A						.						97.0	98.0	97.0					5																	98204197		2203	4300	6503	SO:0001630	splice_region_variant	1105	exon31			AGGCTTACAATGC	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.4248+1T>A	chr5.hg19:g.98204197A>T		90.0	0.0		53.0	4.0	NM_001270	Q17RZ3	Splice_Site	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	A	15.63	2.891018	0.52014	.	.	ENSG00000153922	ENST00000284049	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5806	0.76432	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CHD1	98232097	1.000000	0.71417	1.000000	0.80357	0.549000	0.35272	8.878000	0.92393	2.157000	0.67596	0.533000	0.62120	.	.	.		0.343	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	Intron
ST8SIA4	7903	hgsc.bcm.edu	37	5	100231449	100231449	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:100231449A>G	ENST00000231461.5	-	2	464	c.154T>C	c.(154-156)Tct>Cct	p.S52P	ST8SIA4_ENST00000451528.2_Missense_Mutation_p.S52P	NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	52					axon guidance (GO:0007411)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|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)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	25		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)		ATTTTATCAGAGCTATTGACA	0.383																																					p.S52P		Atlas-SNP	.											.	ST8SIA4	77	.	0			c.T154C						.						114.0	110.0	112.0					5																	100231449		2203	4299	6502	SO:0001583	missense	7903	exon2			TATCAGAGCTATT	L41680	CCDS4091.1, CCDS47252.1	5q21	2013-03-01	2003-01-14	2005-02-07	ENSG00000113532	ENSG00000113532		"""Sialyltransferases"""	10871	protein-coding gene	gene with protein product	"""ST8Sia IV"""	602547	"""sialyltransferase 8 (alpha-2, 8-polysialytransferase) D"""	SIAT8D		7624364	Standard	NM_005668		Approved	PST, PST1	uc003knk.3	Q92187	OTTHUMG00000128727	ENST00000231461.5:c.154T>C	chr5.hg19:g.100231449A>G	ENSP00000231461:p.Ser52Pro	171.0	0.0		105.0	5.0	NM_175052	A8KA07|G3V104|Q8N1F4|Q92693	Missense_Mutation	SNP	ENST00000231461.5	hg19	CCDS4091.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.180082	0.57800	.	.	ENSG00000113532	ENST00000231461;ENST00000451528	T;T	0.37584	2.03;1.19	6.06	4.88	0.63580	.	0.064453	0.64402	D	0.000006	T	0.29190	0.0726	L	0.32530	0.975	0.51233	D	0.999912	P	0.37466	0.596	B	0.37267	0.245	T	0.05084	-1.0907	10	0.52906	T	0.07	.	11.9112	0.52739	0.8696:0.0:0.0:0.1304	.	52	Q92187	SIA8D_HUMAN	P	52	ENSP00000231461:S52P;ENSP00000428914:S52P	ENSP00000231461:S52P	S	-	1	0	ST8SIA4	100259348	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.017000	0.64047	1.064000	0.40671	0.533000	0.62120	TCT	.	.		0.383	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250632.3	NM_005668	
EFNA5	1946	hgsc.bcm.edu	37	5	106723416	106723416	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:106723416T>C	ENST00000333274.6	-	3	756	c.475A>G	c.(475-477)Aga>Gga	p.R159G	EFNA5_ENST00000509503.1_Missense_Mutation_p.R159G|EFNA5_ENST00000510359.1_5'UTR	NM_001962.2	NP_001953.1	P52803	EFNA5_HUMAN	ephrin-A5	159	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|ephrin receptor signaling pathway (GO:0048013)|nervous system development (GO:0007399)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell-cell adhesion (GO:0022407)|regulation of focal adhesion assembly (GO:0051893)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rho GTPase activity (GO:0032319)|retinal ganglion cell axon guidance (GO:0031290)	anchored component of external side of plasma membrane (GO:0031362)|plasma membrane (GO:0005886)	chemorepellent activity (GO:0045499)|ephrin receptor binding (GO:0046875)			large_intestine(6)	6		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		CTTGTTGGTCTCACAAAGACT	0.448																																					p.R159G		Atlas-SNP	.											.	EFNA5	16	.	0			c.A475G						.						169.0	156.0	160.0					5																	106723416		2202	4300	6502	SO:0001583	missense	1946	exon3			TTGGTCTCACAAA	U26403	CCDS4097.1	5q21	2011-03-09			ENSG00000184349	ENSG00000184349		"""Ephrins"""	3225	protein-coding gene	gene with protein product		601535		EPLG7		8661153, 9245480	Standard	NM_001962		Approved	AF1, LERK7	uc003kol.3	P52803	OTTHUMG00000128741	ENST00000333274.6:c.475A>G	chr5.hg19:g.106723416T>C	ENSP00000328777:p.Arg159Gly	168.0	0.0		66.0	4.0	NM_001962		Missense_Mutation	SNP	ENST00000333274.6	hg19	CCDS4097.1	.	.	.	.	.	.	.	.	.	.	T	15.24	2.775925	0.49786	.	.	ENSG00000184349	ENST00000333274;ENST00000509503	D;D	0.93133	-3.17;-3.17	5.56	3.26	0.37387	Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.91372	0.7278	M	0.80028	2.48	0.80722	D	1	P	0.35226	0.491	B	0.30646	0.118	D	0.88244	0.2912	10	0.18276	T	0.48	-13.5014	13.3692	0.60703	0.0:0.0:0.476:0.524	.	159	P52803	EFNA5_HUMAN	G	159	ENSP00000328777:R159G;ENSP00000426989:R159G	ENSP00000328777:R159G	R	-	1	2	EFNA5	106751315	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.711000	0.54868	0.932000	0.37266	0.533000	0.62120	AGA	.	.		0.448	EFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250652.1	NM_001962	
STARD4	134429	hgsc.bcm.edu	37	5	110837775	110837775	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:110837775T>C	ENST00000296632.3	-	4	301	c.167A>G	c.(166-168)cAa>cGa	p.Q56R	STARD4_ENST00000509887.1_Intron|STARD4_ENST00000502322.1_Missense_Mutation_p.Q56R|STARD4_ENST00000511569.1_5'UTR|STARD4_ENST00000512160.1_Intron	NM_139164.1	NP_631903.1	Q96DR4	STAR4_HUMAN	StAR-related lipid transfer (START) domain containing 4	56	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				lipid transport (GO:0006869)		lipid binding (GO:0008289)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	12		all_cancers(142;0.00259)|all_epithelial(76;8.32e-05)|Prostate(80;0.0115)|Colorectal(10;0.0959)|Ovarian(225;0.156)|all_lung(232;0.18)|Lung NSC(167;0.248)		OV - Ovarian serous cystadenocarcinoma(64;4.91e-09)|Epithelial(69;1.39e-08)|all cancers(49;2.34e-06)|COAD - Colon adenocarcinoma(37;0.049)|Colorectal(14;0.138)		TATAACACCTTGGGCTTTGTA	0.383																																					p.Q56R		Atlas-SNP	.											.	STARD4	31	.	0			c.A167G						.						109.0	117.0	114.0					5																	110837775		2202	4300	6502	SO:0001583	missense	134429	exon4			ACACCTTGGGCTT	AF480299	CCDS4104.1	5q22	2011-09-12	2007-08-16		ENSG00000164211	ENSG00000164211		"""StAR-related lipid transfer (START) domain containing"""	18058	protein-coding gene	gene with protein product		607049	"""START domain containing 4, sterol regulated"""			12011452	Standard	NM_139164		Approved		uc003kph.1	Q96DR4	OTTHUMG00000128793	ENST00000296632.3:c.167A>G	chr5.hg19:g.110837775T>C	ENSP00000296632:p.Gln56Arg	99.0	0.0		70.0	4.0	NM_139164	Q86TN9	Missense_Mutation	SNP	ENST00000296632.3	hg19	CCDS4104.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.964345	0.74131	.	.	ENSG00000164211	ENST00000296632;ENST00000505803;ENST00000502322	T;T;T	0.78126	-1.15;-1.15;-1.15	5.94	5.94	0.96194	Lipid-binding START (2);START-like domain (1);	0.081196	0.52532	D	0.000068	D	0.83202	0.5203	M	0.67953	2.075	0.80722	D	1	P;P	0.51449	0.942;0.945	P;P	0.53988	0.739;0.523	T	0.81623	-0.0849	10	0.30854	T	0.27	-6.1773	16.3871	0.83514	0.0:0.0:0.0:1.0	.	56;56	Q86TN9;Q96DR4	.;STAR4_HUMAN	R	56	ENSP00000296632:Q56R;ENSP00000427478:Q56R;ENSP00000427639:Q56R	ENSP00000296632:Q56R	Q	-	2	0	STARD4	110865674	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	6.199000	0.72112	2.276000	0.75962	0.533000	0.62120	CAA	.	.		0.383	STARD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250720.1	NM_139164	
DMXL1	1657	hgsc.bcm.edu	37	5	118576151	118576151	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:118576151A>G	ENST00000311085.8	+	41	8706	c.8626A>G	c.(8626-8628)Aat>Gat	p.N2876D	DMXL1_ENST00000505312.1_3'UTR|DMXL1_ENST00000539542.1_Missense_Mutation_p.N2897D	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2876				N -> D (in Ref. 1; CAA06718). {ECO:0000305}.						breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		AGCACCTGCCAATAGTTTAGT	0.289																																					p.N2876D		Atlas-SNP	.											DMXL1,colon,carcinoma,0,2	DMXL1	268	.	0			c.A8626G						.						84.0	95.0	91.0					5																	118576151		2202	4300	6502	SO:0001583	missense	1657	exon41			CCTGCCAATAGTT	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.8626A>G	chr5.hg19:g.118576151A>G	ENSP00000309690:p.Asn2876Asp	101.0	0.0		40.0	2.0	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	A	14.36	2.512316	0.44660	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.01335	5.0;5.0	5.34	4.19	0.49359	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.097095	0.64402	D	0.000002	T	0.01870	0.0059	L	0.43152	1.355	0.41062	D	0.985381	B;B	0.15141	0.012;0.004	B;B	0.11329	0.006;0.004	T	0.52283	-0.8596	10	0.66056	D	0.02	-22.0096	10.5741	0.45217	0.9243:0.0:0.0757:0.0	.	2897;2876	F5H269;Q9Y485	.;DMXL1_HUMAN	D	2876;2897	ENSP00000309690:N2876D;ENSP00000439479:N2897D	ENSP00000309690:N2876D	N	+	1	0	DMXL1	118604050	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.261000	0.65496	2.031000	0.59945	0.528000	0.53228	AAT	.	.		0.289	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
HSD17B4	3295	hgsc.bcm.edu	37	5	118867101	118867101	+	Splice_Site	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:118867101T>A	ENST00000256216.6	+	22	2126		c.e22+2		HSD17B4_ENST00000522415.1_Splice_Site|HSD17B4_ENST00000504811.1_Splice_Site|HSD17B4_ENST00000513628.1_Splice_Site|HSD17B4_ENST00000414835.2_Splice_Site|HSD17B4_ENST00000510025.1_Splice_Site|HSD17B4_ENST00000509514.1_Splice_Site|HSD17B4_ENST00000515320.1_Splice_Site	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4						alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		CTAAGTGGAGTAAGTTATAGC	0.358																																					.	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											.	HSD17B4	63	.	0			c.1939+2T>A						.						80.0	80.0	80.0					5																	118867101		2202	4300	6502	SO:0001630	splice_region_variant	3295	exon21			GTGGAGTAAGTTA		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5213	protein-coding gene	gene with protein product	"""17beta-estradiol dehydrogenase type IV"", ""peroxisomal multifunctional protein 2"", ""17-beta-HSD IV"", ""17-beta-hydroxysteroid dehydrogenase 4"", ""D-bifunctional protein, peroxisomal"", ""D-3-hydroxyacyl-CoA dehydratase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase"", ""beta-keto-reductase"", ""beta-hydroxyacyl dehydrogenase"", ""short chain dehydrogenase/reductase family 8C, member 1"""	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.1993+2T>A	chr5.hg19:g.118867101T>A		141.0	0.0		84.0	4.0	NM_001199292	B4DNV1|B4DVS5|E9PB82|F5HE57	Splice_Site	SNP	ENST00000256216.6	hg19	CCDS4126.1	.	.	.	.	.	.	.	.	.	.	T	17.90	3.501994	0.64298	.	.	ENSG00000133835	ENST00000256216;ENST00000515320;ENST00000510025;ENST00000504811;ENST00000414835;ENST00000513628;ENST00000509514	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5759	0.68246	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	HSD17B4	118895000	1.000000	0.71417	1.000000	0.80357	0.658000	0.38924	6.937000	0.75898	2.087000	0.62958	0.528000	0.53228	.	.	.		0.358	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414	Intron
SNCAIP	9627	hgsc.bcm.edu	37	5	121739502	121739502	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:121739502A>G	ENST00000261368.8	+	3	334	c.72A>G	c.(70-72)tcA>tcG	p.S24S	SNCAIP_ENST00000414317.2_Missense_Mutation_p.H15R|SNCAIP_ENST00000379533.2_Silent_p.S71S|SNCAIP_ENST00000261367.7_Silent_p.S71S|SNCAIP_ENST00000504884.2_Silent_p.S24S|SNCAIP_ENST00000379538.3_Missense_Mutation_p.H9R|SNCAIP_ENST00000542191.1_5'UTR|SNCAIP_ENST00000503116.2_Silent_p.S71S|SNCAIP_ENST00000379536.2_Silent_p.S24S	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	24					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		CAGTCACATCACTCAAGACGA	0.443																																					p.H9R		Atlas-SNP	.											.	SNCAIP	308	.	0			c.A26G						.						221.0	203.0	209.0					5																	121739502		2203	4300	6503	SO:0001819	synonymous_variant	9627	exon3			CACATCACTCAAG	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"""Ankyrin repeat domain containing"""	11139	protein-coding gene	gene with protein product	"""synphilin"""	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.72A>G	chr5.hg19:g.121739502A>G		142.0	0.0		95.0	6.0	NM_001242935	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	hg19	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	A	15.15	2.749419	0.49257	.	.	ENSG00000064692	ENST00000379538;ENST00000414317;ENST00000447854	T;T	0.01629	5.05;4.72	5.64	-11.3	0.00108	.	.	.	.	.	T	0.01061	0.0035	.	.	.	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.48210	-0.9055	8	0.48119	T	0.1	-14.8217	1.8704	0.03207	0.1616:0.2743:0.3298:0.2343	.	15;9;9	B7Z995;Q9Y6H5-5;Q9Y6H5-2	.;.;.	R	9;15;15	ENSP00000368854:H9R;ENSP00000394392:H15R	ENSP00000368854:H9R	H	+	2	0	SNCAIP	121767401	0.510000	0.26171	0.513000	0.27749	0.993000	0.82548	-0.524000	0.06222	-1.933000	0.01052	-0.290000	0.09829	CAC	.	.		0.443	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1		
GRAMD3	65983	hgsc.bcm.edu	37	5	125813387	125813387	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:125813387T>C	ENST00000285689.3	+	6	951	c.490T>C	c.(490-492)Tct>Cct	p.S164P	GRAMD3_ENST00000515200.1_Missense_Mutation_p.S141P|GRAMD3_ENST00000544396.1_Missense_Mutation_p.S60P|RP11-517I3.1_ENST00000512500.1_RNA|GRAMD3_ENST00000543198.1_Missense_Mutation_p.S141P|RP11-517I3.1_ENST00000515808.1_RNA|GRAMD3_ENST00000502348.1_Missense_Mutation_p.S55P|GRAMD3_ENST00000542322.1_Missense_Mutation_p.S172P|GRAMD3_ENST00000511134.1_Missense_Mutation_p.S148P|GRAMD3_ENST00000513040.1_Missense_Mutation_p.S179P	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	164	GRAM.					cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		GTTTCAGATCTCTATTCCAGC	0.388																																					p.S179P		Atlas-SNP	.											.	GRAMD3	30	.	0			c.T535C						.						117.0	124.0	122.0					5																	125813387		2203	4300	6503	SO:0001583	missense	65983	exon6			CAGATCTCTATTC	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"""HCV NS3 transactivated protein 2"""					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000285689.3:c.490T>C	chr5.hg19:g.125813387T>C	ENSP00000285689:p.Ser164Pro	213.0	0.0		130.0	6.0	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	hg19	CCDS4136.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.964473	0.53507	.	.	ENSG00000155324	ENST00000513040;ENST00000506445;ENST00000543367;ENST00000285689;ENST00000515200;ENST00000542322;ENST00000544396;ENST00000543198;ENST00000502348;ENST00000511134	D;D;D;D;D;D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26;-2.26;-2.26;-2.26;-2.26;-2.26	5.55	4.36	0.52297	GRAM (2);	0.325774	0.36167	N	0.002749	D	0.89818	0.6825	M	0.64404	1.975	0.41316	D	0.987143	D;P;D;D;D	0.64830	0.991;0.952;0.994;0.991;0.991	P;P;D;P;P	0.64506	0.876;0.828;0.926;0.885;0.876	D	0.88502	0.3083	10	0.54805	T	0.06	.	6.1935	0.20538	0.3273:0.0:0.1302:0.5425	.	148;60;172;179;164	B7Z8T2;B7Z1F2;B7Z3R1;B7Z6D8;Q96HH9	.;.;.;.;GRAM3_HUMAN	P	179;178;148;164;141;172;60;141;55;148	ENSP00000426120:S179P;ENSP00000424985:S178P;ENSP00000285689:S164P;ENSP00000426143:S141P;ENSP00000441876:S172P;ENSP00000444049:S60P;ENSP00000442902:S141P;ENSP00000427596:S55P;ENSP00000426088:S148P	ENSP00000285689:S164P	S	+	1	0	GRAMD3	125841286	0.594000	0.26849	0.997000	0.53966	0.984000	0.73092	1.433000	0.34947	1.002000	0.39104	0.533000	0.62120	TCT	.	.		0.388	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927	
ISOC1	51015	hgsc.bcm.edu	37	5	128442751	128442751	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:128442751T>C	ENST00000173527.5	+	4	762	c.746T>C	c.(745-747)cTc>cCc	p.L249P		NM_016048.2	NP_057132.2	Q96CN7	ISOC1_HUMAN	isochorismatase domain containing 1	249						extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	catalytic activity (GO:0003824)			kidney(2)|lung(7)	9		all_cancers(142;0.0813)|Prostate(80;0.0865)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.138)|OV - Ovarian serous cystadenocarcinoma(64;0.164)		ATGTTTGCCCTCGAGGTAATT	0.428																																					p.L249P		Atlas-SNP	.											.	ISOC1	26	.	0			c.T746C						.						132.0	128.0	129.0					5																	128442751		2012	4190	6202	SO:0001583	missense	51015	exon4			TTGCCCTCGAGGT	AF151869	CCDS43357.1	5q22.1-q33.3	2010-03-19			ENSG00000066583	ENSG00000066583			24254	protein-coding gene	gene with protein product						10810093, 18566572	Standard	NM_016048		Approved	CGI-111	uc003kva.3	Q96CN7	OTTHUMG00000163144	ENST00000173527.5:c.746T>C	chr5.hg19:g.128442751T>C	ENSP00000173527:p.Leu249Pro	150.0	0.0		94.0	4.0	NM_016048	Q7Z770	Missense_Mutation	SNP	ENST00000173527.5	hg19	CCDS43357.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.954526	0.73902	.	.	ENSG00000066583	ENST00000506986;ENST00000173527	.	.	.	5.07	3.92	0.45320	Isochorismatase-like (3);	0.174261	0.36482	N	0.002574	T	0.74199	0.3685	M	0.88241	2.94	0.80722	D	1	P	0.37176	0.586	P	0.48089	0.566	T	0.75091	-0.3440	8	.	.	.	-17.3297	10.7276	0.46077	0.0:0.0752:0.0:0.9248	.	249	Q96CN7	ISOC1_HUMAN	P	228;249	.	.	L	+	2	0	ISOC1	128470650	1.000000	0.71417	0.996000	0.52242	0.955000	0.61496	6.461000	0.73522	1.086000	0.41228	0.528000	0.53228	CTC	.	.		0.428	ISOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371826.1	NM_016048	
RAD50	10111	hgsc.bcm.edu	37	5	131911482	131911482	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:131911482C>T	ENST00000265335.6	+	3	614	c.227C>T	c.(226-228)aCa>aTa	p.T76I	RAD50_ENST00000378823.3_5'UTR			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	76					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCTCAAGAAACAGATGTGAGA	0.383								Homologous recombination																													p.T76I		Atlas-SNP	.											.	RAD50	246	.	0			c.C227T						.						101.0	91.0	94.0					5																	131911482		2203	4300	6503	SO:0001583	missense	10111	exon3			AAGAAACAGATGT	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"""RAD50 (S. cerevisiae) homolog"""			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.227C>T	chr5.hg19:g.131911482C>T	ENSP00000265335:p.Thr76Ile	151.0	0.0		92.0	4.0	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	hg19	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.977597	0.92982	.	.	ENSG00000113522	ENST00000265335;ENST00000453394	T;T	0.06608	3.28;3.28	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.21921	0.0528	L	0.52126	1.63	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.00028	-1.2296	10	0.56958	D	0.05	-15.9137	18.9261	0.92546	0.0:1.0:0.0:0.0	.	76	Q92878	RAD50_HUMAN	I	76	ENSP00000265335:T76I;ENSP00000400049:T76I	ENSP00000265335:T76I	T	+	2	0	RAD50	131939381	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	7.497000	0.81536	2.710000	0.92621	0.555000	0.69702	ACA	.	.		0.383	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732	
SEC24A	10802	hgsc.bcm.edu	37	5	134022523	134022523	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:134022523T>C	ENST00000398844.2	+	10	1823	c.1535T>C	c.(1534-1536)gTg>gCg	p.V512A	SEC24A_ENST00000322887.4_Missense_Mutation_p.V512A	NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	512					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTATTTGATGTGTCTCACAAT	0.333																																					p.V512A		Atlas-SNP	.											.	SEC24A	77	.	0			c.T1535C						.						123.0	111.0	115.0					5																	134022523		1854	4105	5959	SO:0001583	missense	10802	exon10			TTGATGTGTCTCA	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"""SEC24 (S. cerevisiae) related gene family, member A"", ""SEC24 family, member A (S. cerevisiae)"""			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.1535T>C	chr5.hg19:g.134022523T>C	ENSP00000381823:p.Val512Ala	202.0	0.0		105.0	5.0	NM_001252231	A8MVW3|Q8WUV2|Q96GP7	Missense_Mutation	SNP	ENST00000398844.2	hg19	CCDS43363.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.3|28.3	4.909637|4.909637	0.92107|0.92107	.|.	.|.	ENSG00000113615|ENSG00000113615	ENST00000513123|ENST00000398844;ENST00000322887	.|T;T	.|0.80653	.|-1.4;-1.4	5.8|5.8	5.8|5.8	0.92144|0.92144	.|Sec23/Sec24, trunk domain (1);	.|0.109172	.|0.64402	.|D	.|0.000009	D|D	0.91744|0.91744	0.7389|0.7389	M|M	0.91459|0.91459	3.21|3.21	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.997	.|D;D	.|0.80764	.|0.994;0.989	D|D	0.93471|0.93471	0.6819|0.6819	5|10	.|0.87932	.|D	.|0	-13.5895|-13.5895	16.1502|16.1502	0.81611|0.81611	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|276;512	.|B4E205;O95486	.|.;SC24A_HUMAN	R|A	58|512	.|ENSP00000381823:V512A;ENSP00000321749:V512A	.|ENSP00000321749:V512A	C|V	+|+	1|2	0|0	SEC24A|SEC24A	134050422|134050422	1.000000|1.000000	0.71417|0.71417	0.965000|0.965000	0.40720|0.40720	0.988000|0.988000	0.76386|0.76386	7.671000|7.671000	0.83941|0.83941	2.203000|2.203000	0.70933|0.70933	0.460000|0.460000	0.39030|0.39030	TGT|GTG	.	.		0.333	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1		
PCDHB16	57717	hgsc.bcm.edu	37	5	140563037	140563037	+	Silent	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:140563037T>A	ENST00000361016.2	+	1	2058	c.903T>A	c.(901-903)gtT>gtA	p.V301V		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	301	Cadherin 3. {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)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGGGGAAGTTCGACTGAGAA	0.438																																					p.V301V		Atlas-SNP	.											.	PCDHB16	159	.	0			c.T903A						.						80.0	87.0	85.0					5																	140563037		2203	4300	6503	SO:0001819	synonymous_variant	57717	exon1			GGAAGTTCGACTG	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.903T>A	chr5.hg19:g.140563037T>A		72.0	0.0		39.0	27.0	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Silent	SNP	ENST00000361016.2	hg19	CCDS4251.1																																																																																			.	.		0.438	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
PCDHGA8	9708	hgsc.bcm.edu	37	5	140774716	140774716	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:140774716T>C	ENST00000398604.2	+	1	2336	c.2336T>C	c.(2335-2337)cTc>cCc	p.L779P	PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	779					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGACATGCTCATCAGTCAG	0.473																																					p.L779P		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.T2336C						.						77.0	81.0	80.0					5																	140774716		2196	4298	6494	SO:0001583	missense	9708	exon1			ACATGCTCATCAG	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.2336T>C	chr5.hg19:g.140774716T>C	ENSP00000381605:p.Leu779Pro	255.0	0.0		163.0	7.0	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	hg19	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	11.79	1.743982	0.30865	.	.	ENSG00000253767	ENST00000398604	T	0.50277	0.75	4.5	4.5	0.54988	.	.	.	.	.	T	0.72252	0.3437	M	0.92169	3.28	0.26051	N	0.981476	D;D	0.89917	1.0;1.0	D;D	0.81914	0.989;0.995	T	0.65450	-0.6165	9	0.62326	D	0.03	.	7.7621	0.28959	0.0:0.0946:0.0:0.9054	.	779;779	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	P	779	ENSP00000381605:L779P	ENSP00000381605:L779P	L	+	2	0	PCDHGA8	140754900	0.722000	0.28017	0.927000	0.36925	0.189000	0.23516	2.857000	0.48349	1.905000	0.55150	0.533000	0.62120	CTC	.	.		0.473	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
PCDHGA12	26025	hgsc.bcm.edu	37	5	140884982	140884982	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:140884982G>T	ENST00000252085.3	+	3	2648	c.2506G>T	c.(2506-2508)Ggc>Tgc	p.G836C	PCDHGA11_ENST00000518882.1_Missense_Mutation_p.G654C|PCDHGB4_ENST00000519479.1_Missense_Mutation_p.G827C|PCDHGB3_ENST00000576222.1_Missense_Mutation_p.G833C|PCDHGB6_ENST00000520790.1_Missense_Mutation_p.G834C|PCDHGA11_ENST00000398587.2_Missense_Mutation_p.G839C|PCDHGA10_ENST00000398610.2_Missense_Mutation_p.G840C|PCDHGA7_ENST00000518325.1_Missense_Mutation_p.G836C|PCDHGB7_ENST00000398594.2_Missense_Mutation_p.G833C|PCDHGA3_ENST00000253812.6_Missense_Mutation_p.G836C|PCDHGB1_ENST00000523390.1_Missense_Mutation_p.G831C|PCDHGB2_ENST00000522605.1_Missense_Mutation_p.G835C|PCDHGA2_ENST00000394576.2_Missense_Mutation_p.G836C|PCDHGA1_ENST00000517417.1_Missense_Mutation_p.G835C|PCDHGA4_ENST00000571252.1_Missense_Mutation_p.G835C|PCDHGA5_ENST00000518069.1_Missense_Mutation_p.G835C|PCDHGA6_ENST00000517434.1_Missense_Mutation_p.G836C|PCDHGA8_ENST00000398604.2_Missense_Mutation_p.G836C|PCDHGC4_ENST00000306593.1_Missense_Mutation_p.G842C|PCDHGC3_ENST00000308177.3_Missense_Mutation_p.G838C|PCDHGC5_ENST00000252087.1_Missense_Mutation_p.G848C|PCDHGA9_ENST00000573521.1_Missense_Mutation_p.G836C	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	836					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGATGACACCGGCACCTGGCC	0.592																																					p.G848C		Atlas-SNP	.											.	PCDHGC5	199	.	0			c.G2542T						.						190.0	184.0	186.0					5																	140884982		2203	4300	6503	SO:0001583	missense	56097	exon3			GACACCGGCACCT	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"""Cadherins / Protocadherins : Clustered"""	8699	other	protocadherin	"""fibroblast cadherin FIB3"""	603059	"""cadherin 21"""	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.2506G>T	chr5.hg19:g.140884982G>T	ENSP00000252085:p.Gly836Cys	161.0	0.0		99.0	4.0	NM_018929	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	hg19	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474072	0.84640	.	.	ENSG00000204956;ENSG00000081853;ENSG00000254245;ENSG00000254221;ENSG00000253910;ENSG00000253485;ENSG00000253731;ENSG00000253537;ENSG00000253953;ENSG00000253767;ENSG00000253305;ENSG00000253846;ENSG00000254122;ENSG00000253873;ENSG00000253873;ENSG00000253159;ENSG00000240184;ENSG00000242419;ENSG00000240764	ENST00000517417;ENST00000394576;ENST00000253812;ENST00000523390;ENST00000522605;ENST00000518069;ENST00000517434;ENST00000518325;ENST00000519479;ENST00000398604;ENST00000520790;ENST00000398610;ENST00000398594;ENST00000398587;ENST00000518882;ENST00000252085;ENST00000308177;ENST00000306593;ENST00000252087	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.96396	-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0	5.32	5.32	0.75619	.	0.000000	0.48767	D	0.000170	D	0.98311	0.9440	M	0.87180	2.865	0.52099	D	0.999947	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;0.995;1.0;0.997;1.0;1.0;1.0;0.998;0.999;0.998;1.0;0.996;0.999;0.997;0.99;1.0;0.998;0.995;0.993;1.0;0.997;0.998;0.984	D	0.99047	1.0826	10	0.87932	D	0	.	17.7507	0.88432	0.0:0.0:1.0:0.0	.	848;842;38;838;836;839;654;833;840;834;836;827;836;827;836;836;833;835;835;835;831;836;836;835	Q9Y5F6;Q9Y5F7;Q9BR81;Q9UN70;O60330;Q9Y5H2;Q9Y5H2-3;Q9Y5F8;Q9Y5H3;Q9Y5F9;Q9Y5G4;Q9Y5G0;Q9Y5G5;Q9UN71;Q9Y5G6;Q9Y5G7;Q9Y5G1;Q9Y5G8;Q9Y5G2;Q9Y5G9;Q9Y5G3;Q9Y5H0;Q9Y5H1;Q9Y5H4	PCDGM_HUMAN;PCDGL_HUMAN;.;PCDGK_HUMAN;PCDGC_HUMAN;PCDGB_HUMAN;.;PCDGJ_HUMAN;PCDGA_HUMAN;PCDGI_HUMAN;PCDG9_HUMAN;PCDGH_HUMAN;PCDG8_HUMAN;PCDGG_HUMAN;PCDG7_HUMAN;PCDG6_HUMAN;PCDGF_HUMAN;PCDG5_HUMAN;PCDGE_HUMAN;PCDG4_HUMAN;PCDGD_HUMAN;PCDG3_HUMAN;PCDG2_HUMAN;PCDG1_HUMAN	C	835;836;836;831;835;835;836;836;827;836;834;840;833;839;654;836;838;842;848	ENSP00000431083:G835C;ENSP00000378077:G836C;ENSP00000253812:G836C;ENSP00000429273:G831C;ENSP00000429018:G835C;ENSP00000429834:G835C;ENSP00000429601:G836C;ENSP00000430024:G836C;ENSP00000428288:G827C;ENSP00000381605:G836C;ENSP00000428603:G834C;ENSP00000381611:G840C;ENSP00000381594:G833C;ENSP00000381589:G839C;ENSP00000428333:G654C;ENSP00000252085:G836C;ENSP00000312070:G838C;ENSP00000306918:G842C;ENSP00000252087:G848C	ENSP00000381611:G840C	G	+	1	0	PCDHGA12;PCDHGA10;PCDHGA11;PCDHGB7;PCDHGA8;PCDHGC5;PCDHGA7;PCDHGB6;PCDHGC4;PCDHGA6;PCDHGC3;PCDHGA5;PCDHGA3;PCDHGB2;PCDHGA2;PCDHGA1;PCDHGB4;PCDHGB1	140865166	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	5.820000	0.69250	2.772000	0.95346	0.650000	0.86243	GGC	.	.		0.592	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735	
PDE6A	5145	hgsc.bcm.edu	37	5	149294528	149294528	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:149294528T>C	ENST00000255266.5	-	6	1095	c.976A>G	c.(976-978)Aaa>Gaa	p.K326E		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	326	GAF 2.				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)	ATGTCCTCTTTGCCATGCAGG	0.328																																					p.K326E		Atlas-SNP	.											.	PDE6A	98	.	0			c.A976G						.						145.0	137.0	140.0					5																	149294528		2203	4300	6503	SO:0001583	missense	5145	exon6			CCTCTTTGCCATG		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.976A>G	chr5.hg19:g.149294528T>C	ENSP00000255266:p.Lys326Glu	126.0	0.0		86.0	4.0	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	hg19	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.094954	0.76870	.	.	ENSG00000132915	ENST00000255266	T	0.67171	-0.25	5.19	5.19	0.71726	GAF (2);	0.123303	0.56097	D	0.000028	T	0.78278	0.4258	M	0.78456	2.415	0.53688	D	0.999972	P	0.49559	0.925	P	0.59012	0.85	T	0.78003	-0.2374	10	0.35671	T	0.21	.	13.2885	0.60258	0.0:0.0:0.0:1.0	.	326	P16499	PDE6A_HUMAN	E	326	ENSP00000255266:K326E	ENSP00000255266:K326E	K	-	1	0	PDE6A	149274721	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	6.664000	0.74437	2.084000	0.62774	0.482000	0.46254	AAA	.	.		0.328	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
SLC36A2	153201	hgsc.bcm.edu	37	5	150712834	150712834	+	Missense_Mutation	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:150712834T>A	ENST00000335244.4	-	7	923	c.794A>T	c.(793-795)tAc>tTc	p.Y265F	SLC36A2_ENST00000521967.1_Missense_Mutation_p.Y265F|SLC36A2_ENST00000450886.1_5'Flank	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	265					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	GAAGAGAGGGTAGGTCTTCCA	0.458																																					p.Y265F		Atlas-SNP	.											.	SLC36A2	71	.	0			c.A794T						.						113.0	111.0	112.0					5																	150712834		2203	4300	6503	SO:0001583	missense	153201	exon7			AGAGGGTAGGTCT	AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"""Solute carriers"""	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.794A>T	chr5.hg19:g.150712834T>A	ENSP00000334223:p.Tyr265Phe	185.0	0.0		123.0	7.0	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Missense_Mutation	SNP	ENST00000335244.4	hg19	CCDS4315.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.77|12.77	2.037639|2.037639	0.35989|0.35989	.|.	.|.	ENSG00000186335|ENSG00000186335	ENST00000523044|ENST00000335244;ENST00000521967	.|T;T	.|0.02085	.|4.46;4.46	4.71|4.71	4.71|4.71	0.59529|0.59529	.|.	.|0.059999	.|0.64402	.|D	.|0.000002	T|T	0.01558|0.01558	0.0050|0.0050	N|N	0.12887|0.12887	0.27|0.27	0.80722|0.80722	D|D	1|1	.|B;B	.|0.15141	.|0.005;0.012	.|B;B	.|0.21360	.|0.023;0.034	T|T	0.56208|0.56208	-0.8017|-0.8017	5|10	.|0.12430	.|T	.|0.62	-14.1951|-14.1951	10.298|10.298	0.43635|0.43635	0.1476:0.0:0.0:0.8524|0.1476:0.0:0.0:0.8524	.|.	.|265;265	.|E5RJJ5;Q495M3	.|.;S36A2_HUMAN	S|F	18|265	.|ENSP00000334223:Y265F;ENSP00000430535:Y265F	.|ENSP00000334223:Y265F	T|Y	-|-	1|2	0|0	SLC36A2|SLC36A2	150693027|150693027	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.751000|2.751000	0.47508|0.47508	2.111000|2.111000	0.64477|0.64477	0.477000|0.477000	0.44152|0.44152	ACC|TAC	.	.		0.458	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1		
FAT2	2196	hgsc.bcm.edu	37	5	150905386	150905386	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:150905386C>A	ENST00000261800.5	-	17	10461	c.10449G>T	c.(10447-10449)ctG>ctT	p.L3483L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3483	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAGCAGTCACCAGCCATCCAT	0.577																																					p.L3483L		Atlas-SNP	.											.	FAT2	465	.	0			c.G10449T						.						82.0	75.0	78.0					5																	150905386		2203	4300	6503	SO:0001819	synonymous_variant	2196	exon17			AGTCACCAGCCAT	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.10449G>T	chr5.hg19:g.150905386C>A		87.0	0.0		64.0	4.0	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	8.305	0.820831	0.16678	.	.	ENSG00000086570	ENST00000520200	.	.	.	5.11	2.33	0.28932	.	.	.	.	.	T	0.54532	0.1864	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46857	-0.9161	4	.	.	.	.	6.3892	0.21577	0.1287:0.6561:0.0:0.2152	.	.	.	.	C	342	.	.	G	-	1	0	FAT2	150885579	0.963000	0.33076	1.000000	0.80357	0.831000	0.47069	0.512000	0.22755	0.667000	0.31107	-0.252000	0.11476	GGT	.	.		0.577	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
FAT2	2196	hgsc.bcm.edu	37	5	150908752	150908752	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:150908752T>C	ENST00000261800.5	-	14	10025	c.10013A>G	c.(10012-10014)gAc>gGc	p.D3338G		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3338	Cadherin 30. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAGGATGACGTCACCCACAAG	0.512																																					p.D3338G		Atlas-SNP	.											.	FAT2	465	.	0			c.A10013G						.						103.0	96.0	98.0					5																	150908752		2203	4300	6503	SO:0001583	missense	2196	exon14			ATGACGTCACCCA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.10013A>G	chr5.hg19:g.150908752T>C	ENSP00000261800:p.Asp3338Gly	134.0	0.0		90.0	4.0	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.202|6.202	0.405372|0.405372	0.11754|0.11754	.|.	.|.	ENSG00000086570|ENSG00000086570	ENST00000261800|ENST00000520200	T|.	0.50277|.	0.75|.	5.78|5.78	3.27|3.27	0.37495|0.37495	Cadherin (3);Cadherin-like (1);|.	0.350897|.	0.27315|.	N|.	0.019932|.	T|.	0.29126|.	0.0724|.	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.12156|.	0.006;0.007|.	T|.	0.17992|.	-1.0351|.	10|.	0.33141|.	T|.	0.24|.	.|.	12.6955|12.6955	0.57001|0.57001	0.0:0.0:0.2595:0.7405|0.0:0.0:0.2595:0.7405	.|.	3338;529|.	Q9NYQ8;E9PDJ8|.	FAT2_HUMAN;.|.	G|W	3338|196	ENSP00000261800:D3338G|.	ENSP00000261800:D3338G|.	D|X	-|-	2|3	0|0	FAT2|FAT2	150888945|150888945	0.079000|0.079000	0.21365|0.21365	0.003000|0.003000	0.11579|0.11579	0.101000|0.101000	0.19017|0.19017	1.767000|1.767000	0.38501|0.38501	0.399000|0.399000	0.25367|0.25367	0.519000|0.519000	0.50382|0.50382	GAC|TGA	.	.		0.512	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
SPARC	6678	hgsc.bcm.edu	37	5	151049257	151049257	+	Missense_Mutation	SNP	T	T	C	rs200223394		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:151049257T>C	ENST00000231061.4	-	6	732	c.419A>G	c.(418-420)aAg>aGg	p.K140R	SPARC_ENST00000537849.1_5'Flank	NM_003118.3	NP_003109.1	P09486	SPRC_HUMAN	secreted protein, acidic, cysteine-rich (osteonectin)	140	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				blood coagulation (GO:0007596)|bone development (GO:0060348)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|inner ear development (GO:0048839)|lung development (GO:0030324)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|regulation of cell morphogenesis (GO:0022604)|response to cadmium ion (GO:0046686)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to gravity (GO:0009629)|response to L-ascorbic acid (GO:0033591)|response to lead ion (GO:0010288)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nuclear matrix (GO:0016363)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|platelet alpha granule membrane (GO:0031092)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)			central_nervous_system(3)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(196;0.109)|all_hematologic(541;0.122)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;0.00118)		CAGGTGGAGCTTGTGGCCCTT	0.557																																					p.K140R		Atlas-SNP	.											.	SPARC	38	.	0			c.A419G						.	T	ARG/LYS	0,4406		0,0,2203	125.0	110.0	115.0		419	5.7	1.0	5		115	2,8598	2.2+/-6.3	0,2,4298	no	missense	SPARC	NM_003118.2	26	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	benign	140/304	151049257	2,13004	2203	4300	6503	SO:0001583	missense	6678	exon6			TGGAGCTTGTGGC		CCDS4318.1	5q31-q33	2012-10-02			ENSG00000113140	ENSG00000113140			11219	protein-coding gene	gene with protein product	"""cysteine-rich protein"", ""osteonectin"""	182120		ON		2838412, 3410046	Standard	NM_003118		Approved		uc003lui.4	P09486	OTTHUMG00000130122	ENST00000231061.4:c.419A>G	chr5.hg19:g.151049257T>C	ENSP00000231061:p.Lys140Arg	163.0	0.0		123.0	5.0	NM_003118	D3DQH9|Q6IBK4	Missense_Mutation	SNP	ENST00000231061.4	hg19	CCDS4318.1	.	.	.	.	.	.	.	.	.	.	T	16.10	3.027083	0.54683	0.0	2.33E-4	ENSG00000113140	ENST00000231061;ENST00000538026;ENST00000521569	T;T;T	0.75367	-0.93;-0.93;-0.93	5.7	5.7	0.88788	Proteinase inhibitor I1, Kazal (2);	0.000000	0.85682	D	0.000000	T	0.64080	0.2566	L	0.27975	0.815	0.80722	D	1	B	0.14805	0.011	B	0.21360	0.034	T	0.58595	-0.7609	10	0.25106	T	0.35	-25.5431	15.9765	0.80071	0.0:0.0:0.0:1.0	.	140	P09486	SPRC_HUMAN	R	140;49;49	ENSP00000231061:K140R;ENSP00000440127:K49R;ENSP00000428119:K49R	ENSP00000231061:K140R	K	-	2	0	SPARC	151029450	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	7.516000	0.81772	2.172000	0.68678	0.533000	0.62120	AAG	.	T|0.999;C|0.001		0.557	SPARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252430.1	NM_003118	
MFAP3	4238	hgsc.bcm.edu	37	5	153432861	153432861	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:153432861T>C	ENST00000436816.1	+	3	896	c.677T>C	c.(676-678)aTg>aCg	p.M226T	MFAP3_ENST00000439768.2_Missense_Mutation_p.M80T|MFAP3_ENST00000322602.5_Missense_Mutation_p.M226T	NM_001242336.1|NM_005927.4	NP_001229265.1|NP_005918.1	P55082	MFAP3_HUMAN	microfibrillar-associated protein 3	226					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)	7	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)		TTTAAGACCATGGAGTTTGCT	0.448																																					p.M226T		Atlas-SNP	.											.	MFAP3	20	.	0			c.T677C						.						109.0	110.0	110.0					5																	153432861		2203	4300	6503	SO:0001583	missense	4238	exon3			AGACCATGGAGTT		CCDS4324.1, CCDS47319.1	5q32-q33.2	2013-01-11			ENSG00000037749	ENSG00000037749		"""Immunoglobulin superfamily / I-set domain containing"""	7034	protein-coding gene	gene with protein product		600491				7782085	Standard	NM_005927		Approved		uc010jib.2	P55082	OTTHUMG00000130149	ENST00000436816.1:c.677T>C	chr5.hg19:g.153432861T>C	ENSP00000409933:p.Met226Thr	206.0	0.0		100.0	4.0	NM_005927	B2RDK0|B4DKA1|Q9NXA7	Missense_Mutation	SNP	ENST00000436816.1	hg19	CCDS4324.1	.	.	.	.	.	.	.	.	.	.	T	19.50	3.839339	0.71488	.	.	ENSG00000037749	ENST00000439768;ENST00000436816;ENST00000322602	T;T	0.27256	1.68;1.68	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.49218	0.1544	M	0.65975	2.015	0.58432	D	0.999995	D	0.71674	0.998	D	0.72338	0.977	T	0.44065	-0.9352	9	.	.	.	-19.8981	15.9374	0.79723	0.0:0.0:0.0:1.0	.	226	P55082	MFAP3_HUMAN	T	80;226;226	ENSP00000409933:M226T;ENSP00000322956:M226T	.	M	+	2	0	MFAP3	153413054	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.063000	0.71162	2.228000	0.72767	0.533000	0.62120	ATG	.	.		0.448	MFAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252457.2	NM_005927	
TIMD4	91937	hgsc.bcm.edu	37	5	156375500	156375500	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:156375500A>G	ENST00000274532.2	-	5	827	c.771T>C	c.(769-771)gtT>gtC	p.V257V	TIMD4_ENST00000407087.3_Intron	NM_138379.2	NP_612388.2	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain containing 4	257	Ser-rich.					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)			GGAGATCCCAAACTTTGGACT	0.423																																					p.V257V		Atlas-SNP	.											.	TIMD4	94	.	0			c.T771C						.						71.0	60.0	64.0					5																	156375500		2203	4300	6503	SO:0001819	synonymous_variant	91937	exon5			ATCCCAAACTTTG	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.771T>C	chr5.hg19:g.156375500A>G		154.0	0.0		93.0	4.0	NM_138379	B5MCL9	Silent	SNP	ENST00000274532.2	hg19	CCDS4332.1																																																																																			.	.		0.423	TIMD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252568.1	NM_138379	
GABRA6	2559	hgsc.bcm.edu	37	5	161128527	161128527	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:161128527G>A	ENST00000274545.5	+	9	1543	c.1110G>A	c.(1108-1110)ctG>ctA	p.L370L	GABRA6_ENST00000523217.1_Silent_p.L360L			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	370					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.L370L(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	AATATCATCTGAAGAAAAGGA	0.383										TCGA Ovarian(5;0.080)																											p.L370L		Atlas-SNP	.											GABRA6,NS,carcinoma,0,1	GABRA6	139	.	1	Substitution - coding silent(1)	lung(1)	c.G1110A						.						105.0	110.0	108.0					5																	161128527		2203	4300	6503	SO:0001819	synonymous_variant	2559	exon9			TCATCTGAAGAAA		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4080	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 6"""	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.1110G>A	chr5.hg19:g.161128527G>A		88.0	0.0		40.0	2.0	NM_000811	A8K096|Q4VAV2	Silent	SNP	ENST00000274545.5	hg19	CCDS4356.1																																																																																			.	.		0.383	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2		
TENM2	57451	hgsc.bcm.edu	37	5	167489119	167489119	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:167489119G>T	ENST00000518659.1	+	7	1403	c.1364G>T	c.(1363-1365)cGg>cTg	p.R455L	TENM2_ENST00000519204.1_Missense_Mutation_p.R334L|TENM2_ENST00000403607.2_Missense_Mutation_p.R288L|TENM2_ENST00000520394.1_Missense_Mutation_p.R223L|TENM2_ENST00000545108.1_Missense_Mutation_p.R455L	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	455					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R288Q(1)									GAAGTTGGTCGGCGGGTAACA	0.463																																					p.R455L		Atlas-SNP	.											ODZ2,colon,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1364T						.						81.0	84.0	83.0					5																	167489119		1851	4098	5949	SO:0001583	missense	57451	exon7			TTGGTCGGCGGGT	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.1364G>T	chr5.hg19:g.167489119G>T	ENSP00000429430:p.Arg455Leu	127.0	1.0		75.0	3.0	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.12	3.033741	0.54896	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05	5.63	5.63	0.86233	.	0.055296	0.64402	D	0.000002	T	0.34861	0.0912	M	0.69823	2.125	0.45979	D	0.998796	P;P;P	0.46784	0.884;0.785;0.853	P;B;P	0.48738	0.588;0.355;0.507	T	0.06110	-1.0845	10	0.56958	D	0.05	.	14.8382	0.70201	0.0705:0.0:0.9295:0.0	.	455;223;334	Q9NT68;F8VNQ3;G3V106	TEN2_HUMAN;.;.	L	455;455;334;223;288	ENSP00000429430:R455L;ENSP00000438635:R455L;ENSP00000428964:R334L;ENSP00000427874:R223L;ENSP00000384905:R288L	ENSP00000384905:R288L	R	+	2	0	ODZ2	167421697	1.000000	0.71417	0.440000	0.26846	0.961000	0.63080	8.017000	0.88712	2.644000	0.89710	0.655000	0.94253	CGG	.	.		0.463	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
WWC1	23286	hgsc.bcm.edu	37	5	167882362	167882362	+	Splice_Site	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:167882362T>C	ENST00000265293.4	+	19	3162	c.2660T>C	c.(2659-2661)gTg>gCg	p.V887A	WWC1_ENST00000522140.1_3'UTR|WWC1_ENST00000521089.1_Splice_Site_p.V887A	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	887	Interaction with histone H3.				cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		CTTCCTCAGGTGGACAAAGAG	0.612																																					p.V887A		Atlas-SNP	.											.	WWC1	98	.	0			c.T2660C						.						108.0	113.0	111.0					5																	167882362		2203	4300	6503	SO:0001630	splice_region_variant	23286	exon19			CTCAGGTGGACAA	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"""WW, C2 and coiled-coil domain containing"""	29435	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 168"""	610533	"""WW, C2 and coiled-coil domain containing 1"""			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2659-1T>C	chr5.hg19:g.167882362T>C		199.0	0.0		99.0	4.0	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	hg19	CCDS4366.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.862617	0.91511	.	.	ENSG00000113645	ENST00000265293;ENST00000521089;ENST00000524038	T;T;T	0.58940	0.3;0.3;0.3	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.72285	0.3441	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.80764	0.99;0.994	T	0.73107	-0.4087	10	0.48119	T	0.1	.	15.5525	0.76164	0.0:0.0:0.0:1.0	.	887;887	Q8IX03-2;Q8IX03	.;KIBRA_HUMAN	A	887;887;213	ENSP00000265293:V887A;ENSP00000427772:V887A;ENSP00000428084:V213A	ENSP00000265293:V887A	V	+	2	0	WWC1	167814940	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.203000	0.72137	2.070000	0.61991	0.533000	0.62120	GTG	.	.		0.612	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	Missense_Mutation
STK10	6793	hgsc.bcm.edu	37	5	171520874	171520874	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:171520874G>A	ENST00000176763.5	-	9	1439	c.1096C>T	c.(1096-1098)Ctg>Ttg	p.L366L	STK10_ENST00000517775.1_5'Flank	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	366					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTGGGTGCCAGCGGGGTGGAA	0.597																																					p.L366L		Atlas-SNP	.											.	STK10	100	.	0			c.C1096T						.						44.0	49.0	47.0					5																	171520874		2202	4299	6501	SO:0001819	synonymous_variant	6793	exon9			GTGCCAGCGGGGT	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.1096C>T	chr5.hg19:g.171520874G>A		150.0	0.0		95.0	4.0	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	hg19	CCDS34290.1																																																																																			.	.		0.597	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990	
TRIM41	90933	hgsc.bcm.edu	37	5	180651508	180651508	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr5:180651508C>T	ENST00000315073.5	+	1	1219	c.509C>T	c.(508-510)cCa>cTa	p.P170L	TRIM41_ENST00000351937.5_Missense_Mutation_p.P170L|MIR4638_ENST00000581158.1_RNA|CTC-338M12.7_ENST00000499096.2_RNA	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	170					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCGTCACCCCACTGCCCCCG	0.642																																					p.P170L		Atlas-SNP	.											.	TRIM41	96	.	0			c.C509T						.						45.0	51.0	49.0					5																	180651508		2203	4300	6503	SO:0001583	missense	90933	exon1			TCACCCCACTGCC	AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19013	protein-coding gene	gene with protein product	"""RING-finger protein that interacts with C kinase"""	610530	"""tripartite motif-containing 41"""			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.509C>T	chr5.hg19:g.180651508C>T	ENSP00000320869:p.Pro170Leu	164.0	0.0		95.0	4.0	NM_201627	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	hg19	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.231936	0.39399	.	.	ENSG00000146063	ENST00000351937;ENST00000315073;ENST00000421508	T;T	0.54279	1.04;0.58	4.55	2.7	0.31948	Zinc finger, RING-type (1);	0.407810	0.20910	N	0.083485	T	0.36608	0.0973	L	0.36672	1.1	0.34627	D	0.719231	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.32402	-0.9908	10	0.21540	T	0.41	.	6.7474	0.23468	0.1827:0.7214:0.0:0.096	.	170;170;170	Q8WV44;Q8WV44-2;Q8WV44-4	TRI41_HUMAN;.;.	L	170;170;49	ENSP00000336749:P170L;ENSP00000320869:P170L	ENSP00000320869:P170L	P	+	2	0	TRIM41	180584114	0.358000	0.24947	0.997000	0.53966	0.767000	0.43475	2.033000	0.41136	0.482000	0.27582	0.491000	0.48974	CCA	.	.		0.642	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627	
HIVEP1	3096	hgsc.bcm.edu	37	6	12161737	12161737	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:12161737G>T	ENST00000379388.2	+	8	6885	c.6553G>T	c.(6553-6555)Gag>Tag	p.E2185*	HIVEP1_ENST00000541134.1_Nonsense_Mutation_p.E50*	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2185					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TGGCCCAGATGAGGATGACAA	0.453																																					p.E2185X		Atlas-SNP	.											.	HIVEP1	242	.	0			c.G6553T						.						79.0	87.0	84.0					6																	12161737		2050	4198	6248	SO:0001587	stop_gained	3096	exon8			CCAGATGAGGATG	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.6553G>T	chr6.hg19:g.12161737G>T	ENSP00000368698:p.Glu2185*	116.0	0.0		99.0	4.0	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Nonsense_Mutation	SNP	ENST00000379388.2	hg19	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	G	36	5.874478	0.97055	.	.	ENSG00000095951	ENST00000379388;ENST00000442081;ENST00000541134;ENST00000542327	.	.	.	5.77	5.77	0.91146	.	0.227351	0.22489	N	0.059383	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-27.6047	19.9827	0.97334	0.0:0.0:1.0:0.0	.	.	.	.	X	2185;112;50;167	.	ENSP00000368698:E2185X	E	+	1	0	HIVEP1	12269723	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	8.955000	0.93058	2.728000	0.93425	0.655000	0.94253	GAG	.	.		0.453	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
GFOD1	54438	hgsc.bcm.edu	37	6	13470694	13470694	+	Intron	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:13470694T>C	ENST00000379287.3	-	1	918				GFOD1_ENST00000379278.3_5'UTR|AL583828.1_ENST00000558378.1_5'UTR|GFOD1_ENST00000603223.1_Missense_Mutation_p.K141R	NM_018988.3	NP_061861.1	Q9NXC2	GFOD1_HUMAN	glucose-fructose oxidoreductase domain containing 1							extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)	18	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)			CCCTAAGGGCTTGAAACCTGT	0.577																																					p.K141R		Atlas-SNP	.											.	GFOD1	38	.	0			c.A422G						.																																			SO:0001627	intron_variant	54438	exon2			AAGGGCTTGAAAC	AK000337	CCDS4524.1, CCDS56397.1, CCDS64351.1	6p24.1-p23	2013-09-19			ENSG00000145990	ENSG00000145990			21096	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 114"""	C6orf114			Standard	NM_018988		Approved	FLJ20330, ADG-90	uc003nat.2	Q9NXC2	OTTHUMG00000014276	ENST00000379287.3:c.253+16175A>G	chr6.hg19:g.13470694T>C		147.0	0.0		98.0	4.0	NM_001242629	A8E4L6|Q5T058|Q96JD4|Q9H5K2	Missense_Mutation	SNP	ENST00000379287.3	hg19	CCDS4524.1																																																																																			.	.		0.577	GFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039902.1	NM_018988	
TDP2	51567	hgsc.bcm.edu	37	6	24653322	24653322	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:24653322C>T	ENST00000378198.4	-	6	866	c.696G>A	c.(694-696)ggG>ggA	p.G232G	TDP2_ENST00000545995.1_Silent_p.G262G|TDP2_ENST00000341060.3_Silent_p.G174G|TDP2_ENST00000478285.1_5'Flank			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	232					cell surface receptor signaling pathway (GO:0007166)|double-strand break repair (GO:0006302)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|PML body (GO:0016605)	5'-tyrosyl-DNA phosphodiesterase activity (GO:0070260)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)|tyrosyl-RNA phosphodiesterase activity (GO:0036317)			kidney(2)|large_intestine(1)|lung(5)|ovary(1)	9						CCGCAGCATGCCCTCTGGTGC	0.423								Direct reversal of damage																													p.G232G		Atlas-SNP	.											.	TDP2	29	.	0			c.G696A						.						231.0	244.0	239.0					6																	24653322		2203	4300	6503	SO:0001819	synonymous_variant	51567	exon6			AGCATGCCCTCTG	AJ269473	CCDS4557.1	6p22.3-p22.1	2010-05-07	2010-05-07	2010-05-07	ENSG00000111802	ENSG00000111802	3.1.4.-		17768	protein-coding gene	gene with protein product		605764	"""TRAF and TNF receptor associated protein"""	TTRAP		11478795	Standard	NM_016614		Approved		uc003nej.3	O95551	OTTHUMG00000014360	ENST00000378198.4:c.696G>A	chr6.hg19:g.24653322C>T		138.0	0.0		113.0	5.0	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Silent	SNP	ENST00000378198.4	hg19	CCDS4557.1																																																																																			.	.		0.423	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1		
BTN2A1	11120	hgsc.bcm.edu	37	6	26463600	26463600	+	Missense_Mutation	SNP	C	C	T	rs368618565		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:26463600C>T	ENST00000312541.5	+	4	807	c.559C>T	c.(559-561)Cct>Tct	p.P187S	BTN2A1_ENST00000469185.1_Missense_Mutation_p.P187S|BTN2A1_ENST00000429381.1_Missense_Mutation_p.P187S|BTN2A1_ENST00000541522.1_Missense_Mutation_p.P126S	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	187					lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						TGGGGTTGCGCCTGCCCTGAA	0.597																																					p.P187S		Atlas-SNP	.											.	BTN2A1	118	.	0			c.C559T						.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	0,4406		0,0,2203	96.0	86.0	89.0		376,559,559,559	2.9	0.0	6		89	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense,missense	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	74,74,74,74	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	126/467,187/331,187/528,187/335	26463600	2,13004	2203	4300	6503	SO:0001583	missense	11120	exon4			GTTGCGCCTGCCC	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.559C>T	chr6.hg19:g.26463600C>T	ENSP00000312158:p.Pro187Ser	79.0	0.0		67.0	4.0	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	hg19	CCDS4613.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.559823	0.27827	0.0	2.33E-4	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	2.88	2.88	0.33553	CD80-like, immunoglobulin C2-set (1);	0.271298	0.27176	N	0.020578	T	0.19208	0.0461	M	0.64170	1.965	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.01225	-1.1413	10	0.41790	T	0.15	.	11.9438	0.52915	0.0:1.0:0.0:0.0	.	187;187	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	S	187;126;187;187;187	ENSP00000312158:P187S;ENSP00000443909:P126S;ENSP00000416945:P187S;ENSP00000419043:P187S	ENSP00000265424:P187S	P	+	1	0	BTN2A1	26571579	0.000000	0.05858	0.018000	0.16275	0.004000	0.04260	0.167000	0.16602	1.896000	0.54893	0.561000	0.74099	CCT	.	.		0.597	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
ZKSCAN8	7745	hgsc.bcm.edu	37	6	28121227	28121227	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:28121227A>G	ENST00000330236.6	+	6	1353	c.1169A>G	c.(1168-1170)aAc>aGc	p.N390S	ZKSCAN8_ENST00000457389.2_Missense_Mutation_p.N390S	NM_001278119.1|NM_001278121.1|NM_001278122.1|NM_006298.2	NP_001265048.1|NP_001265050.1|NP_001265051.1|NP_006289.2	Q15776	ZKSC8_HUMAN	zinc finger with KRAB and SCAN domains 8	390					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)										TTCAGTCAGAACACAGGCCTG	0.483																																					p.N390S		Atlas-SNP	.											.	.	.	.	0			c.A1169G						.						157.0	160.0	159.0					6																	28121227		2203	4300	6503	SO:0001583	missense	7745	exon6			GTCAGAACACAGG		CCDS4645.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000198315	ENSG00000198315		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12983	protein-coding gene	gene with protein product		602240	"""zinc finger protein 192"""	ZNF192			Standard	NM_001278119		Approved	LD5-1, ZSCAN40	uc003nkn.2	Q15776	OTTHUMG00000014510	ENST00000330236.6:c.1169A>G	chr6.hg19:g.28121227A>G	ENSP00000332750:p.Asn390Ser	181.0	0.0		161.0	8.0	NM_006298	A1L3D4|B4DYF1|Q4VAR1|Q4VAR2|Q4VAR3|Q9H4T1	Missense_Mutation	SNP	ENST00000330236.6	hg19	CCDS4645.1	.	.	.	.	.	.	.	.	.	.	A	1.016	-0.686274	0.03328	.	.	ENSG00000198315	ENST00000330236;ENST00000457389	T;T	0.13778	2.56;2.56	5.99	5.99	0.97316	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000004	T	0.01976	0.0062	N	0.01219	-0.95	0.80722	D	1	B	0.25850	0.136	B	0.35859	0.212	T	0.34527	-0.9825	10	0.02654	T	1	.	15.4737	0.75461	1.0:0.0:0.0:0.0	.	390	Q15776	ZN192_HUMAN	S	390	ENSP00000332750:N390S;ENSP00000402948:N390S	ENSP00000332750:N390S	N	+	2	0	ZNF192	28229206	0.000000	0.05858	0.998000	0.56505	0.995000	0.86356	-0.014000	0.12656	2.300000	0.77407	0.533000	0.62120	AAC	.	.		0.483	ZKSCAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040178.2		
NKAPL	222698	hgsc.bcm.edu	37	6	28227461	28227461	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:28227461A>G	ENST00000343684.3	+	1	364	c.312A>G	c.(310-312)gaA>gaG	p.E104E	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	104										breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						ATGCAGAAGAACGGCAGTCAG	0.582																																					p.E104E		Atlas-SNP	.											.	NKAPL	72	.	0			c.A312G						.						69.0	68.0	69.0					6																	28227461		2203	4300	6503	SO:0001819	synonymous_variant	222698	exon1			AGAAGAACGGCAG	BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 194"""	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.312A>G	chr6.hg19:g.28227461A>G		74.0	0.0		92.0	4.0	NM_001007531	Q3MIV1|Q9H4Q7	Silent	SNP	ENST00000343684.3	hg19	CCDS34353.1																																																																																			.	.		0.582	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1		
ZSCAN31	64288	hgsc.bcm.edu	37	6	28297130	28297130	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:28297130C>T	ENST00000414429.1	-	6	1234	c.331G>A	c.(331-333)Gtg>Atg	p.V111M	ZSCAN31_ENST00000344279.6_Missense_Mutation_p.V111M|ZSCAN31_ENST00000439158.1_Missense_Mutation_p.V111M|ZSCAN31_ENST00000396838.2_Missense_Mutation_p.V111M|ZSCAN31_ENST00000446474.1_Intron|ZSCAN31_ENST00000481934.1_5'Flank			Q96LW9	ZSC31_HUMAN	zinc finger and SCAN domain containing 31	111	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				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)										ACTACAGCCACAGCCTCCTCC	0.527																																					p.V111M		Atlas-SNP	.											.	.	.	.	0			c.G331A						.						142.0	159.0	153.0					6																	28297130		2203	4300	6503	SO:0001583	missense	64288	exon2			CAGCCACAGCCTC		CCDS4649.1, CCDS59001.1	6p	2013-01-09	2013-01-08	2013-01-08	ENSG00000235109	ENSG00000235109		"""-"", ""Zinc fingers, C2H2-type"""	14097	protein-coding gene	gene with protein product		610794	"""zinc finger protein 310 pseudogene"", ""zinc finger protein 323"""	ZNF310P, ZNF323			Standard	NM_001135216		Approved		uc003nla.3	Q96LW9	OTTHUMG00000014518	ENST00000414429.1:c.331G>A	chr6.hg19:g.28297130C>T	ENSP00000390076:p.Val111Met	124.0	0.0		99.0	4.0	NM_030899	Q6P178|Q8WWS5	Missense_Mutation	SNP	ENST00000414429.1	hg19	CCDS4649.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.459795	0.84317	.	.	ENSG00000235109	ENST00000396838;ENST00000439158;ENST00000414429;ENST00000344279;ENST00000453745;ENST00000439636;ENST00000447021	T;T;T;T;T;T;T	0.06294	3.32;3.32;3.32;3.32;3.32;3.32;3.32	4.68	2.89	0.33648	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.14874	0.0359	H	0.99404	4.55	0.09310	N	1	P	0.38551	0.636	P	0.44732	0.459	T	0.21245	-1.0251	9	0.87932	D	0	.	7.454	0.27255	0.0:0.7255:0.0:0.2745	.	111	Q96LW9	ZN323_HUMAN	M	111	ENSP00000380050:V111M;ENSP00000413705:V111M;ENSP00000390076:V111M;ENSP00000345339:V111M;ENSP00000389479:V111M;ENSP00000412519:V111M;ENSP00000416108:V111M	ENSP00000345339:V111M	V	-	1	0	ZNF323	28405109	0.002000	0.14202	0.001000	0.08648	0.941000	0.58515	0.911000	0.28584	0.515000	0.28320	0.563000	0.77884	GTG	.	.		0.527	ZSCAN31-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346804.1	NM_030899	
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28333988	28333988	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:28333988A>G	ENST00000377255.3	+	7	1840	c.1543A>G	c.(1543-1545)Aaa>Gaa	p.K515E	ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.K367E|ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.K515E	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	515					autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						TGCGTGTGGAAAAGGCTTCAC	0.423																																					p.K515E		Atlas-SNP	.											.	ZKSCAN3	50	.	0			c.A1543G						.						104.0	103.0	104.0					6																	28333988		2203	4300	6503	SO:0001583	missense	80317	exon6			TGTGGAAAAGGCT	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13853	protein-coding gene	gene with protein product		612791	"""zinc finger protein 306"", ""zinc finger protein 309"""	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.1543A>G	chr6.hg19:g.28333988A>G	ENSP00000366465:p.Lys515Glu	88.0	0.0		72.0	4.0	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	hg19	CCDS4650.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.592151	0.66219	.	.	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.27104	1.69;1.69;1.69	3.97	3.97	0.46021	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32645	0.0836	L	0.53729	1.69	0.31381	N	0.678991	D	0.76494	0.999	D	0.83275	0.996	T	0.09443	-1.0674	9	0.66056	D	0.02	.	11.9945	0.53194	1.0:0.0:0.0:0.0	.	515	Q9BRR0	ZKSC3_HUMAN	E	515;367;515	ENSP00000252211:K515E;ENSP00000341883:K367E;ENSP00000366465:K515E	ENSP00000252211:K515E	K	+	1	0	ZKSCAN3	28441967	1.000000	0.71417	1.000000	0.80357	0.296000	0.27459	4.047000	0.57383	1.666000	0.50821	0.533000	0.62120	AAA	.	.		0.423	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493	
PPP1R10	5514	hgsc.bcm.edu	37	6	30571268	30571268	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:30571268T>C	ENST00000376511.2	-	16	2300	c.1748A>G	c.(1747-1749)gAg>gGg	p.E583G		NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	583	Gly-rich.|Interaction with WDR82. {ECO:0000250}.				protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						GGTGAGGATCTCTTGGACATT	0.567																																					p.E583G		Atlas-SNP	.											.	PPP1R10	60	.	0			c.A1748G						.						97.0	84.0	89.0					6																	30571268		2203	4300	6503	SO:0001583	missense	5514	exon16			AGGATCTCTTGGA	Y13247	CCDS4681.1	6p21.3	2012-04-17	2011-10-04		ENSG00000204569	ENSG00000204569		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9284	protein-coding gene	gene with protein product	"""phosphatase 1 nuclear targeting subunit"", ""HLA-C associated transcript 53"""	603771	"""protein phosphatase 1, regulatory (inhibitor) subunit 10"""			9461602, 9784381	Standard	NM_002714		Approved	PNUTS, FB19, CAT53, p99	uc003nqn.2	Q96QC0	OTTHUMG00000031259	ENST00000376511.2:c.1748A>G	chr6.hg19:g.30571268T>C	ENSP00000365694:p.Glu583Gly	112.0	0.0		72.0	4.0	NM_002714	O00405	Missense_Mutation	SNP	ENST00000376511.2	hg19	CCDS4681.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077578	0.36662	.	.	ENSG00000204569	ENST00000376511	T	0.52295	0.67	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.42877	0.1222	N	0.19112	0.55	0.58432	D	0.999996	D	0.71674	0.998	D	0.78314	0.991	T	0.49634	-0.8919	10	0.49607	T	0.09	-23.2507	13.8155	0.63290	0.0:0.0:0.0:1.0	.	583	Q96QC0	PP1RA_HUMAN	G	583	ENSP00000365694:E583G	ENSP00000365694:E583G	E	-	2	0	PPP1R10	30679247	1.000000	0.71417	1.000000	0.80357	0.172000	0.22775	7.040000	0.76551	1.958000	0.56883	0.383000	0.25322	GAG	.	.		0.567	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714	
GTF2H4	2968	hgsc.bcm.edu	37	6	30876860	30876860	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:30876860G>A	ENST00000259895.4	+	2	270	c.47G>A	c.(46-48)tGc>tAc	p.C16Y	GTF2H4_ENST00000539324.1_Intron|GTF2H4_ENST00000376316.2_Missense_Mutation_p.C16Y|RN7SL175P_ENST00000580375.1_RNA	NM_001517.4	NP_001508.1	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4, 52kDa	16					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						CACCTACAATGCAGGAATCTG	0.547								Nucleotide excision repair (NER)																													p.C16Y		Atlas-SNP	.											GTF2H4_ENST00000259895,colon,carcinoma,0,2	GTF2H4	38	.	0			c.G47A						.						89.0	80.0	83.0					6																	30876860		2203	4300	6503	SO:0001583	missense	2968	exon2			TACAATGCAGGAA	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.47G>A	chr6.hg19:g.30876860G>A	ENSP00000259895:p.Cys16Tyr	43.0	0.0		27.0	2.0	NM_001517	B4DTJ5|Q76KU4	Missense_Mutation	SNP	ENST00000259895.4	hg19	CCDS34386.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454752	0.63290	.	.	ENSG00000213780	ENST00000259895;ENST00000376316;ENST00000453897	T;T	0.45276	0.9;0.9	4.44	4.44	0.53790	.	0.072462	0.56097	U	0.000030	T	0.34948	0.0915	L	0.54323	1.7	0.80722	D	1	P;P;P	0.48998	0.918;0.814;0.814	P;P;P	0.47015	0.534;0.534;0.534	T	0.29671	-1.0004	10	0.59425	D	0.04	-25.7827	14.6358	0.68689	0.0:0.0:1.0:0.0	.	22;16;16	B4DNU0;Q53HH3;Q92759	.;.;TF2H4_HUMAN	Y	16	ENSP00000259895:C16Y;ENSP00000365493:C16Y	ENSP00000259895:C16Y	C	+	2	0	GTF2H4	30984839	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.202000	0.89737	2.300000	0.77407	0.561000	0.74099	TGC	.	.		0.547	GTF2H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076044.3	NM_001517	
CCHCR1	54535	hgsc.bcm.edu	37	6	31113070	31113070	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:31113070T>C	ENST00000376266.5	-	13	1604	c.1482A>G	c.(1480-1482)ctA>ctG	p.L494L	CCHCR1_ENST00000396263.2_Silent_p.L441L|CCHCR1_ENST00000451521.2_Silent_p.L547L|CCHCR1_ENST00000396268.3_Silent_p.L583L	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	494					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						CCGGTGGTGGTAGGGGACAGC	0.597																																					p.L583L		Atlas-SNP	.											.	CCHCR1	68	.	0			c.A1749G						.						36.0	31.0	33.0					6																	31113070		1511	2709	4220	SO:0001819	synonymous_variant	54535	exon13			TGGTGGTAGGGGA	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.1482A>G	chr6.hg19:g.31113070T>C		69.0	0.0		66.0	4.0	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	hg19	CCDS4695.1																																																																																			.	.		0.597	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
TNXB	7148	hgsc.bcm.edu	37	6	32020470	32020470	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:32020470G>A	ENST00000375244.3	-	26	9293	c.9092C>T	c.(9091-9093)cCa>cTa	p.P3031L	TNXB_ENST00000375247.2_Missense_Mutation_p.P3029L			P22105	TENX_HUMAN	tenascin XB	3076	Fibronectin type-III 22. {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						AGCGGACACTGGGCCCACGCG	0.632																																					p.P3029L		Atlas-SNP	.											.	TNXB	553	.	0			c.C9086T						.						54.0	61.0	58.0					6																	32020470		1401	2620	4021	SO:0001583	missense	7148	exon26			GACACTGGGCCCA	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.9092C>T	chr6.hg19:g.32020470G>A	ENSP00000364393:p.Pro3031Leu	182.0	0.0		118.0	5.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	g	20.5	4.002323	0.74932	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.05649	3.41;3.41	4.42	4.42	0.53409	.	0.000000	0.37669	U	0.001999	T	0.22936	0.0554	M	0.93978	3.48	0.41187	D	0.986274	D	0.89917	1.0	D	0.80764	0.994	T	0.16453	-1.0402	10	0.35671	T	0.21	.	13.9305	0.63991	0.0:0.0:1.0:0.0	.	3029	P22105-3	.	L	3031;3029	ENSP00000364393:P3031L;ENSP00000364396:P3029L	ENSP00000364393:P3031L	P	-	2	0	TNXB	32128448	0.998000	0.40836	0.990000	0.47175	0.030000	0.12068	3.413000	0.52686	1.968000	0.57251	0.561000	0.74099	CCA	.	.		0.632	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
TNXB	7148	hgsc.bcm.edu	37	6	32057134	32057134	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:32057134A>G	ENST00000375244.3	-	5	2582	c.2381T>C	c.(2380-2382)tTc>tCc	p.F794S	TNXB_ENST00000375247.2_Missense_Mutation_p.F794S			P22105	TENX_HUMAN	tenascin XB	747	Fibronectin type-III 1. {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						CCGTGCTGTGAATGGGGGGCT	0.612																																					p.F794S		Atlas-SNP	.											.	TNXB	553	.	0			c.T2381C						.						31.0	35.0	33.0					6																	32057134		1947	4146	6093	SO:0001583	missense	7148	exon5			GCTGTGAATGGGG	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.2381T>C	chr6.hg19:g.32057134A>G	ENSP00000364393:p.Phe794Ser	58.0	0.0		65.0	4.0	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	A	18.32	3.597752	0.66332	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.56103	0.48;0.48	5.3	5.3	0.74995	.	.	.	.	.	T	0.36441	0.0967	N	0.05078	-0.115	0.31808	N	0.627477	D	0.76494	0.999	D	0.85130	0.997	T	0.35822	-0.9773	9	0.22706	T	0.39	.	13.2394	0.59987	1.0:0.0:0.0:0.0	.	794	P22105-3	.	S	794	ENSP00000364393:F794S;ENSP00000364396:F794S	ENSP00000364393:F794S	F	-	2	0	TNXB	32165112	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.204000	0.51082	2.231000	0.72958	0.460000	0.39030	TTC	.	.		0.612	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
ATF6B	1388	hgsc.bcm.edu	37	6	32085736	32085736	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:32085736A>G	ENST00000375203.3	-	12	1356	c.1324T>C	c.(1324-1326)Ttc>Ctc	p.F442L	ATF6B_ENST00000375201.4_Missense_Mutation_p.F439L	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	442					response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						TGCTCTGAGAACCCCAGCAAG	0.597																																					p.F442L		Atlas-SNP	.											.	ATF6B	40	.	0			c.T1324C						.						53.0	54.0	54.0					6																	32085736		2203	4300	6503	SO:0001583	missense	1388	exon12			CTGAGAACCCCAG		CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"""basic leucine zipper proteins"""	2349	protein-coding gene	gene with protein product		600984	"""cAMP responsive element binding protein-like 1"""	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.1324T>C	chr6.hg19:g.32085736A>G	ENSP00000364349:p.Phe442Leu	137.0	0.0		91.0	4.0	NM_004381	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Missense_Mutation	SNP	ENST00000375203.3	hg19	CCDS4737.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.623135	0.87460	.	.	ENSG00000213676	ENST00000375203;ENST00000375201	T;T	0.58060	0.36;1.1	5.87	5.87	0.94306	.	0.673373	0.13546	U	0.379841	T	0.48750	0.1517	M	0.79926	2.475	0.36535	D	0.870938	P;P;P	0.47191	0.891;0.553;0.826	P;B;B	0.45610	0.487;0.143;0.292	T	0.53767	-0.8392	10	0.31617	T	0.26	-18.2328	12.6731	0.56878	1.0:0.0:0.0:0.0	.	439;442;442	Q99941-2;Q99941;Q6AZW6	.;ATF6B_HUMAN;.	L	442;439	ENSP00000364349:F442L;ENSP00000364347:F439L	ENSP00000364347:F439L	F	-	1	0	ATF6B	32193714	1.000000	0.71417	0.999000	0.59377	0.947000	0.59692	2.983000	0.49345	2.244000	0.73946	0.533000	0.62120	TTC	.	.		0.597	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2		
TAP1	6890	hgsc.bcm.edu	37	6	32816572	32816572	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:32816572A>G	ENST00000354258.4	-	7	1764	c.1603T>C	c.(1603-1605)Tca>Cca	p.S535P	TAP1_ENST00000425148.2_Missense_Mutation_p.S274P|PSMB9_ENST00000395330.1_Intron|TAPSAR1_ENST00000453426.1_lincRNA	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	535	Involved in peptide-binding site.				antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|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)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	ATTTTCTCTGAGGAGCCCACA	0.522																																					p.S535P		Atlas-SNP	.											.	TAP1	39	.	0			c.T1603C						.						110.0	110.0	110.0					6																	32816572		2203	4300	6503	SO:0001583	missense	6890	exon7			TCTCTGAGGAGCC		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"""ATP binding cassette transporters / subfamily B"""	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.1603T>C	chr6.hg19:g.32816572A>G	ENSP00000346206:p.Ser535Pro	99.0	0.0		89.0	4.0	NM_000593	Q16149|Q96CP4	Missense_Mutation	SNP	ENST00000354258.4	hg19	CCDS4758.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.030456	0.75504	.	.	ENSG00000168394	ENST00000354258;ENST00000425148	T;T	0.80653	-1.4;-1.4	5.02	5.02	0.67125	ABC transporter, transmembrane domain, type 1 (1);	.	.	.	.	D	0.87977	0.6314	M	0.86097	2.795	0.58432	D	0.999999	D	0.89917	1.0	D	0.78314	0.991	D	0.89888	0.4035	9	0.72032	D	0.01	-2.3668	12.7438	0.57268	1.0:0.0:0.0:0.0	.	535	Q03518	TAP1_HUMAN	P	535;274	ENSP00000346206:S535P;ENSP00000401919:S274P	ENSP00000346206:S535P	S	-	1	0	TAP1	32924550	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	5.998000	0.70653	2.106000	0.64143	0.523000	0.50628	TCA	.	.		0.522	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593	
TAP1	6890	hgsc.bcm.edu	37	6	32820940	32820940	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:32820940C>A	ENST00000354258.4	-	1	815	c.654G>T	c.(652-654)ggG>ggT	p.G218G	PSMB9_ENST00000453265.2_5'Flank|PSMB9_ENST00000374859.2_5'Flank|TAP1_ENST00000425148.2_5'Flank|PSMB9_ENST00000395330.1_Intron	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	218					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|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)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	CCCAGAGGCTCCCGAGTTTGT	0.667																																					p.G218G		Atlas-SNP	.											.	TAP1	39	.	0			c.G654T						.						20.0	21.0	21.0					6																	32820940		1508	2707	4215	SO:0001819	synonymous_variant	6890	exon1			GAGGCTCCCGAGT		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"""ATP binding cassette transporters / subfamily B"""	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.654G>T	chr6.hg19:g.32820940C>A		129.0	0.0		103.0	32.0	NM_000593	Q16149|Q96CP4	Silent	SNP	ENST00000354258.4	hg19	CCDS4758.1																																																																																			.	.		0.667	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593	
ZBTB9	221504	hgsc.bcm.edu	37	6	33423704	33423704	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:33423704C>T	ENST00000395064.2	+	2	1095	c.827C>T	c.(826-828)cCt>cTt	p.P276L		NM_152735.3	NP_689948.1	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	276	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(1)|upper_aerodigestive_tract(2)	11						CCTGCCCCTCCTGCACTGCCC	0.562																																					p.P276L		Atlas-SNP	.											.	ZBTB9	23	.	0			c.C827T						.						57.0	59.0	58.0					6																	33423704		2203	4300	6503	SO:0001583	missense	221504	exon2			CCCCTCCTGCACT	AK122644	CCDS4780.1	6p21.31	2013-01-09			ENSG00000213588	ENSG00000213588		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	28323	protein-coding gene	gene with protein product						12477932	Standard	NM_152735		Approved	MGC23166, ZNF919	uc003oeq.3	Q96C00	OTTHUMG00000140180	ENST00000395064.2:c.827C>T	chr6.hg19:g.33423704C>T	ENSP00000378503:p.Pro276Leu	91.0	0.0		96.0	5.0	NM_152735	A2AB19	Missense_Mutation	SNP	ENST00000395064.2	hg19	CCDS4780.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.846482	0.32606	.	.	ENSG00000213588	ENST00000395064	T	0.06608	3.28	4.54	4.54	0.55810	.	7.925470	0.01955	U	0.042929	T	0.02156	0.0067	N	0.19112	0.55	0.21897	N	0.999486	P	0.37423	0.594	B	0.34722	0.188	T	0.32214	-0.9915	10	0.27785	T	0.31	.	12.6515	0.56764	0.0:1.0:0.0:0.0	.	276	Q96C00	ZBTB9_HUMAN	L	276	ENSP00000378503:P276L	ENSP00000378503:P276L	P	+	2	0	ZBTB9	33531682	0.003000	0.15002	0.007000	0.13788	0.850000	0.48378	1.805000	0.38883	2.368000	0.80403	0.655000	0.94253	CCT	.	.		0.562	ZBTB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276533.1	NM_152735	
BRPF3	27154	hgsc.bcm.edu	37	6	36175193	36175193	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:36175193G>T	ENST00000357641.6	+	4	1962	c.1709G>T	c.(1708-1710)cGg>cTg	p.R570L	BRPF3_ENST00000534400.1_Missense_Mutation_p.R570L|BRPF3_ENST00000443324.2_Missense_Mutation_p.R570L|BRPF3_ENST00000534694.1_Missense_Mutation_p.R570L|BRPF3_ENST00000543502.1_Missense_Mutation_p.R570L|BRPF3_ENST00000339717.7_Missense_Mutation_p.R570L	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	570					blood coagulation (GO:0007596)|histone H3 acetylation (GO:0043966)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	cytosol (GO:0005829)|extracellular region (GO:0005576)|MOZ/MORF histone acetyltransferase complex (GO:0070776)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	40						GAGCTGATTCGGAAGAGAGAG	0.547																																					p.R570L		Atlas-SNP	.											.	BRPF3	93	.	0			c.G1709T						.						49.0	47.0	47.0					6																	36175193		2203	4300	6503	SO:0001583	missense	27154	exon4			TGATTCGGAAGAG	AB033112	CCDS34437.1	6p21.31	2008-02-05			ENSG00000096070	ENSG00000096070			14256	protein-coding gene	gene with protein product						10574462	Standard	NM_015695		Approved	KIAA1286	uc003olv.4	Q9ULD4	OTTHUMG00000014589	ENST00000357641.6:c.1709G>T	chr6.hg19:g.36175193G>T	ENSP00000350267:p.Arg570Leu	181.0	0.0		136.0	7.0	NM_015695	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Missense_Mutation	SNP	ENST00000357641.6	hg19	CCDS34437.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.319944	0.81469	.	.	ENSG00000096070	ENST00000357641;ENST00000339717;ENST00000534694;ENST00000543502;ENST00000443324;ENST00000534400	T;T;T;T;T;T	0.20738	2.28;2.31;2.3;2.31;2.3;2.05	4.86	4.86	0.63082	Bromodomain (1);	0.000000	0.85682	D	0.000000	T	0.41604	0.1166	M	0.74546	2.27	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.85130	0.993;0.993;0.997	T	0.43972	-0.9358	10	0.87932	D	0	.	18.3462	0.90322	0.0:0.0:1.0:0.0	.	570;570;570	B7ZLN5;Q17RB6;Q9ULD4	.;.;BRPF3_HUMAN	L	570	ENSP00000350267:R570L;ENSP00000345419:R570L;ENSP00000434501:R570L;ENSP00000445352:R570L;ENSP00000387368:R570L;ENSP00000436504:R570L	ENSP00000345419:R570L	R	+	2	0	BRPF3	36283171	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.751000	0.98889	2.409000	0.81822	0.655000	0.94253	CGG	.	.		0.547	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695	
PPIL1	51645	hgsc.bcm.edu	37	6	36842499	36842499	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:36842499T>C	ENST00000373699.5	-	1	301	c.50A>G	c.(49-51)gAg>gGg	p.E17G	C6orf89_ENST00000359359.2_Intron|C6orf89_ENST00000510325.2_Intron	NM_016059.4	NP_057143.1	Q9Y3C6	PPIL1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 1	17	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			lung(1)|ovary(1)	2						TCACCTGGTCTCCAAGTAAAC	0.657																																					p.E17G		Atlas-SNP	.											.	PPIL1	6	.	0			c.A50G						.						29.0	31.0	30.0					6																	36842499		2203	4300	6503	SO:0001583	missense	51645	exon1			CTGGTCTCCAAGT	AF090992	CCDS4826.1	6p21.1	2008-08-29			ENSG00000137168	ENSG00000137168			9260	protein-coding gene	gene with protein product		601301				10072585, 8978786	Standard	NM_016059		Approved	CYPL1	uc003omu.2	Q9Y3C6	OTTHUMG00000014612	ENST00000373699.5:c.50A>G	chr6.hg19:g.36842499T>C	ENSP00000362803:p.Glu17Gly	158.0	0.0		120.0	5.0	NM_016059	O15001|Q5TDC9	Missense_Mutation	SNP	ENST00000373699.5	hg19	CCDS4826.1	.	.	.	.	.	.	.	.	.	.	T	31	5.063038	0.93898	.	.	ENSG00000137168	ENST00000373699	T	0.24908	1.83	5.62	5.62	0.85841	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.114392	0.56097	D	0.000021	T	0.28896	0.0717	M	0.84846	2.72	0.80722	D	1	P	0.37101	0.582	B	0.41466	0.358	T	0.20273	-1.0280	10	0.66056	D	0.02	.	13.778	0.63066	0.0:0.0:0.0:1.0	.	17	Q9Y3C6	PPIL1_HUMAN	G	17	ENSP00000362803:E17G	ENSP00000362803:E17G	E	-	2	0	PPIL1	36950477	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.465000	0.66725	2.153000	0.67306	0.528000	0.53228	GAG	.	.		0.657	PPIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040382.1		
KIF6	221458	hgsc.bcm.edu	37	6	39552745	39552745	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:39552745A>G	ENST00000287152.7	-	9	1100	c.1006T>C	c.(1006-1008)Tgc>Cgc	p.C336R	KIF6_ENST00000373216.3_Missense_Mutation_p.C336R|KIF6_ENST00000373213.4_Missense_Mutation_p.C175R|KIF6_ENST00000373215.3_Missense_Mutation_p.C336R|KIF6_ENST00000538893.1_Missense_Mutation_p.C336R	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	336	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						GCAAATCTGCAGGTTGATATA	0.303																																					p.C336R		Atlas-SNP	.											.	KIF6	233	.	0			c.T1006C						.						87.0	95.0	92.0					6																	39552745		2203	4300	6503	SO:0001583	missense	221458	exon9			ATCTGCAGGTTGA	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"""Kinesins"""	21202	protein-coding gene	gene with protein product		613919	"""chromosome 6 open reading frame 102"""	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.1006T>C	chr6.hg19:g.39552745A>G	ENSP00000287152:p.Cys336Arg	97.0	0.0		77.0	4.0	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	hg19	CCDS4844.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.163189	0.78226	.	.	ENSG00000164627	ENST00000287152;ENST00000373216;ENST00000373213;ENST00000373215;ENST00000538893;ENST00000441975;ENST00000373211	T;T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66;-0.66	5.65	5.65	0.86999	Kinesin, motor domain (3);	.	.	.	.	T	0.81029	0.4738	M	0.78637	2.42	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.994;0.996;0.996;0.998	D	0.84046	0.0367	9	0.87932	D	0	.	14.4154	0.67145	1.0:0.0:0.0:0.0	.	336;336;336;336	E7EUN7;F6VGH2;Q6ZMV9-3;Q6ZMV9	.;.;.;KIF6_HUMAN	R	336;336;175;336;336;123;127	ENSP00000287152:C336R;ENSP00000362312:C336R;ENSP00000362309:C175R;ENSP00000362311:C336R;ENSP00000441435:C336R;ENSP00000404856:C123R	ENSP00000287152:C336R	C	-	1	0	KIF6	39660723	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.770000	0.91746	2.281000	0.76405	0.528000	0.53228	TGC	.	.		0.303	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027	
GLTSCR1L	23506	hgsc.bcm.edu	37	6	42819934	42819934	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:42819934A>G	ENST00000314073.5	+	7	2120	c.1944A>G	c.(1942-1944)ccA>ccG	p.P648P	GLTSCR1L_ENST00000394168.1_Splice_Site_p.P648P			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	648																	CCACACTGCCAGGTCAGGAGC	0.522																																					p.P648P		Atlas-SNP	.											.	.	.	.	0			c.A1944G						.						92.0	73.0	79.0					6																	42819934		2203	4300	6503	SO:0001630	splice_region_variant	23506	exon6			ACTGCCAGGTCAG	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.1945+1A>G	chr6.hg19:g.42819934A>G		115.0	0.0		123.0	5.0	NM_015349	A1L3W2|Q5TFZ3|Q92514	Silent	SNP	ENST00000314073.5	hg19	CCDS34451.1																																																																																			.	.		0.522	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349	Silent
ZNF318	24149	hgsc.bcm.edu	37	6	43308192	43308192	+	Missense_Mutation	SNP	G	G	T	rs377285454		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:43308192G>T	ENST00000361428.2	-	10	3621	c.3544C>A	c.(3544-3546)Cgc>Agc	p.R1182S	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1182					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			CCAGCTTGGCGGTCCAGATTC	0.443																																					p.R1182S		Atlas-SNP	.											.	ZNF318	175	.	0			c.C3544A						.						41.0	44.0	43.0					6																	43308192		2197	4289	6486	SO:0001583	missense	24149	exon10			CTTGGCGGTCCAG	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"""Zinc fingers, C2H2-type"""	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.3544C>A	chr6.hg19:g.43308192G>T	ENSP00000354964:p.Arg1182Ser	89.0	0.0		59.0	4.0	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	hg19	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	G	17.62	3.435694	0.62955	.	.	ENSG00000171467	ENST00000361428	T	0.49720	0.77	5.69	5.69	0.88448	.	0.057492	0.64402	D	0.000001	T	0.49695	0.1572	M	0.61703	1.905	0.80722	D	1	D	0.54964	0.969	P	0.54460	0.753	T	0.55003	-0.8208	10	0.87932	D	0	-3.3998	13.0671	0.59041	0.0732:0.0:0.9268:0.0	.	1182	Q5VUA4	ZN318_HUMAN	S	1182	ENSP00000354964:R1182S	ENSP00000354964:R1182S	R	-	1	0	ZNF318	43416170	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.058000	0.71126	2.683000	0.91414	0.655000	0.94253	CGC	.	.		0.443	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	
CDC5L	988	hgsc.bcm.edu	37	6	44371614	44371614	+	Missense_Mutation	SNP	A	A	G	rs370695015		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:44371614A>G	ENST00000371477.3	+	6	907	c.608A>G	c.(607-609)aAa>aGa	p.K203R		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	203	Nuclear localization signal. {ECO:0000255}.|Required for interaction with CTNNBL1. {ECO:0000269|PubMed:21385873}.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AAGAAAAGAAAAAGGAAGAGA	0.383																																					p.K203R		Atlas-SNP	.											.	CDC5L	86	.	0			c.A608G						.						57.0	62.0	61.0					6																	44371614		2201	4299	6500	SO:0001583	missense	988	exon6			AAAGAAAAAGGAA	D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"""CDC5 (cell division cycle 5, S. pombe, homolog)-like"", ""CDC5 cell division cycle 5-like (S. pombe)"""			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.608A>G	chr6.hg19:g.44371614A>G	ENSP00000360532:p.Lys203Arg	118.0	0.0		99.0	4.0	NM_001253	Q76N46|Q99974	Missense_Mutation	SNP	ENST00000371477.3	hg19	CCDS4912.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.338606	0.41398	.	.	ENSG00000096401	ENST00000371477	T	0.50277	0.75	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.17365	0.0417	N	0.13140	0.3	0.80722	D	1	B	0.21071	0.051	B	0.24006	0.05	T	0.12293	-1.0553	10	0.13108	T	0.6	-29.085	16.5885	0.84745	1.0:0.0:0.0:0.0	.	203	Q99459	CDC5L_HUMAN	R	203	ENSP00000360532:K203R	ENSP00000360532:K203R	K	+	2	0	CDC5L	44479592	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.093000	0.94163	2.317000	0.78254	0.460000	0.39030	AAA	.	.		0.383	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1		
TNFRSF21	27242	hgsc.bcm.edu	37	6	47202533	47202533	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:47202533C>T	ENST00000296861.2	-	5	2004	c.1611G>A	c.(1609-1611)acG>acA	p.T537T		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	537					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			AAGGCTCCACCGTCAGGAGAG	0.607																																					p.T537T		Atlas-SNP	.											.	TNFRSF21	61	.	0			c.G1611A						.						45.0	42.0	43.0					6																	47202533		2203	4300	6503	SO:0001819	synonymous_variant	27242	exon5			CTCCACCGTCAGG	AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	13469	protein-coding gene	gene with protein product	"""death receptor 6"""	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1611G>A	chr6.hg19:g.47202533C>T		78.0	0.0		48.0	4.0	NM_014452	B2RDI9|Q0D2P5|Q96D86	Silent	SNP	ENST00000296861.2	hg19	CCDS4921.1																																																																																			.	.		0.607	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452	
OPN5	221391	hgsc.bcm.edu	37	6	47763294	47763294	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:47763294A>G	ENST00000371211.2	+	4	779	c.751A>G	c.(751-753)Aca>Gca	p.T251A	OPN5_ENST00000489301.2_Missense_Mutation_p.T251A|OPN5_ENST00000393699.2_Missense_Mutation_p.T251A|OPN5_ENST00000244799.4_3'UTR	NM_181744.3	NP_859528.1	Q6U736	OPN5_HUMAN	opsin 5	251					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|large_intestine(3)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	29						AATGAAACTGACAAAGGTAAG	0.413																																					p.T251A	Melanoma(28;740 973 10870 42660 45347)	Atlas-SNP	.											.	OPN5	58	.	0			c.A751G						.						83.0	74.0	77.0					6																	47763294		2203	4300	6503	SO:0001583	missense	221391	exon4			AAACTGACAAAGG	AY288419	CCDS4923.1	6p12.3	2012-08-08	2004-01-23		ENSG00000124818	ENSG00000124818		"""GPCR / Class A : Opsin receptors"""	19992	protein-coding gene	gene with protein product	"""neuropsin"""	609042	"""transmembrane protein 13"""	TMEM13		14623103, 14623098	Standard	NR_033806		Approved	neuropsin, dJ402H5.1	uc003ozc.3	Q6U736	OTTHUMG00000014803	ENST00000371211.2:c.751A>G	chr6.hg19:g.47763294A>G	ENSP00000360255:p.Thr251Ala	89.0	0.0		92.0	4.0	NM_181744	A0AV33|Q5T5B9|Q5T886|Q7Z603|Q86SL5	Missense_Mutation	SNP	ENST00000371211.2	hg19	CCDS4923.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.165161	0.78339	.	.	ENSG00000124818	ENST00000489301;ENST00000371211;ENST00000393699	T;T;T	0.69926	-0.44;-0.44;-0.44	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.27454	0.0674	N	0.11892	0.195	0.44268	D	0.997121	P	0.36330	0.548	B	0.35727	0.209	T	0.43180	-0.9407	10	0.02654	T	1	.	15.5684	0.76313	1.0:0.0:0.0:0.0	.	251	Q6U736	OPN5_HUMAN	A	251	ENSP00000426991:T251A;ENSP00000360255:T251A;ENSP00000377302:T251A	ENSP00000360255:T251A	T	+	1	0	OPN5	47871253	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	8.962000	0.93254	2.075000	0.62263	0.454000	0.30748	ACA	.	.		0.413	OPN5-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359451.1	NM_181744	
EFHC1	114327	hgsc.bcm.edu	37	6	52329890	52329890	+	Silent	SNP	C	C	A	rs371151471	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:52329890C>A	ENST00000371068.5	+	6	1217	c.1114C>A	c.(1114-1116)Cgg>Agg	p.R372R	EFHC1_ENST00000433625.2_Silent_p.R281R|EFHC1_ENST00000538167.1_Silent_p.R353R	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	372						axoneme (GO:0005930)|neuronal cell body (GO:0043025)	calcium ion binding (GO:0005509)|protein C-terminus binding (GO:0008022)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	27	Lung NSC(77;0.109)					TGTGAGCAAGCGGGAACCACC	0.353																																					p.R372R		Atlas-SNP	.											.	EFHC1	68	.	0			c.C1114A						.						61.0	57.0	58.0					6																	52329890		2203	4300	6503	SO:0001819	synonymous_variant	114327	exon6			AGCAAGCGGGAAC	AK001328	CCDS4942.1, CCDS55021.1	6p12.3	2014-02-04			ENSG00000096093	ENSG00000096093		"""EF-hand domain containing"""	16406	protein-coding gene	gene with protein product	"""myoclonin-1"""	608815	"""epilepsy, juvenile myoclonic 1"""	EJM1, EJM		15258581	Standard	NM_018100		Approved	FLJ10466	uc003pap.4	Q5JVL4	OTTHUMG00000014848	ENST00000371068.5:c.1114C>A	chr6.hg19:g.52329890C>A		121.0	0.0		99.0	4.0	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Silent	SNP	ENST00000371068.5	hg19	CCDS4942.1																																																																																			.	.		0.353	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100	
GFRAL	389400	hgsc.bcm.edu	37	6	55223877	55223877	+	Missense_Mutation	SNP	A	A	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:55223877A>C	ENST00000340465.2	+	6	979	c.893A>C	c.(892-894)cAa>cCa	p.Q298P		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	298					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			ACCATTACACAAAGTGAGGAA	0.393																																					p.Q298P		Atlas-SNP	.											.	GFRAL	91	.	0			c.A893C						.						124.0	115.0	118.0					6																	55223877		2203	4299	6502	SO:0001583	missense	389400	exon6			TTACACAAAGTGA	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 144"""	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.893A>C	chr6.hg19:g.55223877A>C	ENSP00000343636:p.Gln298Pro	134.0	0.0		120.0	63.0	NM_207410	Q5VTF6	Missense_Mutation	SNP	ENST00000340465.2	hg19	CCDS4957.1	.	.	.	.	.	.	.	.	.	.	A	7.534	0.659246	0.14645	.	.	ENSG00000187871	ENST00000340465	T	0.64803	-0.12	5.67	1.57	0.23409	GDNF/GAS1 (2);	0.937809	0.09022	N	0.860045	T	0.24084	0.0583	L	0.39633	1.23	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.13548	-1.0505	10	0.27082	T	0.32	-13.4037	1.733	0.02936	0.3225:0.3345:0.0849:0.2581	.	298	Q6UXV0	GFRAL_HUMAN	P	298	ENSP00000343636:Q298P	ENSP00000343636:Q298P	Q	+	2	0	GFRAL	55331836	0.000000	0.05858	0.113000	0.21522	0.899000	0.52679	0.198000	0.17217	0.385000	0.24970	-0.429000	0.05907	CAA	.	.		0.393	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410	
KIAA1586	57691	hgsc.bcm.edu	37	6	56917492	56917492	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:56917492T>C	ENST00000370733.4	+	4	402	c.195T>C	c.(193-195)ttT>ttC	p.F65F	KIAA1586_ENST00000545356.1_Silent_p.F38F|KIAA1586_ENST00000488682.1_3'UTR	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	65							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			AGATTCTGTTTCCTAAAATGC	0.284																																					p.F65F		Atlas-SNP	.											.	KIAA1586	59	.	0			c.T195C						.						34.0	39.0	37.0					6																	56917492		2196	4297	6493	SO:0001819	synonymous_variant	57691	exon4			TCTGTTTCCTAAA	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.195T>C	chr6.hg19:g.56917492T>C		96.0	0.0		81.0	4.0	NM_020931	A8K4M3|Q8IW25	Silent	SNP	ENST00000370733.4	hg19	CCDS34480.1																																																																																			.	.		0.284	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931	
C6orf165	154313	hgsc.bcm.edu	37	6	88128042	88128042	+	Missense_Mutation	SNP	G	G	A	rs267601154		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:88128042G>A	ENST00000507897.1	+	7	831	c.748G>A	c.(748-750)Gac>Aac	p.D250N	C6ORF165_ENST00000369562.4_Missense_Mutation_p.D250N			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	250										NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		GGCAGCCAACGACCCACTCAT	0.463																																					p.D250N		Atlas-SNP	.											.	C6orf165	116	.	0			c.G748A						.						101.0	100.0	100.0					6																	88128042		2203	4300	6503	SO:0001583	missense	154313	exon7			GCCAACGACCCAC	BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.748G>A	chr6.hg19:g.88128042G>A	ENSP00000426769:p.Asp250Asn	140.0	0.0		81.0	4.0	NM_001031743	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	hg19	CCDS34498.1	.	.	.	.	.	.	.	.	.	.	G	0.023	-1.405130	0.01155	.	.	ENSG00000213204	ENST00000369562;ENST00000480123	T;T	0.32023	1.47;1.49	5.16	3.92	0.45320	.	0.228682	0.49916	N	0.000121	T	0.03136	0.0092	N	0.01817	-0.705	0.22354	N	0.999172	B;B	0.11235	0.003;0.004	B;B	0.06405	0.002;0.002	T	0.44360	-0.9333	10	0.14252	T	0.57	.	9.1397	0.36897	0.8434:0.0:0.1566:0.0	.	250;250	Q8IYR0;E1P509	CF165_HUMAN;.	N	250	ENSP00000358575:D250N;ENSP00000422494:D250N	ENSP00000358575:D250N	D	+	1	0	C6orf165	88184761	0.954000	0.32549	0.606000	0.28943	0.009000	0.06853	2.473000	0.45145	0.908000	0.36671	-0.423000	0.05987	GAC	.	.		0.463	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823	
RARS2	57038	hgsc.bcm.edu	37	6	88229903	88229903	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:88229903T>C	ENST00000369536.5	-	13	1152	c.1107A>G	c.(1105-1107)gcA>gcG	p.A369A	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	369					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		ATTACCTTTCTGCCCAGTCAT	0.353																																					p.A369A		Atlas-SNP	.											.	RARS2	61	.	0			c.A1107G						.						237.0	229.0	232.0					6																	88229903		2203	4300	6503	SO:0001819	synonymous_variant	57038	exon13			CCTTTCTGCCCAG	AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	21406	protein-coding gene	gene with protein product	"""arginine tRNA ligase 2, mitochondrial (putative)"""	611524	"""arginyl-tRNA synthetase-like"""	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.1107A>G	chr6.hg19:g.88229903T>C		179.0	0.0		85.0	4.0	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Silent	SNP	ENST00000369536.5	hg19	CCDS5011.1																																																																																			.	.		0.353	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	
MDN1	23195	hgsc.bcm.edu	37	6	90393616	90393616	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:90393616A>G	ENST00000369393.3	-	72	11952	c.11837T>C	c.(11836-11838)gTt>gCt	p.V3946A	MDN1_ENST00000428876.1_Missense_Mutation_p.V3946A			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3946					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GGAAATCTTAACAAATTCCTG	0.358																																					p.V3946A		Atlas-SNP	.											.	MDN1	478	.	0			c.T11837C						.						86.0	82.0	84.0					6																	90393616		2203	4300	6503	SO:0001583	missense	23195	exon72			ATCTTAACAAATT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.11837T>C	chr6.hg19:g.90393616A>G	ENSP00000358400:p.Val3946Ala	157.0	0.0		93.0	4.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.548634	0.65311	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.50548	0.74;0.74	5.28	5.28	0.74379	.	0.000000	0.64402	D	0.000001	T	0.61553	0.2356	M	0.76838	2.35	0.58432	D	0.999998	D	0.76494	0.999	D	0.78314	0.991	T	0.64373	-0.6423	10	0.42905	T	0.14	.	15.2069	0.73186	1.0:0.0:0.0:0.0	.	3946	Q9NU22	MDN1_HUMAN	A	3946	ENSP00000358400:V3946A;ENSP00000413970:V3946A	ENSP00000358400:V3946A	V	-	2	0	MDN1	90450337	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.339000	0.96797	2.005000	0.58758	0.459000	0.35465	GTT	.	.		0.358	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
GJA10	84694	hgsc.bcm.edu	37	6	90605295	90605295	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:90605295G>T	ENST00000369352.1	+	1	1108	c.1108G>T	c.(1108-1110)Ggt>Tgt	p.G370C	Y_RNA_ENST00000517082.1_RNA	NM_032602.1	NP_115991.1	P57773	CXA9_HUMAN	gap junction protein, alpha 10, 62kDa	407					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|skin(3)|urinary_tract(1)	37		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		GTCCTGGCTAGGTACAACTAC	0.547																																					p.G370C		Atlas-SNP	.											.	GJA10	83	.	0			c.G1108T						.						112.0	105.0	107.0					6																	90605295		2203	4300	6503	SO:0001583	missense	84694	exon1			TGGCTAGGTACAA	AF296766	CCDS5025.1	6q15-q16	2008-02-05			ENSG00000135355	ENSG00000135355		"""Ion channels / Gap junction proteins (connexins)"""	16995	protein-coding gene	gene with protein product	"""connexin 62"""	611924					Standard	NM_032602		Approved	CX62	uc011eaa.2	Q969M2	OTTHUMG00000015210	ENST00000369352.1:c.1108G>T	chr6.hg19:g.90605295G>T	ENSP00000358358:p.Gly370Cys	88.0	0.0		71.0	4.0	NM_032602	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000369352.1	hg19	CCDS5025.1	.	.	.	.	.	.	.	.	.	.	G	10.80	1.453198	0.26161	.	.	ENSG00000135355	ENST00000369352	D	0.99080	-5.4	5.3	3.43	0.39272	.	1.147620	0.06486	N	0.733689	D	0.97832	0.9288	L	0.59436	1.845	0.09310	N	1	D	0.63880	0.993	P	0.53185	0.72	D	0.94379	0.7603	10	0.66056	D	0.02	.	9.0761	0.36522	0.0848:0.1514:0.7638:0.0	.	370	Q969M2	CXA10_HUMAN	C	370	ENSP00000358358:G370C	ENSP00000358358:G370C	G	+	1	0	GJA10	90662016	0.027000	0.19231	0.011000	0.14972	0.199000	0.23934	2.165000	0.42396	1.319000	0.45190	0.563000	0.77884	GGT	.	.		0.547	GJA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041505.1	NM_032602	
EPHA7	2045	hgsc.bcm.edu	37	6	93967190	93967190	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:93967190G>A	ENST00000369303.4	-	12	2346	c.2162C>T	c.(2161-2163)gCa>gTa	p.A721V		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	721	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		CCTGAGAAATGCATCTAGGGC	0.343																																					p.A721V		Atlas-SNP	.											.	EPHA7	251	.	0			c.C2162T						.						84.0	87.0	86.0					6																	93967190		2203	4300	6503	SO:0001583	missense	2045	exon12			AGAAATGCATCTA	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3390	protein-coding gene	gene with protein product		602190	"""EphA7"""			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.2162C>T	chr6.hg19:g.93967190G>A	ENSP00000358309:p.Ala721Val	173.0	0.0		100.0	4.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	hg19	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.972590	0.74246	.	.	ENSG00000135333	ENST00000369303	T	0.62498	0.02	5.87	5.87	0.94306	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.055365	0.64402	D	0.000001	T	0.44829	0.1312	L	0.41236	1.265	0.80722	D	1	B;P;D	0.53619	0.315;0.951;0.961	B;B;B	0.37267	0.025;0.158;0.245	T	0.57051	-0.7877	10	0.87932	D	0	.	20.2119	0.98289	0.0:0.0:1.0:0.0	.	717;716;721	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	V	721	ENSP00000358309:A721V	ENSP00000358309:A721V	A	-	2	0	EPHA7	94023911	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.721000	0.84768	2.784000	0.95788	0.585000	0.79938	GCA	.	.		0.343	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1		
MMS22L	253714	hgsc.bcm.edu	37	6	97613138	97613138	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:97613138T>C	ENST00000275053.4	-	21	3470	c.3205A>G	c.(3205-3207)Att>Gtt	p.I1069V	MMS22L_ENST00000369251.2_Missense_Mutation_p.I1029V	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1069					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						ACTTGCACAATGCATTTCTTT	0.343																																					p.I1069V		Atlas-SNP	.											.	MMS22L	102	.	0			c.A3205G						.						101.0	101.0	101.0					6																	97613138		2203	4300	6503	SO:0001583	missense	253714	exon21			GCACAATGCATTT		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"""chromosome 6 open reading frame 167"""	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.3205A>G	chr6.hg19:g.97613138T>C	ENSP00000275053:p.Ile1069Val	104.0	0.0		73.0	4.0	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	hg19	CCDS5039.1	.	.	.	.	.	.	.	.	.	.	T	1.018	-0.685723	0.03328	.	.	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.30182	1.54;1.54	5.79	-1.5	0.08691	.	0.209158	0.47455	D	0.000227	T	0.06781	0.0173	L	0.34521	1.04	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.39187	-0.9626	10	0.25751	T	0.34	-15.3407	9.128	0.36828	0.0:0.2479:0.0949:0.6572	.	1029;1069	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	V	1069;1029	ENSP00000275053:I1069V;ENSP00000358254:I1029V	ENSP00000275053:I1069V	I	-	1	0	MMS22L	97719859	0.995000	0.38212	0.144000	0.22314	0.083000	0.17756	0.611000	0.24268	-0.404000	0.07610	-1.139000	0.01908	ATT	.	.		0.343	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468	
PNISR	25957	hgsc.bcm.edu	37	6	99856127	99856127	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:99856127G>T	ENST00000369239.5	-	7	898	c.694C>A	c.(694-696)Ctt>Att	p.L232I	PNISR_ENST00000438806.1_Missense_Mutation_p.L232I	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	232						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						CAAGCGGGAAGAGTCCTGCGT	0.363																																					p.L232I		Atlas-SNP	.											.	PNISR	74	.	0			c.C694A						.						85.0	79.0	81.0					6																	99856127		2203	4300	6503	SO:0001583	missense	25957	exon6			CGGGAAGAGTCCT	AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 111"", ""splicing factor, arginine/serine-rich 18"""	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.694C>A	chr6.hg19:g.99856127G>T	ENSP00000358242:p.Leu232Ile	173.0	0.0		121.0	5.0	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Missense_Mutation	SNP	ENST00000369239.5	hg19	CCDS5043.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.028756	0.93518	.	.	ENSG00000132424	ENST00000369239;ENST00000438806	T;T	0.44482	0.92;0.92	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.65873	0.2733	M	0.83483	2.645	0.80722	D	1	D	0.67145	0.996	D	0.80764	0.994	T	0.68062	-0.5508	10	0.87932	D	0	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	232	Q8TF01	PNISR_HUMAN	I	232	ENSP00000358242:L232I;ENSP00000387997:L232I	ENSP00000358242:L232I	L	-	1	0	PNISR	99962848	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.328000	0.65887	2.941000	0.99782	0.655000	0.94253	CTT	.	.		0.363	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870	
HACE1	57531	hgsc.bcm.edu	37	6	105259252	105259252	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:105259252A>G	ENST00000262903.4	-	7	827	c.551T>C	c.(550-552)cTa>cCa	p.L184P	HACE1_ENST00000369125.2_Missense_Mutation_p.L184P	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	184					cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		ACCACTGTCTAGCAAGCACTG	0.358																																					p.L184P		Atlas-SNP	.											.	HACE1	96	.	0			c.T551C						.						107.0	106.0	106.0					6																	105259252		2203	4299	6502	SO:0001583	missense	57531	exon7			CTGTCTAGCAAGC	BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"""Ankyrin repeat domain containing"""	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.551T>C	chr6.hg19:g.105259252A>G	ENSP00000262903:p.Leu184Pro	117.0	0.0		67.0	4.0	NM_020771	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Missense_Mutation	SNP	ENST00000262903.4	hg19	CCDS5050.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.094336	0.56075	.	.	ENSG00000085382	ENST00000262903;ENST00000369125;ENST00000519645	T;T;T	0.72725	-0.68;-0.68;-0.68	5.34	5.34	0.76211	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000001	D	0.87597	0.6217	H	0.96777	3.88	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.81914	0.995;0.977	D	0.91854	0.5494	10	0.87932	D	0	.	14.9585	0.71138	1.0:0.0:0.0:0.0	.	184;184	E9PGP0;Q8IYU2	.;HACE1_HUMAN	P	184;184;140	ENSP00000262903:L184P;ENSP00000358121:L184P;ENSP00000429765:L140P	ENSP00000262903:L184P	L	-	2	0	HACE1	105365945	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.563000	0.82314	2.008000	0.58898	0.460000	0.39030	CTA	.	.		0.358	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095	
AIM1	202	hgsc.bcm.edu	37	6	106999726	106999726	+	Splice_Site	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:106999726G>T	ENST00000369066.3	+	12	4575		c.e12-1		AIM1_ENST00000535438.1_Splice_Site|AIM1_ENST00000487681.1_Splice_Site	NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1						developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		TTGTTTCTTAGATGGGTAGCC	0.328																																					.		Atlas-SNP	.											.	AIM1	161	.	0			c.4089-1G>T						.						79.0	88.0	85.0					6																	106999726		2203	4298	6501	SO:0001630	splice_region_variant	202	exon12			TTCTTAGATGGGT	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.4089-1G>T	chr6.hg19:g.106999726G>T		161.0	0.0		98.0	4.0	NM_001624	Q6P2P0|Q9BTM3	Splice_Site	SNP	ENST00000369066.3	hg19	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	G	36	5.621912	0.96660	.	.	ENSG00000112297	ENST00000369066;ENST00000457437;ENST00000535438	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2723	0.98479	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AIM1	107106419	1.000000	0.71417	0.770000	0.31555	0.944000	0.59088	9.463000	0.97652	2.793000	0.96121	0.563000	0.77884	.	.	.		0.328	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		Intron
REV3L	5980	hgsc.bcm.edu	37	6	111686477	111686477	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:111686477T>C	ENST00000358835.3	-	16	7198	c.6744A>G	c.(6742-6744)acA>acG	p.T2248T	REV3L_ENST00000368805.1_Silent_p.T2248T|REV3L_ENST00000368802.3_Silent_p.T2248T|REV3L_ENST00000435970.1_Silent_p.T2170T			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2248					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CCTTTGCTTGTGTTAACAGTA	0.294								DNA polymerases (catalytic subunits)																													p.T2248T		Atlas-SNP	.											.	REV3L	386	.	0			c.A6744G						.						129.0	120.0	123.0					6																	111686477		2198	4297	6495	SO:0001819	synonymous_variant	5980	exon15			TGCTTGTGTTAAC	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.6744A>G	chr6.hg19:g.111686477T>C		162.0	0.0		89.0	4.0	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	hg19	CCDS5091.2																																																																																			.	.		0.294	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
LAMA4	3910	hgsc.bcm.edu	37	6	112466014	112466014	+	Silent	SNP	G	G	T	rs189313630	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:112466014G>T	ENST00000230538.7	-	19	2872	c.2475C>A	c.(2473-2475)acC>acA	p.T825T	LAMA4_ENST00000389463.4_Silent_p.T818T|LAMA4_ENST00000424408.2_Silent_p.T818T|LAMA4_ENST00000522006.1_Silent_p.T818T	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	825	Domain II and I.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		CAACACTTCTGGTCTGAGCAA	0.517																																					p.T825T		Atlas-SNP	.											LAMA4,right_upper_lobe,carcinoma,0,1	LAMA4	227	.	0			c.C2475A						.						111.0	110.0	110.0					6																	112466014		2203	4300	6503	SO:0001819	synonymous_variant	3910	exon19			ACTTCTGGTCTGA		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.2475C>A	chr6.hg19:g.112466014G>T		45.0	0.0		39.0	2.0	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	hg19	CCDS43491.1																																																																																			.	G|1.000;A|0.000		0.517	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
RSPH4A	345895	hgsc.bcm.edu	37	6	116943931	116943931	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:116943931A>G	ENST00000229554.5	+	2	824	c.687A>G	c.(685-687)ctA>ctG	p.L229L	RSPH4A_ENST00000368581.4_Splice_Site_p.L229L|RSPH4A_ENST00000368580.4_Splice_Site_p.L229L	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	229					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)				breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						GTTTGGATAGATATGATCATC	0.328									Kartagener syndrome																												p.L229L		Atlas-SNP	.											.	RSPH4A	54	.	0			c.A687G						.						56.0	61.0	60.0					6																	116943931		2203	4298	6501	SO:0001630	splice_region_variant	345895	exon2	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGATAGATATGAT		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"""radial spokehead-like 3"""	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.687-1A>G	chr6.hg19:g.116943931A>G		113.0	0.0		97.0	4.0	NM_001161664	B4DSI1|Q3KP24|Q5TD95	Silent	SNP	ENST00000229554.5	hg19	CCDS34521.1																																																																																			.	.		0.328	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892	Silent
SOGA3	387104	hgsc.bcm.edu	37	6	127837004	127837004	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:127837004T>C	ENST00000525778.1	-	2	1501	c.756A>G	c.(754-756)gaA>gaG	p.E252E	SOGA3_ENST00000556132.1_Silent_p.E252E|SOGA3_ENST00000465909.2_Silent_p.E252E|SOGA3_ENST00000481848.2_Silent_p.E252E|SOGA3_ENST00000368268.2_Silent_p.E252E			Q5TF21	SOGA3_HUMAN	SOGA family member 3	252					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											GCAGACATCCTTCTTTCCAGT	0.657																																					p.E252E		Atlas-SNP	.											.	.	.	.	0			c.A756G						.						19.0	24.0	23.0					6																	127837004		1927	4111	6038	SO:0001819	synonymous_variant	387104	exon2			ACATCCTTCTTTC	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.756A>G	chr6.hg19:g.127837004T>C		139.0	0.0		82.0	4.0	NM_001012279		Silent	SNP	ENST00000525778.1	hg19	CCDS43505.1																																																																																			.	.		0.657	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
C6orf58	352999	hgsc.bcm.edu	37	6	127902353	127902353	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:127902353T>C	ENST00000329722.7	+	4	612	c.600T>C	c.(598-600)ttT>ttC	p.F200F		NM_001010905.1	NP_001010905.1	Q6P5S2	CF058_HUMAN	chromosome 6 open reading frame 58	200						extracellular vesicular exosome (GO:0070062)				kidney(3)|large_intestine(3)|liver(1)|lung(7)|pancreas(1)	15				GBM - Glioblastoma multiforme(226;0.0405)|all cancers(137;0.156)		TTAGTAAGTTTGATGATCTGT	0.328																																					p.F200F		Atlas-SNP	.											.	C6orf58	35	.	0			c.T600C						.						108.0	104.0	105.0					6																	127902353		2203	4295	6498	SO:0001819	synonymous_variant	352999	exon4			TAAGTTTGATGAT	BC062712	CCDS34533.1	6q22.33	2011-12-13			ENSG00000184530	ENSG00000184530			20960	protein-coding gene	gene with protein product							Standard	NM_001010905		Approved		uc003qbh.4	Q6P5S2	OTTHUMG00000015530	ENST00000329722.7:c.600T>C	chr6.hg19:g.127902353T>C		128.0	0.0		89.0	4.0	NM_001010905	B4E1I0|Q5VUP2	Silent	SNP	ENST00000329722.7	hg19	CCDS34533.1																																																																																			.	.		0.328	C6orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042152.1	NM_001010905	
PTPRK	5796	hgsc.bcm.edu	37	6	128643368	128643368	+	Missense_Mutation	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:128643368T>A	ENST00000368215.3	-	3	310	c.311A>T	c.(310-312)cAc>cTc	p.H104L	PTPRK_ENST00000368213.5_Missense_Mutation_p.H104L|PTPRK_ENST00000368227.3_Missense_Mutation_p.H104L|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000532331.1_Missense_Mutation_p.H104L|PTPRK_ENST00000368207.3_Missense_Mutation_p.H104L|PTPRK_ENST00000368210.3_Missense_Mutation_p.H104L|PTPRK_ENST00000368226.4_Missense_Mutation_p.H104L|PTPRK_ENST00000525459.1_Missense_Mutation_p.H104L			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	104	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		ATCAATGCAGTGAGTGTCGTT	0.418																																					p.H104L		Atlas-SNP	.											.	PTPRK	330	.	0			c.A311T						.						156.0	147.0	150.0					6																	128643368		2203	4299	6502	SO:0001583	missense	5796	exon3			ATGCAGTGAGTGT	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.311A>T	chr6.hg19:g.128643368T>A	ENSP00000357198:p.His104Leu	134.0	0.0		95.0	4.0	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	hg19		.	.	.	.	.	.	.	.	.	.	T	32	5.151204	0.94645	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000525459	T;T;T;T;T;T;T;T	0.02140	4.43;4.43;4.43;4.43;4.43;4.43;4.43;4.43	6.06	6.06	0.98353	Concanavalin A-like lectin/glucanase (1);MAM domain (5);	0.122378	0.53938	D	0.000045	T	0.06188	0.0160	L	0.54965	1.715	0.58432	D	0.999993	D;D;D;D;D;D	0.89917	1.0;0.994;0.998;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.969;0.948;0.999;1.0;0.999	T	0.15694	-1.0428	10	0.87932	D	0	.	15.8056	0.78506	0.0:0.0:0.0:1.0	.	104;104;104;104;104;104	B4DHC3;B7ZMG0;Q15262-3;E9PRW2;Q15262;Q15262-2	.;.;.;.;PTPRK_HUMAN;.	L	104	ENSP00000357209:H104L;ENSP00000357210:H104L;ENSP00000432973:H104L;ENSP00000357196:H104L;ENSP00000357193:H104L;ENSP00000357198:H104L;ENSP00000357190:H104L;ENSP00000434116:H104L	ENSP00000357190:H104L	H	-	2	0	PTPRK	128685061	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.040000	0.89188	2.323000	0.78572	0.528000	0.53228	CAC	.	.		0.418	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1		
ARHGAP18	93663	hgsc.bcm.edu	37	6	129950526	129950526	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:129950526T>C	ENST00000368149.2	-	5	846	c.758A>G	c.(757-759)aAg>aGg	p.K253R		NM_033515.2	NP_277050.2			Rho GTPase activating protein 18											NS(2)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(3)	18				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)		GCCTTTGCTCTTCTGGATTTT	0.413																																					p.K253R		Atlas-SNP	.											.	ARHGAP18	52	.	0			c.A758G						.						130.0	128.0	129.0					6																	129950526		2203	4300	6503	SO:0001583	missense	93663	exon5			TTGCTCTTCTGGA	AB053293	CCDS34535.1	6q23.1	2011-06-29			ENSG00000146376	ENSG00000146376		"""Rho GTPase activating proteins"""	21035	protein-coding gene	gene with protein product		613351					Standard	NM_033515		Approved	MacGAP, bA307O14.2	uc003qbr.3	Q8N392	OTTHUMG00000015547	ENST00000368149.2:c.758A>G	chr6.hg19:g.129950526T>C	ENSP00000357131:p.Lys253Arg	158.0	0.0		89.0	4.0	NM_033515		Missense_Mutation	SNP	ENST00000368149.2	hg19	CCDS34535.1	.	.	.	.	.	.	.	.	.	.	T	4.882	0.163997	0.09287	.	.	ENSG00000146376	ENST00000368149;ENST00000275189	.	.	.	5.49	-1.45	0.08828	.	0.471085	0.25561	N	0.029835	T	0.05593	0.0147	N	0.17723	0.515	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.36456	-0.9747	8	.	.	.	.	4.3617	0.11205	0.2118:0.2751:0.0:0.5131	.	253;253	A9UK01;Q8N392	.;RHG18_HUMAN	R	208;253	.	.	K	-	2	0	ARHGAP18	129992219	0.000000	0.05858	0.013000	0.15412	0.058000	0.15608	0.200000	0.17257	-0.083000	0.12618	-0.250000	0.11733	AAG	.	.		0.413	ARHGAP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042185.2	NM_033515	
L3MBTL3	84456	hgsc.bcm.edu	37	6	130407320	130407320	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:130407320T>C	ENST00000529410.1	+	18	1922	c.1443T>C	c.(1441-1443)ctT>ctC	p.L481L	L3MBTL3_ENST00000368136.2_Silent_p.L481L|L3MBTL3_ENST00000368139.2_Silent_p.L456L|L3MBTL3_ENST00000361794.2_Silent_p.L481L|L3MBTL3_ENST00000533560.1_Silent_p.L456L|L3MBTL3_ENST00000526019.1_Silent_p.L456L			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	481					chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		AAATGAAGCTTGAGGTTGTAG	0.398																																					p.L481L		Atlas-SNP	.											.	L3MBTL3	99	.	0			c.T1443C						.						151.0	171.0	164.0					6																	130407320		2203	4300	6503	SO:0001819	synonymous_variant	84456	exon16			GAAGCTTGAGGTT	AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"""Sterile alpha motif (SAM) domain containing"""	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.1443T>C	chr6.hg19:g.130407320T>C		159.0	0.0		98.0	4.0	NM_032438	Q4VXE1|Q5VUM9|Q6P9B5	Silent	SNP	ENST00000529410.1	hg19	CCDS34537.1																																																																																			.	.		0.398	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074	
TMEM200A	114801	hgsc.bcm.edu	37	6	130762130	130762130	+	Nonsense_Mutation	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:130762130T>A	ENST00000296978.3	+	3	1434	c.563T>A	c.(562-564)tTg>tAg	p.L188*	TMEM200A_ENST00000392429.1_Nonsense_Mutation_p.L188*|TMEM200A_ENST00000545622.1_Nonsense_Mutation_p.L188*	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	188						integral component of membrane (GO:0016021)				NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		TACACTGGTTTGATGGGAGAA	0.448																																					p.L188X		Atlas-SNP	.											.	TMEM200A	108	.	0			c.T563A						.						96.0	89.0	91.0					6																	130762130		2203	4300	6503	SO:0001587	stop_gained	114801	exon3			CTGGTTTGATGGG	AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"""KIAA1913"""	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.563T>A	chr6.hg19:g.130762130T>A	ENSP00000296978:p.Leu188*	194.0	0.0		80.0	4.0	NM_001258277	Q96PX5	Nonsense_Mutation	SNP	ENST00000296978.3	hg19	CCDS5140.1	.	.	.	.	.	.	.	.	.	.	T	53	20.462260	0.99931	.	.	ENSG00000164484	ENST00000296978;ENST00000545622;ENST00000392429	.	.	.	5.46	3.01	0.34805	.	0.596635	0.18460	N	0.140553	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.0425	0.30529	0.0:0.0706:0.1365:0.7928	.	.	.	.	X	188	.	ENSP00000296978:L188X	L	+	2	0	TMEM200A	130803823	0.172000	0.23043	0.109000	0.21407	0.920000	0.55202	1.661000	0.37408	0.348000	0.23949	0.533000	0.62120	TTG	.	.		0.448	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913	
TBPL1	9519	hgsc.bcm.edu	37	6	134304019	134304019	+	Splice_Site	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:134304019G>A	ENST00000237264.4	+	4	557		c.e4+1		TBPL1_ENST00000477527.1_Splice_Site|TBPL1_ENST00000367871.1_Splice_Site	NM_001253676.1|NM_004865.3	NP_001240605.1|NP_004856.1	P62380	TBPL1_HUMAN	TBP-like 1						acrosome assembly (GO:0001675)|DNA-templated transcription, initiation (GO:0006352)|dTTP biosynthetic process (GO:0006235)|regulation of transcription, DNA-templated (GO:0006355)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	6	Colorectal(23;0.221)|Breast(56;0.247)			GBM - Glioblastoma multiforme(68;0.00591)|OV - Ovarian serous cystadenocarcinoma(155;0.00848)		AGGTTTTCAGGTAACGTTTTC	0.323																																					.		Atlas-SNP	.											.	TBPL1	20	.	0			c.282+1G>A						.						68.0	66.0	67.0					6																	134304019		2201	4299	6500	SO:0001630	splice_region_variant	9519	exon4			TTTCAGGTAACGT	AB020881	CCDS5168.1	6q22.1-q22.3	2008-05-23			ENSG00000028839	ENSG00000028839			11589	protein-coding gene	gene with protein product		605521				10082669, 10220372, 15767669	Standard	NM_001253676		Approved	TLP, STUD, TRF2, TLF	uc010kgg.3	P62380	OTTHUMG00000015609	ENST00000237264.4:c.282+1G>A	chr6.hg19:g.134304019G>A		195.0	0.0		121.0	5.0	NM_001253676	A8K8F5|O95753|Q9BWD5|Q9Z2Z0	Splice_Site	SNP	ENST00000237264.4	hg19	CCDS5168.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.193057	0.58017	.	.	ENSG00000028839	ENST00000416965;ENST00000367871;ENST00000237264	.	.	.	5.99	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4606	0.61225	0.0:0.0:0.8431:0.1569	.	.	.	.	.	-1	.	.	.	+	.	.	TBPL1	134345712	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	7.371000	0.79600	1.501000	0.48654	0.655000	0.94253	.	.	.		0.323	TBPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042294.2		Intron
HBS1L	10767	hgsc.bcm.edu	37	6	135358603	135358603	+	Intron	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:135358603T>C	ENST00000367837.5	-	4	637				HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367822.5_Missense_Mutation_p.E331G|HBS1L_ENST00000367824.4_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		AGTCATATTTTCCAACGAGCT	0.289																																					p.E331G		Atlas-SNP	.											.	HBS1L	75	.	0			c.A992G						.						32.0	26.0	28.0					6																	135358603		692	1590	2282	SO:0001627	intron_variant	10767	exon5			ATATTTTCCAACG	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+2107A>G	chr6.hg19:g.135358603T>C		214.0	0.0		122.0	5.0	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	hg19	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	T	13.07	2.128182	0.37533	.	.	ENSG00000112339	ENST00000367822	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	T	0.31104	0.0786	.	.	.	0.80722	D	1	B	0.27559	0.181	B	0.30646	0.118	T	0.42599	-0.9442	7	0.54805	T	0.06	.	4.8834	0.13690	0.0:0.1141:0.1863:0.6996	.	331	Q9Y450-2	.	G	331	.	ENSP00000356796:E331G	E	-	2	0	HBS1L	135400296	1.000000	0.71417	0.998000	0.56505	0.510000	0.34073	2.111000	0.41883	2.194000	0.70268	0.533000	0.62120	GAA	.	.		0.289	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
MAP3K5	4217	hgsc.bcm.edu	37	6	136882716	136882716	+	Silent	SNP	G	G	T	rs371929460		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:136882716G>T	ENST00000359015.4	-	28	4302	c.3942C>A	c.(3940-3942)acC>acA	p.T1314T	MAP3K5_ENST00000355845.4_Silent_p.T561T	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	1314			T -> I (in dbSNP:rs45599539). {ECO:0000269|PubMed:17344846}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		TCAGCCAGTCGGTAAGTTCAG	0.373																																					p.T1314T		Atlas-SNP	.											.	MAP3K5	136	.	0			c.C3942A						.						94.0	93.0	93.0					6																	136882716		2203	4300	6503	SO:0001819	synonymous_variant	4217	exon28			CCAGTCGGTAAGT	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6857	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 1"""	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.3942C>A	chr6.hg19:g.136882716G>T		218.0	0.0		128.0	9.0	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	hg19	CCDS5179.1																																																																																			.	.		0.373	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1		
HECA	51696	hgsc.bcm.edu	37	6	139487731	139487731	+	Silent	SNP	G	G	T	rs529104889		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:139487731G>T	ENST00000367658.2	+	2	867	c.582G>T	c.(580-582)gtG>gtT	p.V194V	RP1-225E12.2_ENST00000589192.1_RNA|RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000586229.1_RNA|RP1-225E12.2_ENST00000590679.1_RNA|RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.3_ENST00000585874.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.2_ENST00000591102.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	194					respiratory tube development (GO:0030323)	membrane (GO:0016020)				endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		GGTATCAGGTGAAGCGGATGC	0.577																																					p.V194V		Atlas-SNP	.											.	HECA	45	.	0			c.G582T						.						71.0	77.0	75.0					6																	139487731		2203	4300	6503	SO:0001819	synonymous_variant	51696	exon2			TCAGGTGAAGCGG	AB033492	CCDS5194.1	6q23-q24	2010-11-25			ENSG00000112406	ENSG00000112406			21041	protein-coding gene	gene with protein product		607977				11696983, 19643820	Standard	NM_016217		Approved	HDCL, hHDC, HDC, dJ225E12.1	uc003qin.3	Q9UBI9	OTTHUMG00000015686	ENST00000367658.2:c.582G>T	chr6.hg19:g.139487731G>T		162.0	0.0		65.0	4.0	NM_016217		Silent	SNP	ENST00000367658.2	hg19	CCDS5194.1																																																																																			.	.		0.577	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217	
ADAT2	134637	hgsc.bcm.edu	37	6	143755117	143755117	+	Splice_Site	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:143755117G>A	ENST00000237283.8	-	3	217	c.203C>T	c.(202-204)gCt>gTt	p.A68V	ADAT2_ENST00000606514.1_Splice_Site_p.A21V	NM_182503.2	NP_872309.2	Q7Z6V5	ADAT2_HUMAN	adenosine deaminase, tRNA-specific 2	68					tRNA wobble adenosine to inosine editing (GO:0002100)		tRNA-specific adenosine deaminase activity (GO:0008251)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(3)|lung(3)	8				OV - Ovarian serous cystadenocarcinoma(155;5.61e-06)|GBM - Glioblastoma multiforme(68;0.0115)		ATGTCGAGTAGCCTGAAAAGA	0.418																																					p.A68V		Atlas-SNP	.											.	ADAT2	18	.	0			c.C203T						.						131.0	125.0	127.0					6																	143755117		1979	4158	6137	SO:0001630	splice_region_variant	134637	exon3			CGAGTAGCCTGAA	BC037955	CCDS43511.1, CCDS69219.1	6q24.2	2014-01-28	2011-05-19	2007-08-16	ENSG00000189007	ENSG00000189007			21172	protein-coding gene	gene with protein product	tRNA-specific adenosine deaminase 2 homolog (S. cerevisiae)	615388	"""deaminase domain containing 1"", ""adenosine deaminase, tRNA-specific 2, TAD2 homolog (S. cerevisiae)"""	DEADC1		12457566	Standard	NM_182503		Approved	dJ20N2.1, TAD2	uc003qjj.3	Q7Z6V5	OTTHUMG00000015725	ENST00000237283.8:c.202-1C>T	chr6.hg19:g.143755117G>A		37.0	0.0		25.0	17.0	NM_182503	A6NL12|B3KWY3|Q7Z327|Q8IY39	Missense_Mutation	SNP	ENST00000237283.8	hg19	CCDS43511.1	.	.	.	.	.	.	.	.	.	.	G	32	5.119043	0.94385	.	.	ENSG00000189007	ENST00000367594;ENST00000237283	T	0.41758	0.99	4.37	4.37	0.52481	Cytidine deaminase-like (1);CMP/dCMP deaminase, zinc-binding (1);	0.000000	0.85682	D	0.000000	T	0.52853	0.1760	L	0.55017	1.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.56811	-0.7917	10	0.59425	D	0.04	-17.6129	17.1223	0.86705	0.0:0.0:1.0:0.0	.	68	Q7Z6V5	ADAT2_HUMAN	V	21;68	ENSP00000237283:A68V	ENSP00000237283:A68V	A	-	2	0	ADAT2	143796810	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.782000	0.91809	2.254000	0.74563	0.650000	0.86243	GCT	.	.		0.418	ADAT2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042517.1	XM_059727	Missense_Mutation
SHPRH	257218	hgsc.bcm.edu	37	6	146243830	146243830	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:146243830G>T	ENST00000367505.2	-	19	3952	c.3688C>A	c.(3688-3690)Cac>Aac	p.H1230N	SHPRH_ENST00000438092.2_Missense_Mutation_p.H1234N|SHPRH_ENST00000275233.7_Missense_Mutation_p.H1230N|SHPRH_ENST00000367503.3_Missense_Mutation_p.H1234N			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1230					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		GGTCGGAGGTGACAGACTGTT	0.403																																					p.H1234N		Atlas-SNP	.											.	SHPRH	169	.	0			c.C3700A						.						87.0	87.0	87.0					6																	146243830		1888	4104	5992	SO:0001583	missense	257218	exon19			GGAGGTGACAGAC	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.3688C>A	chr6.hg19:g.146243830G>T	ENSP00000356475:p.His1230Asn	94.0	0.0		82.0	4.0	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	hg19	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	G	23.1	4.379883	0.82682	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.74526	-0.84;-0.85;-0.84;-0.84	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.83188	0.5200	M	0.66939	2.045	0.80722	D	1	P;D;D	0.76494	0.956;0.999;0.999	P;D;D	0.83275	0.63;0.991;0.996	T	0.83196	-0.0081	10	0.52906	T	0.07	-17.2231	19.0974	0.93258	0.0:0.0:1.0:0.0	.	429;1230;1234	B3KX98;Q149N8;Q149N8-4	.;SHPRH_HUMAN;.	N	1230;1234;1234;1230	ENSP00000356475:H1230N;ENSP00000356473:H1234N;ENSP00000412797:H1234N;ENSP00000275233:H1230N	ENSP00000275233:H1230N	H	-	1	0	SHPRH	146285523	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.599000	0.98280	2.593000	0.87608	0.650000	0.86243	CAC	.	.		0.403	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	
NUP43	348995	hgsc.bcm.edu	37	6	150067096	150067096	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:150067096C>T	ENST00000340413.2	-	2	299	c.223G>A	c.(223-225)Ggt>Agt	p.G75S	NUP43_ENST00000460354.2_Missense_Mutation_p.G75S|NUP43_ENST00000367403.3_Missense_Mutation_p.G136S|NUP43_ENST00000463048.3_5'UTR|NUP43_ENST00000367404.4_Missense_Mutation_p.G75S	NM_198887.1	NP_942590.1	Q8NFH3	NUP43_HUMAN	nucleoporin 43kDa	75					carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|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)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)		p.G75C(1)		breast(1)|large_intestine(2)|lung(8)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;4.71e-13)|GBM - Glioblastoma multiforme(68;0.101)		ATTACATCACCATGGTGTCTG	0.363																																					p.G75S		Atlas-SNP	.											NUP43,NS,carcinoma,0,1	NUP43	32	.	1	Substitution - Missense(1)	lung(1)	c.G223A						.						127.0	124.0	125.0					6																	150067096		2203	4300	6503	SO:0001583	missense	348995	exon2			CATCACCATGGTG	AF514997	CCDS5218.1	6q25.1	2013-01-10			ENSG00000120253	ENSG00000120253		"""WD repeat domain containing"""	21182	protein-coding gene	gene with protein product		608141				12196509	Standard	XM_005266961		Approved	bA350J20.1, FLJ13287	uc003qmz.3	Q8NFH3	OTTHUMG00000015795	ENST00000340413.2:c.223G>A	chr6.hg19:g.150067096C>T	ENSP00000342262:p.Gly75Ser	80.0	0.0		44.0	2.0	NM_198887	B4E2F0|Q9H8S0	Missense_Mutation	SNP	ENST00000340413.2	hg19	CCDS5218.1	.	.	.	.	.	.	.	.	.	.	C	36	5.940959	0.97128	.	.	ENSG00000120253	ENST00000340413;ENST00000460354;ENST00000367403;ENST00000367404;ENST00000543637	T;T;T;T;T	0.70869	-0.06;-0.06;-0.52;-0.52;-0.52	6.08	6.08	0.98989	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.82536	0.5058	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.81265	-0.1011	10	0.56958	D	0.05	-26.5731	20.6647	0.99678	0.0:1.0:0.0:0.0	.	75;75	B4E2F0;Q8NFH3	.;NUP43_HUMAN	S	75;75;136;75;82	ENSP00000342262:G75S;ENSP00000432401:G75S;ENSP00000356373:G136S;ENSP00000356374:G75S;ENSP00000438031:G82S	ENSP00000342262:G75S	G	-	1	0	NUP43	150108789	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	7.487000	0.81328	2.890000	0.99128	0.655000	0.94253	GGT	.	.		0.363	NUP43-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396947.1	NM_198887	
LRP11	84918	hgsc.bcm.edu	37	6	150147437	150147437	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:150147437A>G	ENST00000239367.2	-	6	1316	c.1311T>C	c.(1309-1311)ggT>ggC	p.G437G	LRP11_ENST00000546019.1_Silent_p.G182G|LRP11_ENST00000463728.1_5'UTR	NM_032832.5	NP_116221.3	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein 11	437						integral component of membrane (GO:0016021)				cervix(1)|kidney(5)|large_intestine(1)|lung(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		CTCCTCCATCACCCTTTGACT	0.448																																					p.G437G		Atlas-SNP	.											.	LRP11	27	.	0			c.T1311C						.						197.0	190.0	192.0					6																	150147437		2203	4300	6503	SO:0001819	synonymous_variant	84918	exon6			TCCATCACCCTTT	AK027641	CCDS5220.1	6q24.3	2013-02-27			ENSG00000120256	ENSG00000120256		"""Low density lipoprotein receptors"""	16936	protein-coding gene	gene with protein product							Standard	NM_032832		Approved	bA350J20.3, MANSC3	uc003qng.2	Q86VZ4	OTTHUMG00000015801	ENST00000239367.2:c.1311T>C	chr6.hg19:g.150147437A>G		168.0	0.0		99.0	5.0	NM_032832	Q5VYC0|Q96SN6	Silent	SNP	ENST00000239367.2	hg19	CCDS5220.1																																																																																			.	.		0.448	LRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042664.1	NM_032832	
ESR1	2099	hgsc.bcm.edu	37	6	152382169	152382169	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:152382169A>G	ENST00000206249.3	+	6	1641	c.1279A>G	c.(1279-1281)Atg>Gtg	p.M427V	ESR1_ENST00000338799.5_Missense_Mutation_p.M427V|ESR1_ENST00000406599.1_Missense_Mutation_p.M166V|ESR1_ENST00000427531.2_Missense_Mutation_p.M254V|ESR1_ENST00000456483.2_Missense_Mutation_p.M315V|ESR1_ENST00000443427.1_Missense_Mutation_p.M427V|ESR1_ENST00000440973.1_Missense_Mutation_p.M427V	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	427	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)	GATCTTCGACATGCTGCTGGC	0.373																																					p.M427V		Atlas-SNP	.											.	ESR1	94	.	0			c.A1279G						.						110.0	99.0	103.0					6																	152382169		2203	4300	6503	SO:0001583	missense	2099	exon6			TTCGACATGCTGC	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.1279A>G	chr6.hg19:g.152382169A>G	ENSP00000206249:p.Met427Val	147.0	0.0		74.0	4.0	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Missense_Mutation	SNP	ENST00000206249.3	hg19	CCDS5234.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.528128	0.85706	.	.	ENSG00000091831	ENST00000440973;ENST00000338799;ENST00000456483;ENST00000443427;ENST00000206249;ENST00000406599;ENST00000431590;ENST00000544394;ENST00000415488	D;D;D;D;D;D;D;D	0.96396	-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0;-4.0	5.38	5.38	0.77491	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.97291	0.9114	M	0.65498	2.005	0.58432	D	0.999999	P;D;D;P;P;P;P	0.65815	0.704;0.968;0.995;0.607;0.514;0.458;0.514	P;P;D;B;B;B;B	0.72075	0.543;0.906;0.976;0.227;0.34;0.311;0.438	D	0.98336	1.0536	10	0.87932	D	0	.	15.4108	0.74917	1.0:0.0:0.0:0.0	.	331;122;166;354;426;427;427	B0QYW6;C8CJL6;Q9H2M1;B4E3R5;A8KAF4;G4XH65;P03372	.;.;.;.;.;.;ESR1_HUMAN	V	427;427;315;427;427;166;355;254;100	ENSP00000405330:M427V;ENSP00000342630:M427V;ENSP00000415934:M315V;ENSP00000387500:M427V;ENSP00000206249:M427V;ENSP00000384064:M166V;ENSP00000445454:M254V;ENSP00000401995:M100V	ENSP00000206249:M427V	M	+	1	0	ESR1	152423862	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.323000	0.96364	2.039000	0.60335	0.533000	0.62120	ATG	.	.		0.373	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		
SYNE1	23345	hgsc.bcm.edu	37	6	152457873	152457873	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:152457873G>A	ENST00000367255.5	-	141	26140	c.25539C>T	c.(25537-25539)gaC>gaT	p.D8513D	SYNE1_ENST00000341594.5_Silent_p.D8125D|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000265368.4_Silent_p.D8513D|SYNE1_ENST00000354674.4_Silent_p.D691D|SYNE1_ENST00000448038.1_Silent_p.D8465D|SYNE1_ENST00000423061.1_Silent_p.D8465D|SYNE1_ENST00000356820.4_Silent_p.D3037D|SYNE1_ENST00000539504.1_Silent_p.D668D	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8513					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCTCCTTGCTGTCAGCCTGGG	0.587										HNSCC(10;0.0054)																											p.D8513D		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C25539T						.						93.0	87.0	89.0					6																	152457873		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon141			CTTGCTGTCAGCC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.25539C>T	chr6.hg19:g.152457873G>A		155.0	0.0		82.0	5.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.587	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
SYNE1	23345	hgsc.bcm.edu	37	6	152577846	152577846	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:152577846C>T	ENST00000367255.5	-	102	19628	c.19027G>A	c.(19027-19029)Gtg>Atg	p.V6343M	SYNE1_ENST00000341594.5_Missense_Mutation_p.V5955M|SYNE1_ENST00000265368.4_Missense_Mutation_p.V6343M|SYNE1_ENST00000448038.1_Missense_Mutation_p.V6272M|SYNE1_ENST00000423061.1_Missense_Mutation_p.V6272M|SYNE1_ENST00000356820.4_Missense_Mutation_p.V867M	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6343					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.V6343L(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGGGTTGGCACGTCCCCTTTG	0.468										HNSCC(10;0.0054)																											p.V6343M		Atlas-SNP	.											SYNE1_ENST00000423061,rectum,carcinoma,0,5	SYNE1	3227	.	2	Substitution - Missense(2)	prostate(2)	c.G19027A						.						179.0	149.0	159.0					6																	152577846		2203	4300	6503	SO:0001583	missense	23345	exon102			TTGGCACGTCCCC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.19027G>A	chr6.hg19:g.152577846C>T	ENSP00000356224:p.Val6343Met	92.0	0.0		46.0	2.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	5.689	0.311623	0.10789	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.53857	0.7;0.69;0.6;0.69;0.79;2.65	5.29	4.43	0.53597	.	0.206659	0.33854	N	0.004500	T	0.15522	0.0374	N	0.08118	0	0.09310	N	1	P;P;P	0.44578	0.75;0.75;0.838	B;B;B	0.40565	0.115;0.115;0.333	T	0.02721	-1.1119	10	0.44086	T	0.13	.	9.6366	0.39811	0.0:0.7808:0.0:0.2192	.	6343;6343;6272	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	M	6343;6272;6343;6272;5955;867	ENSP00000356224:V6343M;ENSP00000396024:V6272M;ENSP00000265368:V6343M;ENSP00000390975:V6272M;ENSP00000341887:V5955M;ENSP00000349276:V867M	ENSP00000265368:V6343M	V	-	1	0	SYNE1	152619539	0.005000	0.15991	0.013000	0.15412	0.233000	0.25261	1.384000	0.34396	1.373000	0.46208	-0.142000	0.14014	GTG	.	.		0.468	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
SYNJ2	8871	hgsc.bcm.edu	37	6	158449995	158449995	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:158449995A>G	ENST00000355585.4	+	3	497	c.422A>G	c.(421-423)gAc>gGc	p.D141G	SYNJ2_ENST00000367122.2_Missense_Mutation_p.D141G|SYNJ2_ENST00000449859.2_Missense_Mutation_p.D90G|SYNJ2_ENST00000367121.3_Missense_Mutation_p.D141G	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	141	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		TCTCGCTTTGACCTGACTGTC	0.582																																					p.D141G		Atlas-SNP	.											.	SYNJ2	111	.	0			c.A422G						.						66.0	68.0	68.0					6																	158449995		2203	4300	6503	SO:0001583	missense	8871	exon3			GCTTTGACCTGAC	AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.422A>G	chr6.hg19:g.158449995A>G	ENSP00000347792:p.Asp141Gly	114.0	0.0		61.0	5.0	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	hg19	CCDS5254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.57|16.57	3.160442|3.160442	0.57368|0.57368	.|.	.|.	ENSG00000078269|ENSG00000078269	ENST00000367122;ENST00000367121;ENST00000355585;ENST00000449320;ENST00000449859|ENST00000367113	T;T;T;T;T|.	0.72167|.	-0.63;-0.63;-0.63;-0.63;-0.63|.	4.62|4.62	4.62|4.62	0.57501|0.57501	Synaptojanin, N-terminal (2);|.	0.000000|.	0.64402|.	D|.	0.000018|.	D|D	0.85579|0.85579	0.5729|0.5729	H|H	0.98027|0.98027	4.13|4.13	0.49915|0.49915	D|D	0.999838|0.999838	D;D;D;D|.	0.58620|.	0.969;0.983;0.983;0.962|.	P;D;P;P|.	0.63113|.	0.676;0.911;0.676;0.547|.	D|D	0.90043|0.90043	0.4143|0.4143	10|5	0.87932|.	D|.	0|.	.|.	14.2246|14.2246	0.65850|0.65850	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	90;141;141;141|.	B4DJU8;E7ER60;O15056;O15056-3|.	.;.;SYNJ2_HUMAN;.|.	G|A	141;141;141;90;90|116	ENSP00000356089:D141G;ENSP00000356088:D141G;ENSP00000347792:D141G;ENSP00000411202:D90G;ENSP00000388371:D90G|.	ENSP00000347792:D141G|.	D|T	+|+	2|1	0|0	SYNJ2|SYNJ2	158369983|158369983	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.017000|0.017000	0.09413|0.09413	8.614000|8.614000	0.90917|0.90917	0.546000|0.546000	0.28920|0.28920	0.655000|0.655000	0.94253|0.94253	GAC|ACC	.	.		0.582	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2		
IGF2R	3482	hgsc.bcm.edu	37	6	160491044	160491044	+	Missense_Mutation	SNP	G	G	T	rs368697729		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:160491044G>T	ENST00000356956.1	+	31	4545	c.4397G>T	c.(4396-4398)cGg>cTg	p.R1466L		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1466					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	GATGGGATTCGGAAAAAGTCA	0.522																																					p.R1466L		Atlas-SNP	.											.	IGF2R	251	.	0			c.G4397T						.						106.0	87.0	93.0					6																	160491044		2203	4300	6503	SO:0001583	missense	3482	exon31			GGATTCGGAAAAA	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.4397G>T	chr6.hg19:g.160491044G>T	ENSP00000349437:p.Arg1466Leu	175.0	0.0		95.0	4.0	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.840838	0.91197	.	.	ENSG00000197081	ENST00000356956	T	0.13089	2.62	5.62	5.62	0.85841	Mannose-6-phosphate receptor, binding (1);	0.058799	0.64402	D	0.000005	T	0.34077	0.0885	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.06023	-1.0850	10	0.54805	T	0.06	-11.632	19.6758	0.95932	0.0:0.0:1.0:0.0	.	1466	P11717	MPRI_HUMAN	L	1466	ENSP00000349437:R1466L	ENSP00000349437:R1466L	R	+	2	0	IGF2R	160411034	1.000000	0.71417	0.971000	0.41717	0.723000	0.41478	5.738000	0.68613	2.644000	0.89710	0.561000	0.74099	CGG	.	.		0.522	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
LPA	4018	hgsc.bcm.edu	37	6	160978594	160978594	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:160978594G>T	ENST00000316300.5	-	29	4685	c.4641C>A	c.(4639-4641)acC>acA	p.T1547T	LPA_ENST00000447678.1_Silent_p.T1547T			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4055	Kringle 14. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	AGTAGTTCTCGGTCAGGCCAC	0.478																																					p.T1547T		Atlas-SNP	.											.	LPA	237	.	0			c.C4641A						.						67.0	69.0	68.0					6																	160978594		2113	4264	6377	SO:0001819	synonymous_variant	4018	exon30			GTTCTCGGTCAGG	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4641C>A	chr6.hg19:g.160978594G>T		173.0	0.0		100.0	4.0	NM_005577	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	hg19	CCDS43523.1																																																																																			.	.		0.478	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
RPS6KA2	6196	hgsc.bcm.edu	37	6	166912091	166912091	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:166912091A>G	ENST00000265678.4	-	8	875	c.652T>C	c.(652-654)Tcc>Ccc	p.S218P	RPS6KA2_ENST00000503859.1_Missense_Mutation_p.S226P|RPS6KA2_ENST00000481261.2_Missense_Mutation_p.S129P|RPS6KA2_ENST00000510118.1_Missense_Mutation_p.S243P|RPS6KA2_ENST00000405189.3_Missense_Mutation_p.S129P|RPS6KA2_ENST00000366863.2_Missense_Mutation_p.S64P	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	218	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|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)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		CCGCAGAAGGAGTACGCTCTC	0.597																																					p.S226P		Atlas-SNP	.											.	RPS6KA2	212	.	0			c.T676C						.						212.0	143.0	167.0					6																	166912091		2203	4300	6503	SO:0001583	missense	6196	exon9			AGAAGGAGTACGC	L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"""ribosomal protein S6 kinase, 90kD, polypeptide 2"""			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.652T>C	chr6.hg19:g.166912091A>G	ENSP00000265678:p.Ser218Pro	144.0	0.0		85.0	4.0	NM_001006932	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Missense_Mutation	SNP	ENST00000265678.4	hg19	CCDS5294.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.002768	0.93287	.	.	ENSG00000071242	ENST00000265678;ENST00000510118;ENST00000503859;ENST00000481261;ENST00000405189;ENST00000366863	T;T;T;T;T;T	0.67345	1.74;1.74;1.74;1.74;1.74;-0.26	4.89	4.89	0.63831	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	0.77445	0.4131	M	0.77820	2.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.998;0.997;0.996	T	0.81627	-0.0847	10	0.87932	D	0	.	13.9945	0.64388	1.0:0.0:0.0:0.0	.	243;226;218	F2Z2J1;Q15349-3;Q15349	.;.;KS6A2_HUMAN	P	218;243;226;129;129;64	ENSP00000265678:S218P;ENSP00000422435:S243P;ENSP00000427015:S226P;ENSP00000422484:S129P;ENSP00000386050:S129P;ENSP00000355828:S64P	ENSP00000265678:S218P	S	-	1	0	RPS6KA2	166832081	1.000000	0.71417	0.832000	0.32986	0.955000	0.61496	8.576000	0.90770	1.947000	0.56498	0.533000	0.62120	TCC	.	.		0.597	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135	
ERMARD	55780	hgsc.bcm.edu	37	6	170154032	170154032	+	Nonsense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr6:170154032C>T	ENST00000366773.3	+	2	112	c.79C>T	c.(79-81)Caa>Taa	p.Q27*	ERMARD_ENST00000392095.4_Intron|ERMARD_ENST00000588451.1_5'UTR|ERMARD_ENST00000366772.2_Nonsense_Mutation_p.Q27*|ERMARD_ENST00000418781.3_Nonsense_Mutation_p.Q27*|TCTE3_ENST00000366774.3_5'Flank	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	27					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TCTTGGGTTTCAACTCAGAGA	0.348																																					p.Q27X		Atlas-SNP	.											.	C6orf70	63	.	0			c.C79T						.						82.0	78.0	79.0					6																	170154032		2203	4300	6503	SO:0001587	stop_gained	55780	exon2			GGGTTTCAACTCA	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"""chromosome 6 open reading frame 70"""	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.79C>T	chr6.hg19:g.170154032C>T	ENSP00000355735:p.Gln27*	124.0	0.0		62.0	4.0	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Nonsense_Mutation	SNP	ENST00000366773.3	hg19	CCDS34576.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.939366	0.73557	.	.	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781	.	.	.	5.66	4.79	0.61399	.	0.212077	0.32802	N	0.005635	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	14.4984	0.67704	0.0:0.1503:0.8497:0.0	.	.	.	.	X	27	.	ENSP00000355734:Q27X	Q	+	1	0	C6orf70	169895957	1.000000	0.71417	0.965000	0.40720	0.389000	0.30415	4.290000	0.59019	1.388000	0.46506	-0.153000	0.13522	CAA	.	.		0.348	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
PRKAR1B	5575	hgsc.bcm.edu	37	7	635799	635799	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:635799T>C	ENST00000406797.1	-	7	866	c.692A>G	c.(691-693)tAc>tGc	p.Y231C	PRKAR1B_ENST00000544935.1_Missense_Mutation_p.Y231C|PRKAR1B_ENST00000360274.4_Missense_Mutation_p.Y231C|PRKAR1B_ENST00000403562.1_Missense_Mutation_p.Y231C|PRKAR1B_ENST00000537384.1_Missense_Mutation_p.Y231C	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	231					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)		GATGCGCCGGTAGCTGTCCCG	0.637																																					p.Y231C		Atlas-SNP	.											.	PRKAR1B	32	.	0			c.A692G						.						97.0	76.0	83.0					7																	635799		2203	4296	6499	SO:0001583	missense	5575	exon7			CGCCGGTAGCTGT	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.692A>G	chr7.hg19:g.635799T>C	ENSP00000385749:p.Tyr231Cys	176.0	0.0		121.0	5.0	NM_001164760	Q8N422	Missense_Mutation	SNP	ENST00000406797.1	hg19	CCDS34579.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.4|21.4	4.148129|4.148129	0.78001|0.78001	.|.	.|.	ENSG00000188191|ENSG00000188191	ENST00000400758|ENST00000537384;ENST00000544935;ENST00000406797;ENST00000403562;ENST00000360274;ENST00000430040	.|D;D;D;D;D;D	.|0.84873	.|-1.91;-1.91;-1.91;-1.91;-1.91;-1.91	4.88|4.88	4.88|4.88	0.63580|0.63580	.|Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	.|0.000000	.|0.85682	.|U	.|0.000000	D|D	0.91646|0.91646	0.7360|0.7360	M|M	0.75777|0.75777	2.31|2.31	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	D|D	0.92734|0.92734	0.6202|0.6202	5|10	.|0.87932	.|D	.|0	-2.1353|-2.1353	14.5236|14.5236	0.67870|0.67870	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|231	.|P31321	.|KAP1_HUMAN	A|C	92|231	.|ENSP00000440449:Y231C;ENSP00000444487:Y231C;ENSP00000385749:Y231C;ENSP00000385349:Y231C;ENSP00000353415:Y231C;ENSP00000402648:Y231C	.|ENSP00000353415:Y231C	T|Y	-|-	1|2	0|0	PRKAR1B|PRKAR1B	602325|602325	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.960000|0.960000	0.62799|0.62799	7.487000|7.487000	0.81328|0.81328	1.851000|1.851000	0.53745|0.53745	0.449000|0.449000	0.29647|0.29647	ACC|TAC	.	.		0.637	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322525.1		
SUN1	23353	hgsc.bcm.edu	37	7	881715	881715	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:881715T>C	ENST00000405266.1	+	3	423	c.399T>C	c.(397-399)ccT>ccC	p.P133P	SUN1_ENST00000403868.1_Silent_p.P133P|SUN1_ENST00000452783.2_Silent_p.P133P|SUN1_ENST00000425407.2_Silent_p.P83P|SUN1_ENST00000401592.1_Silent_p.P133P|SUN1_ENST00000389574.3_Silent_p.P83P|SUN1_ENST00000457378.2_Silent_p.P154P|SUN1_ENST00000456758.2_Silent_p.P191P			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	133	LMNA-binding.				cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GACGGCCTCCTGTATTGGACG	0.572																																					p.P154P		Atlas-SNP	.											.	SUN1	157	.	0			c.T462C						.						79.0	80.0	79.0					7																	881715		2072	4211	6283	SO:0001819	synonymous_variant	23353	exon5			GCCTCCTGTATTG	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.399T>C	chr7.hg19:g.881715T>C		111.0	0.0		69.0	4.0	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Silent	SNP	ENST00000405266.1	hg19																																																																																				.	.		0.572	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
CHST12	55501	hgsc.bcm.edu	37	7	2472863	2472863	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:2472863C>A	ENST00000258711.6	+	2	724	c.589C>A	c.(589-591)Cgc>Agc	p.R197S		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	197					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		TGCGCCCTACCGCGACCCGCT	0.677																																					p.R197S		Atlas-SNP	.											.	CHST12	39	.	0			c.C589A						.						49.0	41.0	44.0					7																	2472863		2203	4299	6502	SO:0001583	missense	55501	exon2			CCCTACCGCGACC	AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"""Sulfotransferases, membrane-bound"""	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.589C>A	chr7.hg19:g.2472863C>A	ENSP00000258711:p.Arg197Ser	145.0	0.0		94.0	4.0	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	hg19	CCDS5333.1	.	.	.	.	.	.	.	.	.	.	C	6.407	0.443189	0.12164	.	.	ENSG00000136213	ENST00000258711;ENST00000432336	T;T	0.72835	-0.69;-0.69	5.23	4.25	0.50352	.	0.422384	0.25792	N	0.028274	T	0.52549	0.1741	N	0.20845	0.615	0.32470	N	0.542986	P	0.37158	0.585	B	0.39419	0.299	T	0.55964	-0.8057	10	0.05525	T	0.97	-8.4503	12.9136	0.58192	0.1318:0.7528:0.1154:0.0	.	197	Q9NRB3	CHSTC_HUMAN	S	197	ENSP00000258711:R197S;ENSP00000411207:R197S	ENSP00000258711:R197S	R	+	1	0	CHST12	2439389	0.717000	0.27966	1.000000	0.80357	0.894000	0.52154	2.056000	0.41355	2.451000	0.82905	0.561000	0.74099	CGC	.	.		0.677	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641	
LFNG	3955	hgsc.bcm.edu	37	7	2552813	2552813	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:2552813A>G	ENST00000402506.1	+	2	196	c.70A>G	c.(70-72)Agc>Ggc	p.S24G		NM_001166355.1	NP_001159827.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0					compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		CTGGGCATGGAGCAAATGCTC	0.542																																					p.S24G		Atlas-SNP	.											.	LFNG	57	.	0			c.A70G						.						150.0	138.0	141.0					7																	2552813		1568	3582	5150	SO:0001583	missense	3955	exon2			GCATGGAGCAAAT	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"""Beta 3-glycosyltransferases"""	6560	protein-coding gene	gene with protein product		602576	"""lunatic fringe (Drosophila) homolog"", ""lunatic fringe homolog (Drosophila)"""			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000402506.1:c.70A>G	chr7.hg19:g.2552813A>G	ENSP00000385764:p.Ser24Gly	140.0	0.0		98.0	4.0	NM_001166355	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Missense_Mutation	SNP	ENST00000402506.1	hg19	CCDS55081.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.386861	0.25031	.	.	ENSG00000106003	ENST00000402506	T	0.56275	0.47	2.87	-5.74	0.02391	.	.	.	.	.	T	0.23330	0.0564	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.15954	-1.0419	7	0.30078	T	0.28	.	3.2979	0.06973	0.231:0.0:0.2547:0.5143	.	.	.	.	G	24	ENSP00000385764:S24G	ENSP00000385764:S24G	S	+	1	0	LFNG	2519339	0.013000	0.17824	0.000000	0.03702	0.010000	0.07245	0.353000	0.20130	-0.999000	0.03442	-0.415000	0.06103	AGC	.	.		0.542	LFNG-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000325023.1	NM_002304	
TNRC18	84629	hgsc.bcm.edu	37	7	5391469	5391469	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:5391469C>A	ENST00000430969.1	-	17	5799	c.5451G>T	c.(5449-5451)tcG>tcT	p.S1817S	TNRC18_ENST00000399537.4_Silent_p.S1817S	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1817							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		ACGATTCCTCCGAAGAGTCGC	0.582																																					p.S1817S		Atlas-SNP	.											.	TNRC18	311	.	0			c.G5451T						.						18.0	16.0	17.0					7																	5391469		1567	3582	5149	SO:0001819	synonymous_variant	84629	exon17			TTCCTCCGAAGAG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.5451G>T	chr7.hg19:g.5391469C>A		163.0	0.0		99.0	4.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	hg19	CCDS47534.1																																																																																			.	.		0.582	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
TNRC18	84629	hgsc.bcm.edu	37	7	5396822	5396822	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:5396822T>C	ENST00000430969.1	-	16	5267	c.4919A>G	c.(4918-4920)gAc>gGc	p.D1640G	TNRC18_ENST00000399537.4_Missense_Mutation_p.D1640G	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1640							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CTTCAACTTGTCCTGCTTGGT	0.552																																					p.D1640G		Atlas-SNP	.											.	TNRC18	311	.	0			c.A4919G						.						45.0	45.0	45.0					7																	5396822		2033	4184	6217	SO:0001583	missense	84629	exon16			AACTTGTCCTGCT	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4919A>G	chr7.hg19:g.5396822T>C	ENSP00000395538:p.Asp1640Gly	212.0	0.0		199.0	9.0	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	t	15.07	2.725089	0.48833	.	.	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000440081	T;T;T	0.42900	2.67;2.69;0.96	5.25	5.25	0.73442	.	0.000000	0.41938	D	0.000788	T	0.39759	0.1090	M	0.61703	1.905	0.33662	D	0.609793	B;B	0.33940	0.433;0.236	B;B	0.30029	0.11;0.031	T	0.53830	-0.8383	10	0.23891	T	0.37	.	15.1664	0.72828	0.0:0.0:0.0:1.0	.	695;1640	A8MSW5;O15417	.;TNC18_HUMAN	G	1640;1640;695;130	ENSP00000382452:D1640G;ENSP00000395538:D1640G;ENSP00000395990:D130G	ENSP00000382452:D1640G	D	-	2	0	TNRC18	5363348	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.801000	0.62532	1.988000	0.58038	0.459000	0.35465	GAC	.	.		0.552	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
EIF2AK1	27102	hgsc.bcm.edu	37	7	6078226	6078226	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:6078226T>C	ENST00000199389.6	-	10	1342	c.1196A>G	c.(1195-1197)aAc>aGc	p.N399S	EIF2AK1_ENST00000495565.1_5'Flank|EIF2AK1_ENST00000536084.1_Missense_Mutation_p.N275S	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	399	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		GCCCCGCTTGTTTCTCTCGAC	0.562																																					p.N399S		Atlas-SNP	.											.	EIF2AK1	76	.	0			c.A1196G						.						136.0	127.0	130.0					7																	6078226		2203	4300	6503	SO:0001583	missense	27102	exon10			CGCTTGTTTCTCT	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"""heme regulated initiation factor 2 alpha kinase"""	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.1196A>G	chr7.hg19:g.6078226T>C	ENSP00000199389:p.Asn399Ser	84.0	0.0		86.0	4.0	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Missense_Mutation	SNP	ENST00000199389.6	hg19	CCDS5345.1	.	.	.	.	.	.	.	.	.	.	.	22.6	4.317420	0.81469	.	.	ENSG00000086232	ENST00000199389;ENST00000536084;ENST00000426957	T;T	0.69175	-0.38;1.88	5.74	5.74	0.90152	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.042140	0.85682	D	0.000000	T	0.75583	0.3869	L	0.47078	1.49	0.54753	D	0.999984	D;D;P	0.71674	0.998;0.981;0.62	D;P;B	0.66196	0.942;0.661;0.422	T	0.75071	-0.3447	10	0.41790	T	0.15	-22.7794	15.7044	0.77565	0.0:0.0:0.0:1.0	.	275;398;399	B4DIP4;Q9BQI3-2;Q9BQI3	.;.;E2AK1_HUMAN	S	399;275;26	ENSP00000199389:N399S;ENSP00000445784:N275S	ENSP00000199389:N399S	N	-	2	0	EIF2AK1	6044752	1.000000	0.71417	0.443000	0.26883	0.060000	0.15804	4.807000	0.62576	2.181000	0.69327	0.528000	0.53228	AAC	.	.		0.562	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413	
COL28A1	340267	hgsc.bcm.edu	37	7	7572478	7572478	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:7572478A>G	ENST00000399429.3	-	2	169	c.29T>C	c.(28-30)cTc>cCc	p.L10P		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	10					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)		CAAAAGCAGGAGATAGAAGAC	0.353																																					p.L10P		Atlas-SNP	.											.	COL28A1	113	.	0			c.T29C						.						134.0	124.0	127.0					7																	7572478		1867	4112	5979	SO:0001583	missense	340267	exon2			AGCAGGAGATAGA	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.29T>C	chr7.hg19:g.7572478A>G	ENSP00000382356:p.Leu10Pro	81.0	0.0		81.0	4.0	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	hg19	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	A	8.338	0.828124	0.16749	.	.	ENSG00000215018	ENST00000399429;ENST00000399419;ENST00000448652	D	0.89617	-2.54	4.28	3.11	0.35812	.	0.536026	0.15628	U	0.252502	D	0.87589	0.6215	N	0.24115	0.695	0.30233	N	0.795696	D	0.64830	0.994	P	0.59288	0.855	T	0.82855	-0.0251	10	0.72032	D	0.01	-4.7079	9.4504	0.38723	0.8389:0.0:0.1611:0.0	.	10	Q2UY09	COSA1_HUMAN	P	10	ENSP00000382356:L10P	ENSP00000382347:L10P	L	-	2	0	COL28A1	7539003	0.265000	0.24102	0.648000	0.29521	0.008000	0.06430	1.247000	0.32815	0.284000	0.22305	-1.450000	0.01041	CTC	.	.		0.353	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
SCIN	85477	hgsc.bcm.edu	37	7	12662452	12662452	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:12662452A>G	ENST00000297029.5	+	5	794	c.693A>G	c.(691-693)ccA>ccG	p.P231P	SCIN_ENST00000519209.1_5'UTR|SCIN_ENST00000445618.2_5'UTR|SCIN_ENST00000473722.1_3'UTR	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	231	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		CAGAGCTTCCAGATGGAGGTG	0.383																																					p.P231P		Atlas-SNP	.											.	SCIN	105	.	0			c.A693G						.						160.0	156.0	157.0					7																	12662452		1887	4124	6011	SO:0001819	synonymous_variant	85477	exon5			GCTTCCAGATGGA	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.693A>G	chr7.hg19:g.12662452A>G		83.0	0.0		89.0	4.0	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Silent	SNP	ENST00000297029.5	hg19	CCDS47545.1																																																																																			.	.		0.383	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
KLHL7	55975	hgsc.bcm.edu	37	7	23180386	23180386	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:23180386A>G	ENST00000339077.5	+	5	685		c.e5-1		KLHL7_ENST00000409689.1_Splice_Site|KLHL7_ENST00000539124.1_Splice_Site|KLHL7_ENST00000322231.7_Splice_Site|KLHL7_ENST00000545443.1_Splice_Site|KLHL7_ENST00000542558.1_Splice_Site|KLHL7_ENST00000479288.1_Splice_Site	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7						protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TTCTGTGTTTAGGTATAAGTG	0.318																																					.		Atlas-SNP	.											KLHL7_ENST00000339077,NS,carcinoma,0,4	KLHL7	102	.	0			c.443-2A>G						.						59.0	59.0	59.0					7																	23180386		2203	4300	6503	SO:0001630	splice_region_variant	55975	exon5			GTGTTTAGGTATA		CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"""Kelch-like"", ""BTB/POZ domain containing"""	15646	protein-coding gene	gene with protein product	"""retinitis pigmentosa 42"""	611119	"""kelch-like 7 (Drosophila)"""			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.443-1A>G	chr7.hg19:g.23180386A>G		77.0	0.0		70.0	3.0	NM_001031710	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Splice_Site	SNP	ENST00000339077.5	hg19	CCDS34609.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.220187	0.39201	.	.	ENSG00000122550	ENST00000322231;ENST00000339077;ENST00000539124;ENST00000409689;ENST00000545443	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1304	0.72517	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KLHL7	23146911	1.000000	0.71417	0.978000	0.43139	0.327000	0.28475	8.606000	0.90888	2.032000	0.59987	0.379000	0.24179	.	.	.		0.318	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846	Intron
HIBADH	11112	hgsc.bcm.edu	37	7	27672052	27672052	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:27672052G>T	ENST00000265395.2	-	3	471	c.265C>A	c.(265-267)Cca>Aca	p.P89T		NM_152740.3	NP_689953.1	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase	89					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	3-hydroxyisobutyrate dehydrogenase activity (GO:0008442)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(4)|kidney(2)|lung(3)|ovary(2)|prostate(1)	12			GBM - Glioblastoma multiforme(3;0.0368)			ACATCTGCTGGGGAAGATACT	0.368																																					p.P89T		Atlas-SNP	.											.	HIBADH	28	.	0			c.C265A						.						110.0	106.0	107.0					7																	27672052		2203	4300	6503	SO:0001583	missense	11112	exon3			CTGCTGGGGAAGA	AF529362	CCDS5414.1	7p15	2009-06-12			ENSG00000106049	ENSG00000106049	1.1.1.31		4907	protein-coding gene	gene with protein product		608475					Standard	NM_152740		Approved	NS5ATP1	uc003szf.3	P31937	OTTHUMG00000097035	ENST00000265395.2:c.265C>A	chr7.hg19:g.27672052G>T	ENSP00000265395:p.Pro89Thr	86.0	0.0		76.0	4.0	NM_152740	Q546Z2|Q9UDN3	Missense_Mutation	SNP	ENST00000265395.2	hg19	CCDS5414.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.759483	0.49468	.	.	ENSG00000106049	ENST00000265395	T	0.37915	1.17	5.8	5.8	0.92144	6-phosphogluconate dehydrogenase, NADP-binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.50633	0.1627	M	0.77103	2.36	0.80722	D	1	P;P	0.37997	0.614;0.614	B;B	0.43155	0.41;0.41	T	0.47129	-0.9141	10	0.39692	T	0.17	-23.3127	20.0643	0.97702	0.0:0.0:1.0:0.0	.	89;89	Q546Z2;P31937	.;3HIDH_HUMAN	T	89	ENSP00000265395:P89T	ENSP00000265395:P89T	P	-	1	0	HIBADH	27638577	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.138000	0.94501	2.737000	0.93849	0.650000	0.86243	CCA	.	.		0.368	HIBADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214132.1	NM_152740	
TAX1BP1	8887	hgsc.bcm.edu	37	7	27832797	27832797	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:27832797T>C	ENST00000396319.2	+	10	1464	c.1376T>C	c.(1375-1377)cTc>cCc	p.L459P	TAX1BP1_ENST00000433216.2_Missense_Mutation_p.L302P|TAX1BP1_ENST00000543117.1_Missense_Mutation_p.L459P|TAX1BP1_ENST00000265393.6_Missense_Mutation_p.L459P|TAX1BP1_ENST00000409980.1_Missense_Mutation_p.L459P	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	459					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			TGCCAAAGGCTCCAAAAACAA	0.313																																					p.L459P		Atlas-SNP	.											.	TAX1BP1	71	.	0			c.T1376C						.						34.0	36.0	35.0					7																	27832797		2203	4300	6503	SO:0001583	missense	8887	exon10			AAAGGCTCCAAAA	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.1376T>C	chr7.hg19:g.27832797T>C	ENSP00000379612:p.Leu459Pro	142.0	0.0		122.0	5.0	NM_006024	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Missense_Mutation	SNP	ENST00000396319.2	hg19	CCDS5415.1	.	.	.	.	.	.	.	.	.	.	T	16.88	3.245160	0.59103	.	.	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319;ENST00000457186	T;T;T;T;T	0.16457	2.34;2.34;2.34;2.34;2.34	5.9	4.74	0.60224	.	0.000000	0.48286	D	0.000193	T	0.39963	0.1098	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.998	T	0.23476	-1.0187	10	0.87932	D	0	-6.0552	13.3552	0.60623	0.0:0.0:0.1316:0.8684	.	302;459;459	E7ENV2;Q86VP1;Q86VP1-2	.;TAXB1_HUMAN;.	P	459;459;459;302;459;14	ENSP00000444811:L459P;ENSP00000265393:L459P;ENSP00000386515:L459P;ENSP00000391907:L302P;ENSP00000379612:L459P	ENSP00000265393:L459P	L	+	2	0	TAX1BP1	27799322	1.000000	0.71417	1.000000	0.80357	0.500000	0.33767	7.537000	0.82033	1.038000	0.40049	0.528000	0.53228	CTC	.	.		0.313	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024	
ADCYAP1R1	117	hgsc.bcm.edu	37	7	31125006	31125006	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:31125006A>G	ENST00000304166.4	+	9	907	c.618A>G	c.(616-618)aaA>aaG	p.K206K	ADCYAP1R1_ENST00000396211.2_Silent_p.K206K|ADCYAP1R1_ENST00000409363.1_Silent_p.K185K|ADCYAP1R1_ENST00000409489.1_Silent_p.K206K	NM_001118.4|NM_001199635.1|NM_001199636.1	NP_001109.2|NP_001186564.1|NP_001186565.1	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary) receptor type I	206					activation of adenylate cyclase activity (GO:0007190)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(1)|large_intestine(4)|liver(2)|lung(24)|ovary(1)|skin(2)|stomach(1)	35						TCTTCATCAAAGACTGGATTC	0.552																																					p.K206K	Ovarian(44;225 1186 2158 11092)	Atlas-SNP	.											.	ADCYAP1R1	78	.	0			c.A618G						.						191.0	152.0	165.0					7																	31125006		2203	4300	6503	SO:0001819	synonymous_variant	117	exon9			CATCAAAGACTGG		CCDS5433.1, CCDS56480.1, CCDS56481.1	7p14.3	2012-09-20			ENSG00000078549	ENSG00000078549		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	242	protein-coding gene	gene with protein product	"""PACAP receptor 1"""	102981				7902709	Standard	NM_001199635		Approved	PAC1, PACAPR, PAC1R	uc003tcg.3	P41586	OTTHUMG00000023884	ENST00000304166.4:c.618A>G	chr7.hg19:g.31125006A>G		39.0	0.0		39.0	4.0	NM_001118	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Silent	SNP	ENST00000304166.4	hg19	CCDS5433.1																																																																																			.	.		0.552	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118	
FKBP9	11328	hgsc.bcm.edu	37	7	33028263	33028263	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:33028263A>G	ENST00000242209.4	+	6	1207	c.1038A>G	c.(1036-1038)agA>agG	p.R346R	FKBP9_ENST00000538443.1_Splice_Site_p.R208R|FKBP9_ENST00000490776.2_Splice_Site_p.R114R|AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538336.1_Splice_Site_p.R399R|FKBP9_ENST00000489038.1_3'UTR	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	346	PPIase FKBP-type 3. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			AGGAAGGAAGAGGTGAGCATC	0.478																																					p.R346R		Atlas-SNP	.											.	FKBP9	335	.	0			c.A1038G						.						108.0	91.0	97.0					7																	33028263		2203	4300	6503	SO:0001630	splice_region_variant	11328	exon6			AGGAAGAGGTGAG	AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642		"""EF-hand domain containing"""	3725	protein-coding gene	gene with protein product			"""FK506-binding protein 9 (63 kD)"""			12036304	Standard	NM_007270		Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	ENST00000242209.4:c.1039+1A>G	chr7.hg19:g.33028263A>G		106.0	0.0		70.0	4.0	NM_007270	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Silent	SNP	ENST00000242209.4	hg19	CCDS5439.1																																																																																			.	.		0.478	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270	Silent
NT5C3A	51251	hgsc.bcm.edu	37	7	33057200	33057200	+	Missense_Mutation	SNP	T	T	C	rs186325627	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:33057200T>C	ENST00000242210.7	-	7	635	c.559A>G	c.(559-561)Aat>Gat	p.N187D	NT5C3A_ENST00000405342.1_Missense_Mutation_p.N148D|NT5C3A_ENST00000381626.2_Missense_Mutation_p.N136D|NT5C3A_ENST00000396152.2_Missense_Mutation_p.N148D|NT5C3A_ENST00000409467.1_Missense_Mutation_p.N136D|AVL9_ENST00000404479.1_Intron|NT5C3A_ENST00000409787.1_Missense_Mutation_p.N148D|NT5C3A_ENST00000610140.1_Missense_Mutation_p.N182D	NM_001002009.2|NM_001002010.2	NP_001002009.1|NP_001002010.1	Q9H0P0	5NT3A_HUMAN	5'-nucleotidase, cytosolic IIIA	187					dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside metabolic process (GO:0006213)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	2'-phosphotransferase activity (GO:0008665)|5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)										TCAAAGAAATTCTCATATCCT	0.363																																					p.N187D		Atlas-SNP	.											.	.	.	.	0			c.A559G						.						128.0	126.0	127.0					7																	33057200		2203	4300	6503	SO:0001583	missense	0	exon7			AGAAATTCTCATA	AF312735	CCDS34616.1, CCDS34617.1, CCDS55101.1	7p14.3	2013-03-06	2013-03-06	2013-03-06	ENSG00000122643	ENSG00000122643	3.1.3.5		17820	protein-coding gene	gene with protein product	"""lupin"""	606224	"""5'-nucleotidase, cytosolic III"""	NT5C3		11042152, 10942414	Standard	NM_001002010		Approved	UMPH1, PSN1, PN-I, UMPH, P5'N-1, cN-III, p36, POMP, hUMP1	uc003tdk.4	Q9H0P0	OTTHUMG00000152983	ENST00000242210.7:c.559A>G	chr7.hg19:g.33057200T>C	ENSP00000242210:p.Asn187Asp	124.0	0.0		99.0	4.0	NM_001002010	A8K253|B2RAA5|B8ZZC4|Q6IPZ1|Q6NXS6|Q7L3G6|Q9P0P5|Q9UC42|Q9UC43|Q9UC44|Q9UC45	Missense_Mutation	SNP	ENST00000242210.7	hg19	CCDS34616.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.337953	0.24253	.	.	ENSG00000122643	ENST00000381626;ENST00000396152;ENST00000242210;ENST00000405342;ENST00000409467;ENST00000409787	D;D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62;-1.62	5.19	-2.49	0.06403	HAD-like domain (2);	0.456245	0.25532	N	0.030036	T	0.58906	0.2155	N	0.16567	0.415	0.25846	N	0.983995	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41840	-0.9486	10	0.14252	T	0.57	.	2.588	0.04835	0.0942:0.2194:0.1763:0.5101	.	187;148	Q9H0P0;Q9H0P0-1	5NT3_HUMAN;.	D	136;148;187;148;136;148	ENSP00000371039:N136D;ENSP00000379456:N148D;ENSP00000242210:N187D;ENSP00000385261:N148D;ENSP00000387166:N136D;ENSP00000387205:N148D	ENSP00000242210:N187D	N	-	1	0	NT5C3	33023725	0.199000	0.23386	0.995000	0.50966	0.991000	0.79684	0.377000	0.20552	-0.239000	0.09710	0.533000	0.62120	AAT	.	T|0.999;G|0.001		0.363	NT5C3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328880.1	NM_016489	
AOAH	313	hgsc.bcm.edu	37	7	36763688	36763688	+	Silent	SNP	C	C	A	rs2228411	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:36763688C>A	ENST00000258749.5	-	1	465	c.66G>T	c.(64-66)tcG>tcT	p.S22S	AOAH_ENST00000535891.1_Silent_p.S22S|AOAH_ENST00000431169.1_Silent_p.S22S	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	22					inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|lipopolysaccharide metabolic process (GO:0008653)|negative regulation of inflammatory response (GO:0050728)	extracellular region (GO:0005576)	acyloxyacyl hydrolase activity (GO:0050528)|catalytic activity (GO:0003824)|lipoprotein lipase activity (GO:0004465)	p.S22S(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(21)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	41						CTGGAGAGGCCGAGGACTGAA	0.512																																					p.S22S		Atlas-SNP	.											AOAH,NS,carcinoma,0,2	AOAH	79	.	1	Substitution - coding silent(1)	stomach(1)	c.G66T						.						57.0	63.0	61.0					7																	36763688		2203	4300	6503	SO:0001819	synonymous_variant	313	exon1			AGAGGCCGAGGAC	BC025698	CCDS5448.1, CCDS55102.1, CCDS75584.1	7p14-p12	2014-03-14			ENSG00000136250	ENSG00000136250	3.1.1.77		548	protein-coding gene	gene with protein product		102593				1883828	Standard	NM_001637		Approved		uc022abu.1	P28039	OTTHUMG00000023566	ENST00000258749.5:c.66G>T	chr7.hg19:g.36763688C>A		79.0	0.0		70.0	3.0	NM_001177507	A4D1Y5|B7Z490|Q53F13	Silent	SNP	ENST00000258749.5	hg19	CCDS5448.1																																																																																			.	C|0.590;T|0.410		0.512	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637	
VPS41	27072	hgsc.bcm.edu	37	7	38781711	38781711	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:38781711A>G	ENST00000310301.4	-	25	2187	c.2133T>C	c.(2131-2133)acT>acC	p.T711T	VPS41_ENST00000395969.2_Silent_p.T686T	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	711					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						TTAACAAGCCAGTAATAAATG	0.318																																					p.T711T		Atlas-SNP	.											.	VPS41	102	.	0			c.T2133C						.						53.0	53.0	53.0					7																	38781711		2203	4299	6502	SO:0001819	synonymous_variant	27072	exon25			CAAGCCAGTAATA	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.2133T>C	chr7.hg19:g.38781711A>G		135.0	0.0		96.0	4.0	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Silent	SNP	ENST00000310301.4	hg19	CCDS5457.1																																																																																			.	.		0.318	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
STK17A	9263	hgsc.bcm.edu	37	7	43663335	43663335	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:43663335G>T	ENST00000319357.5	+	6	947	c.768G>T	c.(766-768)atG>atT	p.M256I		NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	256	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						CATATGTCATGCTTACAGGAA	0.289																																					p.M256I		Atlas-SNP	.											.	STK17A	31	.	0			c.G768T						.						97.0	96.0	96.0					7																	43663335		2201	4297	6498	SO:0001583	missense	9263	exon6			TGTCATGCTTACA	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.768G>T	chr7.hg19:g.43663335G>T	ENSP00000319192:p.Met256Ile	81.0	0.0		82.0	5.0	NM_004760	A4D1V6|Q8IVC8	Missense_Mutation	SNP	ENST00000319357.5	hg19	CCDS5470.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.863338	0.91511	.	.	ENSG00000164543	ENST00000319357	T	0.41758	0.99	4.98	4.98	0.66077	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	0.64402	D	0.000020	T	0.52901	0.1763	N	0.25031	0.7	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.59904	-0.7366	10	0.87932	D	0	.	18.2488	0.89996	0.0:0.0:1.0:0.0	.	256	Q9UEE5	ST17A_HUMAN	I	256	ENSP00000319192:M256I	ENSP00000319192:M256I	M	+	3	0	STK17A	43629860	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.183000	0.94887	2.278000	0.76064	0.563000	0.77884	ATG	.	.		0.289	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760	
DBNL	28988	hgsc.bcm.edu	37	7	44098959	44098959	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:44098959T>C	ENST00000448521.1	+	10	940	c.842T>C	c.(841-843)cTg>cCg	p.L281P	DBNL_ENST00000456905.1_Missense_Mutation_p.L233P|DBNL_ENST00000468694.1_Missense_Mutation_p.L290P|DBNL_ENST00000452943.1_Missense_Mutation_p.L257P|DBNL_ENST00000440166.1_Missense_Mutation_p.L178P|DBNL_ENST00000494774.1_Missense_Mutation_p.L282P|DBNL_ENST00000497184.1_3'UTR|DBNL_ENST00000490734.2_Missense_Mutation_p.L187P	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	281					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|endocytosis (GO:0006897)|immune system process (GO:0002376)|neuron projection morphogenesis (GO:0048812)|podosome assembly (GO:0071800)|Rac protein signal transduction (GO:0016601)|synapse assembly (GO:0007416)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|podosome (GO:0002102)|postsynaptic density (GO:0014069)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|enzyme activator activity (GO:0008047)			breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						GCAGGCAAGCTGAGGAGCCCC	0.597																																					p.L290P	NSCLC(68;573 1327 18604 34760 37992)	Atlas-SNP	.											.	DBNL	26	.	0			c.T869C						.						38.0	39.0	38.0					7																	44098959		2203	4300	6503	SO:0001583	missense	28988	exon10			GCAAGCTGAGGAG	AF151364	CCDS34622.1, CCDS34623.1, CCDS47579.1, CCDS64633.1, CCDS64634.1	7p13	2004-07-22			ENSG00000136279	ENSG00000136279			2696	protein-coding gene	gene with protein product		610106				10087302	Standard	NM_014063		Approved	SH3P7, HIP-55	uc003tjq.4	Q9UJU6	OTTHUMG00000155350	ENST00000448521.1:c.842T>C	chr7.hg19:g.44098959T>C	ENSP00000411701:p.Leu281Pro	86.0	0.0		58.0	4.0	NM_001122956	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Missense_Mutation	SNP	ENST00000448521.1	hg19	CCDS34623.1	.	.	.	.	.	.	.	.	.	.	T	16.59	3.166408	0.57476	.	.	ENSG00000136279	ENST00000448521;ENST00000456905;ENST00000440166;ENST00000452943;ENST00000468694;ENST00000494774;ENST00000490734;ENST00000539475	T;T;T;T;T;T;T	0.35048	1.71;2.04;1.99;2.03;1.33;1.73;2.0	5.32	5.32	0.75619	.	0.800992	0.11347	N	0.573412	T	0.60183	0.2249	M	0.66939	2.045	0.80722	D	1	D;D;P;D;P;D;D;B;D	0.89917	1.0;1.0;0.488;0.999;0.919;0.999;0.997;0.36;1.0	D;D;B;D;P;D;D;B;D	0.75484	0.957;0.959;0.23;0.959;0.548;0.959;0.973;0.173;0.986	T	0.53961	-0.8364	10	0.48119	T	0.1	-29.9077	14.9982	0.71449	0.0:0.0:0.0:1.0	.	178;230;211;233;187;257;290;281;282	B4DEM2;B4DXL9;B4DDU5;B4DDP6;C9J7P1;B4DDD6;Q9UJU6-3;Q9UJU6;Q9UJU6-2	.;.;.;.;.;.;.;DBNL_HUMAN;.	P	281;233;178;257;290;282;187;211	ENSP00000411701:L281P;ENSP00000416421:L233P;ENSP00000415173:L178P;ENSP00000405343:L257P;ENSP00000417653:L290P;ENSP00000419992:L282P;ENSP00000417749:L187P	ENSP00000415173:L178P	L	+	2	0	DBNL	44065484	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.929000	0.70096	2.024000	0.59613	0.456000	0.33151	CTG	.	.		0.597	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063	
OGDH	4967	hgsc.bcm.edu	37	7	44687303	44687303	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:44687303T>C	ENST00000222673.5	+	4	504	c.462T>C	c.(460-462)gaT>gaC	p.D154D	OGDH_ENST00000543843.1_Intron|OGDH_ENST00000443864.2_Silent_p.D154D|OGDH_ENST00000439616.2_Intron|OGDH_ENST00000444676.1_Silent_p.D154D|OGDH_ENST00000449767.1_Intron|OGDH_ENST00000447398.1_Intron	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	154					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	GGATTTTGGATGCTGATCTGG	0.537																																					p.D154D		Atlas-SNP	.											.	OGDH	145	.	0			c.T462C						.						121.0	112.0	115.0					7																	44687303		2203	4300	6503	SO:0001819	synonymous_variant	4967	exon4			TTTGGATGCTGAT	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.462T>C	chr7.hg19:g.44687303T>C		96.0	0.0		94.0	4.0	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Silent	SNP	ENST00000222673.5	hg19	CCDS34627.1																																																																																			.	.		0.537	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1		
ZNF727	442319	hgsc.bcm.edu	37	7	63538877	63538877	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:63538877A>G	ENST00000550760.3	+	4	1629	c.1450A>G	c.(1450-1452)Aat>Gat	p.N484D	RP11-3N2.13_ENST00000445978.1_RNA	NM_001159522.1	NP_001152994.1	A8MUV8	ZN727_HUMAN	zinc finger protein 727	484					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|skin(1)|stomach(1)|urinary_tract(1)	8						AAGTGCAAAGAATGTGGCAAA	0.388																																					p.N484D		Atlas-SNP	.											.	ZNF727	35	.	0			c.A1450G						.						53.0	49.0	50.0					7																	63538877		692	1591	2283	SO:0001583	missense	442319	exon4			GCAAAGAATGTGG			7q11.21	2014-09-09	2014-09-09	2014-09-09	ENSG00000214652	ENSG00000214652		"""Zinc fingers, C2H2-type"", ""-"""	22785	pseudogene	pseudogene			"""zinc finger protein 727, pseudogene"""	ZNF727P			Standard	NM_001159522		Approved		uc011kdm.2	A8MUV8	OTTHUMG00000156536	ENST00000550760.3:c.1450A>G	chr7.hg19:g.63538877A>G	ENSP00000447987:p.Asn484Asp	104.0	0.0		84.0	4.0	NM_001159522		Missense_Mutation	SNP	ENST00000550760.3	hg19	CCDS55113.1	.	.	.	.	.	.	.	.	.	.	A	8.341	0.828632	0.16749	.	.	ENSG00000257482	ENST00000550760	T	0.04502	3.61	0.988	0.988	0.19796	.	.	.	.	.	T	0.02304	0.0071	N	0.08118	0	0.09310	N	1	B	0.17852	0.024	B	0.06405	0.002	T	0.48896	-0.8994	8	.	.	.	.	5.7933	0.18373	1.0:0.0:0.0:0.0	.	484	A8MUV8	ZN727_HUMAN	D	484	ENSP00000447987:N484D	.	N	+	1	0	ZNF727	63176312	0.000000	0.05858	0.124000	0.21820	0.119000	0.20118	0.706000	0.25690	0.363000	0.24346	0.352000	0.21897	AAT	.	.		0.388	ZNF727-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001159522	
STX1A	6804	hgsc.bcm.edu	37	7	73119552	73119552	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:73119552T>C	ENST00000222812.3	-	4	237	c.211A>G	c.(211-213)Acg>Gcg	p.T71A	STX1A_ENST00000395156.3_Missense_Mutation_p.T71A|STX1A_ENST00000395154.3_Missense_Mutation_p.T71A|STX1A_ENST00000395155.3_Missense_Mutation_p.T71A	NM_004603.3	NP_004594.1	Q16623	STX1A_HUMAN	syntaxin 1A (brain)	71					calcium ion-dependent exocytosis (GO:0017156)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of insulin secretion (GO:0050796)|response to gravity (GO:0009629)|secretion by cell (GO:0032940)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)	actomyosin (GO:0042641)|cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|SNARE complex (GO:0031201)|synaptic vesicle membrane (GO:0030672)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033)	calcium channel inhibitor activity (GO:0019855)			large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(55;0.0908)|all_lung(88;0.198)				TCCTCCTTCGTCTCTGGGGAG	0.587																																					p.T71A		Atlas-SNP	.											.	STX1A	16	.	0			c.A211G						.						149.0	130.0	136.0					7																	73119552		2203	4300	6503	SO:0001583	missense	6804	exon4			CCTTCGTCTCTGG		CCDS34655.1, CCDS55120.1	7q11.2	2008-07-18			ENSG00000106089	ENSG00000106089			11433	protein-coding gene	gene with protein product		186590		STX1		1321498	Standard	NM_001165903		Approved	HPC-1, p35-1	uc003tyx.3	Q16623	OTTHUMG00000137422	ENST00000222812.3:c.211A>G	chr7.hg19:g.73119552T>C	ENSP00000222812:p.Thr71Ala	171.0	0.0		112.0	5.0	NM_004603	O15447|O15448|Q12936|Q75MD9|Q7Z5K3|Q9BPZ6	Missense_Mutation	SNP	ENST00000222812.3	hg19	CCDS34655.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.392774	0.62066	.	.	ENSG00000106089	ENST00000222812;ENST00000395156;ENST00000395154;ENST00000395155	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.67	4.67	0.58626	t-SNARE (1);Syntaxin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.39682	0.1087	M	0.71036	2.16	0.80722	D	1	B;B;B	0.12630	0.006;0.002;0.0	B;B;B	0.10450	0.005;0.001;0.003	T	0.25813	-1.0121	10	0.12103	T	0.63	-27.0427	12.1051	0.53807	0.0:0.0:0.0:1.0	.	71;71;71	Q7Z5K3;Q16623-3;Q16623	.;.;STX1A_HUMAN	A	71	ENSP00000222812:T71A;ENSP00000378585:T71A;ENSP00000378583:T71A;ENSP00000378584:T71A	ENSP00000222812:T71A	T	-	1	0	STX1A	72757488	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	5.965000	0.70387	1.961000	0.56991	0.454000	0.30748	ACG	.	.		0.587	STX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268422.1	NM_004603	
HIP1	3092	hgsc.bcm.edu	37	7	75186064	75186064	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:75186064T>C	ENST00000336926.6	-	17	1659	c.1633A>G	c.(1633-1635)Agc>Ggc	p.S545G	HIP1_ENST00000434438.2_Missense_Mutation_p.S545G	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	545					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						TCCCGTTGGCTTGTGGCAAGT	0.463			T	PDGFRB	CMML																																p.S545G		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.A1633G						.						113.0	115.0	114.0					7																	75186064		2203	4300	6503	SO:0001583	missense	3092	exon17			GTTGGCTTGTGGC	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.1633A>G	chr7.hg19:g.75186064T>C	ENSP00000336747:p.Ser545Gly	70.0	0.0		43.0	4.0	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Missense_Mutation	SNP	ENST00000336926.6	hg19	CCDS34669.1	.	.	.	.	.	.	.	.	.	.	T	8.497	0.863309	0.17250	.	.	ENSG00000127946	ENST00000336926;ENST00000434438	T;T	0.14516	2.72;2.5	5.93	5.93	0.95920	.	0.226266	0.64402	D	0.000011	T	0.14270	0.0345	L	0.50919	1.6	0.45502	D	0.998461	B;B	0.21225	0.0;0.053	B;B	0.19391	0.0;0.025	T	0.08371	-1.0725	10	0.15952	T	0.53	-15.3367	13.7453	0.62872	0.0:0.0:0.0:1.0	.	545;545	E7ES17;O00291	.;HIP1_HUMAN	G	545	ENSP00000336747:S545G;ENSP00000410300:S545G	ENSP00000336747:S545G	S	-	1	0	HIP1	75024000	1.000000	0.71417	0.983000	0.44433	0.051000	0.14879	4.648000	0.61425	2.257000	0.74773	0.533000	0.62120	AGC	.	.		0.463	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338	
FGL2	10875	hgsc.bcm.edu	37	7	76829024	76829024	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:76829024T>C	ENST00000248598.5	-	1	119	c.87A>G	c.(85-87)gaA>gaG	p.E29E	RP11-467H10.2_ENST00000459742.1_RNA|CCDC146_ENST00000431197.1_Intron|CCDC146_ENST00000285871.4_Intron	NM_006682.2	NP_006673.1	Q14314	FGL2_HUMAN	fibrinogen-like 2	29						extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	13						CATCTTTAATTTCCTCTGTTT	0.498																																					p.E29E		Atlas-SNP	.											.	FGL2	40	.	0			c.A87G						.						96.0	95.0	95.0					7																	76829024		2203	4300	6503	SO:0001819	synonymous_variant	10875	exon1			TTTAATTTCCTCT	Z36531	CCDS5591.1	7q11.23	2013-02-06			ENSG00000127951	ENSG00000127951		"""Fibrinogen C domain containing"""	3696	protein-coding gene	gene with protein product		605351				7642106	Standard	NM_006682		Approved	pT49, T49	uc003ugb.3	Q14314	OTTHUMG00000130681	ENST00000248598.5:c.87A>G	chr7.hg19:g.76829024T>C		79.0	0.0		78.0	4.0	NM_006682		Silent	SNP	ENST00000248598.5	hg19	CCDS5591.1																																																																																			.	.		0.498	FGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253176.1	NM_006682	
SEMA3D	223117	hgsc.bcm.edu	37	7	84666257	84666257	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:84666257T>C	ENST00000284136.6	-	10	1182	c.1139A>G	c.(1138-1140)gAc>gGc	p.D380G	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	380	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						CCAACGATGGTCTGCACTTTC	0.398																																					p.D380G	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.A1139G						.						138.0	121.0	127.0					7																	84666257		2203	4300	6503	SO:0001583	missense	223117	exon10			CGATGGTCTGCAC	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"""Semaphorins"", ""Immunoglobulin superfamily / V-set domain containing"""	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.1139A>G	chr7.hg19:g.84666257T>C	ENSP00000284136:p.Asp380Gly	157.0	0.0		120.0	5.0	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	hg19	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.319342	0.81469	.	.	ENSG00000153993	ENST00000284136	T	0.22743	1.94	5.89	5.89	0.94794	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.43389	0.1245	L	0.55990	1.75	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.28459	-1.0043	10	0.72032	D	0.01	.	16.3071	0.82852	0.0:0.0:0.0:1.0	.	380	O95025	SEM3D_HUMAN	G	380	ENSP00000284136:D380G	ENSP00000284136:D380G	D	-	2	0	SEMA3D	84504193	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.965000	0.87945	2.250000	0.74265	0.477000	0.44152	GAC	.	.		0.398	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754	
ABCB1	5243	hgsc.bcm.edu	37	7	87214929	87214929	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:87214929C>A	ENST00000265724.3	-	5	602	c.185G>T	c.(184-186)gGg>gTg	p.G62V	ABCB1_ENST00000543898.1_Missense_Mutation_p.G62V	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	62	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	AAGTCCAGCCCCATGGATGAT	0.393																																					p.G62V		Atlas-SNP	.											.	ABCB1	263	.	0			c.G185T						.						93.0	94.0	94.0					7																	87214929		2203	4300	6503	SO:0001583	missense	5243	exon5			CCAGCCCCATGGA	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"""CD molecules"", ""ATP binding cassette transporters / subfamily B"""	40	protein-coding gene	gene with protein product	"""multidrug resistance protein 1"""	171050	"""colchicin sensitivity"""	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.185G>T	chr7.hg19:g.87214929C>A	ENSP00000265724:p.Gly62Val	106.0	0.0		116.0	6.0	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	hg19	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.467954	0.26335	.	.	ENSG00000085563	ENST00000265724;ENST00000543898	T;T	0.79033	-1.23;-1.23	5.72	5.72	0.89469	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	0.92283	0.7552	H	0.97440	4.005	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.949;1.0	D	0.94357	0.7584	10	0.72032	D	0.01	-22.2302	15.3886	0.74723	0.0:1.0:0.0:0.0	.	62;62	B5AK60;P08183	.;MDR1_HUMAN	V	62	ENSP00000265724:G62V;ENSP00000444095:G62V	ENSP00000265724:G62V	G	-	2	0	ABCB1	87052865	1.000000	0.71417	0.928000	0.36995	0.477000	0.33069	3.949000	0.56668	2.700000	0.92200	0.563000	0.77884	GGG	.	.		0.393	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	
HEPACAM2	253012	hgsc.bcm.edu	37	7	92825188	92825188	+	Nonsense_Mutation	SNP	C	C	A	rs145244580	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:92825188C>A	ENST00000394468.2	-	8	1305	c.1228G>T	c.(1228-1230)Gga>Tga	p.G410*	HEPACAM2_ENST00000341723.4_Nonsense_Mutation_p.G398*|HEPACAM2_ENST00000440868.1_Silent_p.S389S|HEPACAM2_ENST00000492616.1_5'UTR|HEPACAM2_ENST00000453812.2_Nonsense_Mutation_p.G433*	NM_001039372.1	NP_001034461.1	A8MVW5	HECA2_HUMAN	HEPACAM family member 2	410					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|midbody (GO:0030496)|spindle (GO:0005819)				breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(4)|skin(1)	28						TCATATATTCCGAAGTCATCC	0.383																																					p.G410X		Atlas-SNP	.											.	HEPACAM2	132	.	0			c.G1228T						.						116.0	113.0	114.0					7																	92825188		2203	4300	6503	SO:0001587	stop_gained	253012	exon8			ATATTCCGAAGTC	AK096002	CCDS5629.1, CCDS43616.1, CCDS75631.1, CCDS75632.1	7q21.3	2013-01-29	2008-07-11		ENSG00000188175	ENSG00000188175		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27364	protein-coding gene	gene with protein product		614133				12975309	Standard	NM_001288804		Approved	FLJ38683	uc003umm.3	A8MVW5	OTTHUMG00000131732	ENST00000394468.2:c.1228G>T	chr7.hg19:g.92825188C>A	ENSP00000377980:p.Gly410*	70.0	0.0		79.0	4.0	NM_001039372	B3KTT4|B4DPJ1|B9EG93|E9PDV5|Q6UXI0	Nonsense_Mutation	SNP	ENST00000394468.2	hg19	CCDS43616.1	.	.	.	.	.	.	.	.	.	.	C	37	6.197908	0.97367	.	.	ENSG00000188175	ENST00000394468;ENST00000341723;ENST00000453812	.	.	.	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-15.3871	16.7918	0.85591	0.0:1.0:0.0:0.0	.	.	.	.	X	410;398;433	.	ENSP00000340532:G398X	G	-	1	0	HEPACAM2	92663124	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.510000	0.60455	2.692000	0.91855	0.650000	0.86243	GGA	.	C|0.998;T|0.002		0.383	HEPACAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254651.1	NM_198151	
SMURF1	57154	hgsc.bcm.edu	37	7	98628253	98628253	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:98628253T>C	ENST00000361125.1	-	19	2547	c.2228A>G	c.(2227-2229)aAg>aGg	p.K743R	AC004893.11_ENST00000360902.1_RNA|AC004893.11_ENST00000468960.2_RNA|SMURF1_ENST00000361368.2_Missense_Mutation_p.K717R	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	743	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			TGTCAGCAGCTTCTCGTAGAG	0.522																																					p.K743R		Atlas-SNP	.											.	SMURF1	58	.	0			c.A2228G						.						122.0	111.0	115.0					7																	98628253		2203	4300	6503	SO:0001583	missense	57154	exon19			AGCAGCTTCTCGT	AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.2228A>G	chr7.hg19:g.98628253T>C	ENSP00000354621:p.Lys743Arg	96.0	0.0		74.0	5.0	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Missense_Mutation	SNP	ENST00000361125.1	hg19	CCDS34690.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.981217	0.93044	.	.	ENSG00000198742	ENST00000361368;ENST00000361125	T;T	0.52526	0.66;0.66	5.26	5.26	0.73747	HECT (4);	0.000000	0.85682	D	0.000000	T	0.61714	0.2369	L	0.43646	1.37	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	0.64859	-0.6308	10	0.72032	D	0.01	.	15.1696	0.72862	0.0:0.0:0.0:1.0	.	717;743;714	Q9HCE7-2;Q9HCE7;B9EGV3	.;SMUF1_HUMAN;.	R	717;743	ENSP00000355326:K717R;ENSP00000354621:K743R	ENSP00000354621:K743R	K	-	2	0	SMURF1	98466189	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.668000	0.83897	1.993000	0.58246	0.391000	0.25812	AAG	.	.		0.522	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429	
AP4M1	9179	hgsc.bcm.edu	37	7	99703069	99703069	+	Splice_Site	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:99703069T>C	ENST00000359593.4	+	11	994	c.836T>C	c.(835-837)cTg>cCg	p.L279P	AP4M1_ENST00000429084.1_Splice_Site_p.L286P|AP4M1_ENST00000421755.1_Splice_Site_p.L279P|AP4M1_ENST00000422582.1_Splice_Site_p.L151P	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	279	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|Golgi trans cisterna (GO:0000138)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GTCTCTCAGCTGACTGTGATG	0.612																																					p.L279P	Pancreas(174;1182 2812 29595 49511)	Atlas-SNP	.											.	AP4M1	39	.	0			c.T836C						.						120.0	101.0	108.0					7																	99703069		2203	4300	6503	SO:0001630	splice_region_variant	9179	exon11			CTCAGCTGACTGT	Y08387	CCDS5685.1	7q22.1	2012-06-29			ENSG00000221838	ENSG00000221838			574	protein-coding gene	gene with protein product	"""mu-adaptin-related protein-2"", ""mu subunit of AP-4"", ""AP-4 adapter complex mu subunit"", ""adaptor-related protein complex AP-4 mu4 subunit"""	602296				9013859, 10066790, 21620353	Standard	NM_004722		Approved	MU-ARP2, MU-4, SPG50	uc003utb.4	O00189	OTTHUMG00000154722	ENST00000359593.4:c.835-1T>C	chr7.hg19:g.99703069T>C		117.0	0.0		90.0	4.0	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Missense_Mutation	SNP	ENST00000359593.4	hg19	CCDS5685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.4|20.4	3.985015|3.985015	0.74474|0.74474	.|.	.|.	ENSG00000221838|ENSG00000221838	ENST00000438383;ENST00000429084;ENST00000359593;ENST00000439416;ENST00000421755;ENST00000422582;ENST00000450807|ENST00000445295	T;T;T;T;T;T;T|.	0.20598|.	2.06;2.06;2.06;2.06;2.06;2.06;2.06|.	5.38|5.38	5.38|5.38	0.77491|0.77491	Clathrin adaptor, mu subunit, conserved site (1);Clathrin adaptor, mu subunit, C-terminal (3);|.	0.071876|.	0.56097|.	D|.	0.000023|.	T|.	0.56572|.	0.1994|.	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.998;1.0;1.0|.	D;D;D|.	0.69307|.	0.947;0.963;0.963|.	T|.	0.53436|.	-0.8439|.	10|.	0.87932|.	D|.	0|.	2.8916|2.8916	13.3999|13.3999	0.60876|0.60876	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	235;286;279|.	C9JMG3;C9JC87;O00189|.	.;.;AP4M1_HUMAN|.	P|R	211;286;279;235;279;151;31|5	ENSP00000401613:L211P;ENSP00000403663:L286P;ENSP00000352603:L279P;ENSP00000414286:L235P;ENSP00000412185:L279P;ENSP00000406676:L151P;ENSP00000391585:L31P|.	ENSP00000352603:L279P|.	L|X	+|+	2|1	0|0	AP4M1|AP4M1	99541005|99541005	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	5.015000|5.015000	0.64035|0.64035	2.254000|2.254000	0.74563|0.74563	0.533000|0.533000	0.62120|0.62120	CTG|TGA	.	.		0.612	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722	Missense_Mutation
TFR2	7036	hgsc.bcm.edu	37	7	100225214	100225214	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:100225214A>G	ENST00000462107.1	-	16	2040	c.1753T>C	c.(1753-1755)Ttc>Ctc	p.F585L	TFR2_ENST00000431692.1_3'UTR|TFR2_ENST00000223051.3_Missense_Mutation_p.F585L|TFR2_ENST00000544242.1_Missense_Mutation_p.F126L			Q9UP52	TFR2_HUMAN	transferrin receptor 2	585					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	ATAAAGGAGAACTCGACGGCA	0.642																																					p.F585L		Atlas-SNP	.											.	TFR2	53	.	0			c.T1753C						.						58.0	58.0	58.0					7																	100225214		2203	4300	6503	SO:0001583	missense	7036	exon15			AGGAGAACTCGAC	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.1753T>C	chr7.hg19:g.100225214A>G	ENSP00000420525:p.Phe585Leu	64.0	0.0		65.0	4.0	NM_003227	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Missense_Mutation	SNP	ENST00000462107.1	hg19	CCDS34707.1	.	.	.	.	.	.	.	.	.	.	A	15.07	2.723543	0.48728	.	.	ENSG00000106327	ENST00000223051;ENST00000462107;ENST00000544242	T;T;T	0.37915	1.17;1.17;1.17	4.9	4.9	0.64082	Peptidase M28 (1);	0.132555	0.51477	D	0.000085	T	0.29190	0.0726	L	0.28649	0.875	0.80722	D	1	B	0.28667	0.219	B	0.31946	0.138	T	0.10086	-1.0645	10	0.44086	T	0.13	-28.6179	12.5712	0.56339	1.0:0.0:0.0:0.0	.	585	Q9UP52	TFR2_HUMAN	L	585;585;126	ENSP00000223051:F585L;ENSP00000420525:F585L;ENSP00000443656:F126L	ENSP00000223051:F585L	F	-	1	0	TFR2	100063150	1.000000	0.71417	1.000000	0.80357	0.475000	0.33008	2.953000	0.49105	2.077000	0.62373	0.374000	0.22700	TTC	.	.		0.642	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227	
GNB2	2783	hgsc.bcm.edu	37	7	100275432	100275432	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:100275432A>G	ENST00000303210.4	+	7	970	c.488A>G	c.(487-489)gAt>gGt	p.D163G	GNB2_ENST00000427895.1_Missense_Mutation_p.D63G|GNB2_ENST00000419828.1_Missense_Mutation_p.D63G|GNB2_ENST00000436220.1_Missense_Mutation_p.D119G|GNB2_ENST00000393926.1_Missense_Mutation_p.D163G|GNB2_ENST00000393924.1_Missense_Mutation_p.D163G|GNB2_ENST00000424361.1_Missense_Mutation_p.D119G	NM_005273.3	NP_005264.2	P62879	GBB2_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2	163					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell body (GO:0044297)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|lung(3)|ovary(2)|prostate(1)	7	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)	Ovarian(593;0.238)				AGCTCTGGGGATACCACCTGG	0.622																																					p.D163G		Atlas-SNP	.											.	GNB2	29	.	0			c.A488G						.						55.0	45.0	49.0					7																	100275432		2203	4300	6503	SO:0001583	missense	2783	exon7			CTGGGGATACCAC	M16514	CCDS5703.1	7q21.3-q22.1	2013-01-10			ENSG00000172354	ENSG00000172354		"""WD repeat domain containing"""	4398	protein-coding gene	gene with protein product	"""G protein, beta-2 subunit"", ""guanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 2"", ""signal-transducing guanine nucleotide-binding regulatory protein beta subunit"", ""transducin beta chain 2"""	139390				9799793	Standard	NM_005273		Approved		uc003uwb.3	P62879	OTTHUMG00000137419	ENST00000303210.4:c.488A>G	chr7.hg19:g.100275432A>G	ENSP00000305260:p.Asp163Gly	105.0	0.0		93.0	4.0	NM_005273	B3KPU1|P11016|P54312	Missense_Mutation	SNP	ENST00000303210.4	hg19	CCDS5703.1	.	.	.	.	.	.	.	.	.	.	.	25.9	4.680853	0.88542	.	.	ENSG00000172354	ENST00000303210;ENST00000451587;ENST00000436220;ENST00000424361;ENST00000419828;ENST00000427895;ENST00000393926;ENST00000431068;ENST00000393924	D;D;D;D;D;D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49;-2.49	4.79	4.79	0.61399	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.95959	0.8684	H	0.96430	3.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96816	0.9600	10	0.87932	D	0	-1.7218	12.3252	0.55007	1.0:0.0:0.0:0.0	.	163	P62879	GBB2_HUMAN	G	163;163;119;119;63;63;163;163;163	ENSP00000305260:D163G;ENSP00000399904:D163G;ENSP00000401873:D119G;ENSP00000389391:D119G;ENSP00000390543:D63G;ENSP00000400286:D63G;ENSP00000377503:D163G;ENSP00000390077:D163G;ENSP00000377501:D163G	ENSP00000305260:D163G	D	+	2	0	GNB2	100113368	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.088000	0.76901	2.014000	0.59158	0.379000	0.24179	GAT	.	.		0.622	GNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268391.2	NM_005273	
ACHE	43	hgsc.bcm.edu	37	7	100487872	100487872	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:100487872T>C	ENST00000412389.1	-	4	1963	c.1808A>G	c.(1807-1809)gAc>gGc	p.D603G	ACHE_ENST00000302913.4_3'UTR|UFSP1_ENST00000388761.2_5'Flank|ACHE_ENST00000428317.1_Missense_Mutation_p.D603G|ACHE_ENST00000241069.5_Missense_Mutation_p.D603G|ACHE_ENST00000419336.2_Missense_Mutation_p.D515G			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	603					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	GCTGTAGTGGTCGAACTGGTT	0.632																																					p.D603G		Atlas-SNP	.											.	ACHE	80	.	0			c.A1808G						.						66.0	57.0	60.0					7																	100487872		2203	4300	6503	SO:0001583	missense	43	exon5			TAGTGGTCGAACT		CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"""Blood group antigens"""	108	protein-coding gene	gene with protein product	"""Yt blood group"""	100740	"""acetylcholinesterase (YT blood group)"", ""acetylcholinesterase (Yt blood group)"", ""acetylcholinesterase"""	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.1808A>G	chr7.hg19:g.100487872T>C	ENSP00000394976:p.Asp603Gly	207.0	0.0		141.0	6.0	NM_000665	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Missense_Mutation	SNP	ENST00000412389.1	hg19	CCDS5709.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.2|25.2	4.615153|4.615153	0.87359|0.87359	.|.	.|.	ENSG00000087085|ENSG00000087085	ENST00000419336;ENST00000241069;ENST00000428317;ENST00000412389|ENST00000426415;ENST00000430554	T;T;T;T|T;T	0.69435|0.68479	-0.4;-0.28;-0.28;-0.28|-0.33;-0.1	4.32|4.32	4.32|4.32	0.51571|0.51571	Acetylcholinesterase, tetramerisation (2);|.	0.000000|.	0.64402|.	U|.	0.000003|.	T|T	0.71082|0.71082	0.3298|0.3298	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.987;0.999|.	P;D|.	0.74674|.	0.797;0.984|.	T|T	0.74150|0.74150	-0.3758|-0.3758	10|7	0.56958|0.87932	D|D	0.05|0	.|.	11.4294|11.4294	0.50032|0.50032	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	515;603|.	P22303-3;P22303|.	.;ACES_HUMAN|.	G|A	515;603;603;603|385;422	ENSP00000403474:D515G;ENSP00000241069:D603G;ENSP00000414858:D603G;ENSP00000394976:D603G|ENSP00000397143:T385A;ENSP00000399725:T422A	ENSP00000241069:D603G|ENSP00000397143:T385A	D|T	-|-	2|1	0|0	ACHE|ACHE	100325808|100325808	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	5.040000|5.040000	0.64191|0.64191	1.599000|1.599000	0.50093|0.50093	0.260000|0.260000	0.18958|0.18958	GAC|ACC	.	.		0.632	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831	
CUX1	1523	hgsc.bcm.edu	37	7	101840082	101840082	+	Missense_Mutation	SNP	C	C	A	rs569218052		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:101840082C>A	ENST00000292535.7	+	15	1429	c.1391C>A	c.(1390-1392)tCc>tAc	p.S464Y	CUX1_ENST00000556210.1_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000360264.3_Missense_Mutation_p.S475Y|CUX1_ENST00000549414.2_Missense_Mutation_p.S464Y|CUX1_ENST00000550008.2_Missense_Mutation_p.S464Y|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000546411.2_Intron|CUX1_ENST00000292538.4_Intron|SNORA48_ENST00000517015.1_RNA	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	464					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						TTCAGCTCATCCCTGGCAAGC	0.532													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16575	0.0		0.0	False		,,,				2504	0.0				p.S475Y		Atlas-SNP	.											.	CUX1	253	.	0			c.C1424A						.						70.0	73.0	72.0					7																	101840082		2203	4300	6503	SO:0001583	missense	1523	exon15			GCTCATCCCTGGC	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1391C>A	chr7.hg19:g.101840082C>A	ENSP00000292535:p.Ser464Tyr	174.0	0.0		138.0	44.0	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476486	0.44044	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008	T;T;T;T	0.60797	0.18;0.17;0.16;0.17	5.71	4.8	0.61643	.	0.294006	0.28635	N	0.014644	T	0.52500	0.1738	N	0.22421	0.69	0.80722	D	1	P;P	0.42649	0.681;0.786	B;P	0.47251	0.254;0.542	T	0.53012	-0.8498	10	0.40728	T	0.16	-6.8901	15.6421	0.77012	0.1423:0.8577:0.0:0.0	.	464;475	P39880;P39880-3	CUX1_HUMAN;.	Y	475;464;464;464	ENSP00000353401:S475Y;ENSP00000292535:S464Y;ENSP00000446630:S464Y;ENSP00000447373:S464Y	ENSP00000292535:S464Y	S	+	2	0	CUX1	101626802	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.111000	0.50360	1.350000	0.45770	0.561000	0.74099	TCC	.	.		0.532	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913	
NRCAM	4897	hgsc.bcm.edu	37	7	107807398	107807398	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:107807398A>G	ENST00000425651.2	-	27	3433	c.3434T>C	c.(3433-3435)gTg>gCg	p.V1145A	NRCAM_ENST00000351718.4_Intron|NRCAM_ENST00000379024.4_Intron|NRCAM_ENST00000379028.3_Missense_Mutation_p.V1145A|NRCAM_ENST00000413765.2_Intron|NRCAM_ENST00000379022.4_Missense_Mutation_p.V1145A	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1145	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						CTCTGAACTCACAAAACCAGA	0.537																																					p.V1145A		Atlas-SNP	.											.	NRCAM	267	.	0			c.T3434C						.						53.0	58.0	57.0					7																	107807398		2060	4191	6251	SO:0001583	missense	4897	exon27			GAACTCACAAAAC		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3434T>C	chr7.hg19:g.107807398A>G	ENSP00000401244:p.Val1145Ala	111.0	0.0		86.0	4.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	hg19	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	A	10.03	1.240010	0.22711	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000425651;ENST00000379022	T;T;T	0.58358	0.34;0.34;0.38	5.67	5.67	0.87782	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.382752	0.29892	N	0.010929	T	0.26376	0.0644	N	0.08118	0	0.31329	N	0.685032	B	0.02656	0.0	B	0.09377	0.004	T	0.27640	-1.0068	10	0.07644	T	0.81	.	7.4738	0.27363	0.6361:0.2434:0.0:0.1205	.	1145	Q92823	NRCAM_HUMAN	A	1145	ENSP00000368314:V1145A;ENSP00000401244:V1145A;ENSP00000368308:V1145A	ENSP00000368308:V1145A	V	-	2	0	NRCAM	107594634	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.123000	0.41996	2.284000	0.76573	0.523000	0.50628	GTG	.	.		0.537	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121679517	121679517	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:121679517G>A	ENST00000393386.2	+	20	5923	c.5512G>A	c.(5512-5514)Gat>Aat	p.D1838N	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.D971N	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1838	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						GAGAAAATGTGATCAGTACTG	0.418																																					p.D1838N		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G5512A						.						87.0	86.0	86.0					7																	121679517		2203	4300	6503	SO:0001583	missense	5803	exon20			AAATGTGATCAGT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.5512G>A	chr7.hg19:g.121679517G>A	ENSP00000377047:p.Asp1838Asn	39.0	0.0		53.0	4.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	G	36	5.724235	0.96847	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	D;D	0.84070	-1.8;-1.8	5.88	5.88	0.94601	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.92296	0.7556	M	0.82923	2.615	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.994;0.997	D	0.92393	0.5923	10	0.72032	D	0.01	.	20.2441	0.98394	0.0:0.0:1.0:0.0	.	977;971;1838	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	N	1838;971	ENSP00000377047:D1838N;ENSP00000410000:D971N	ENSP00000377047:D1838N	D	+	1	0	PTPRZ1	121466753	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.813000	0.99286	2.774000	0.95407	0.655000	0.94253	GAT	.	.		0.418	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
FLNC	2318	hgsc.bcm.edu	37	7	128494663	128494663	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:128494663G>A	ENST00000325888.8	+	41	7185	c.6924G>A	c.(6922-6924)ccG>ccA	p.P2308P	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.P2275P	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2308					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CTGTGGGGCCGCTGGGTGAAG	0.692																																					p.P2308P		Atlas-SNP	.											.	FLNC	339	.	0			c.G6924A						.						13.0	16.0	15.0					7																	128494663		2147	4249	6396	SO:0001819	synonymous_variant	2318	exon41			GGGGCCGCTGGGT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.6924G>A	chr7.hg19:g.128494663G>A		160.0	0.0		107.0	5.0	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	hg19	CCDS43644.1																																																																																			.	.		0.692	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
KIAA1147	57189	hgsc.bcm.edu	37	7	141362629	141362629	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:141362629G>T	ENST00000536163.1	-	9	1194	c.1195C>A	c.(1195-1197)Cgg>Agg	p.R399R	KIAA1147_ENST00000482493.1_Silent_p.R295R|RP5-894A10.6_ENST00000602609.1_RNA	NM_001080392.1	NP_001073861.1	A4D1U4	LCHN_HUMAN	KIAA1147	399										breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|ovary(1)|skin(1)	12	Melanoma(164;0.0171)					TGAAATATCCGGTTGTTTTGT	0.502																																					p.R399R		Atlas-SNP	.											.	KIAA1147	32	.	0			c.C1195A						.						30.0	30.0	30.0					7																	141362629		1845	4088	5933	SO:0001819	synonymous_variant	57189	exon9			ATATCCGGTTGTT	AB032973	CCDS47726.1	7q34	2012-10-04			ENSG00000257093	ENSG00000257093			29472	protein-coding gene	gene with protein product							Standard	NM_001080392		Approved	LCHN	uc003vwk.3	A4D1U4	OTTHUMG00000157539	ENST00000536163.1:c.1195C>A	chr7.hg19:g.141362629G>T		117.0	0.0		95.0	4.0	NM_001080392	Q9ULS3	Silent	SNP	ENST00000536163.1	hg19	CCDS47726.1																																																																																			.	.		0.502	KIAA1147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349104.1		
TRPV6	55503	hgsc.bcm.edu	37	7	142569466	142569466	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:142569466C>T	ENST00000359396.3	-	15	2417	c.2172G>A	c.(2170-2172)caG>caA	p.Q724Q		NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	724					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					GCAGTCAGATCTGATATTCCC	0.527																																					p.Q724Q		Atlas-SNP	.											.	TRPV6	108	.	0			c.G2172A						.						76.0	75.0	75.0					7																	142569466		2203	4300	6503	SO:0001819	synonymous_variant	55503	exon15			TCAGATCTGATAT	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	14006	protein-coding gene	gene with protein product		606680	"""epithelial calcium channel 2"""	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.2172G>A	chr7.hg19:g.142569466C>T		126.0	0.0		91.0	5.0	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Silent	SNP	ENST00000359396.3	hg19	CCDS5874.1																																																																																			.	.		0.527	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274	
CUL1	8454	hgsc.bcm.edu	37	7	148451110	148451110	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:148451110A>G	ENST00000325222.4	+	3	462	c.183A>G	c.(181-183)caA>caG	p.Q61Q	CUL1_ENST00000602748.1_Silent_p.Q61Q|CUL1_ENST00000409469.1_Silent_p.Q61Q	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	61				Missing (in Ref. 1; AAC50544). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			AGTCAAACCAAGCACGAGGAG	0.413																																					p.Q61Q		Atlas-SNP	.											.	CUL1	80	.	0			c.A183G						.						59.0	56.0	57.0					7																	148451110		2203	4300	6503	SO:0001819	synonymous_variant	8454	exon3			AAACCAAGCACGA	U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	ENST00000325222.4:c.183A>G	chr7.hg19:g.148451110A>G		100.0	0.0		93.0	5.0	NM_003592	D3DWG3|O60719|Q08AL6|Q8IYW1	Silent	SNP	ENST00000325222.4	hg19	CCDS34772.1																																																																																			.	.		0.413	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592	
ZNF862	643641	hgsc.bcm.edu	37	7	149545056	149545056	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:149545056T>C	ENST00000223210.4	+	4	719	c.474T>C	c.(472-474)gcT>gcC	p.A158A		NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	158					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)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						AGCAGACGGCTCTGTTCTGCT	0.507																																					p.A158A		Atlas-SNP	.											.	ZNF862	97	.	0			c.T474C						.						49.0	49.0	49.0					7																	149545056		2022	4180	6202	SO:0001819	synonymous_variant	643641	exon4			GACGGCTCTGTTC	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"""Zinc fingers, C2H2-type"", ""-"""	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.474T>C	chr7.hg19:g.149545056T>C		128.0	0.0		119.0	6.0	NM_001099220	A0AUL8	Silent	SNP	ENST00000223210.4	hg19	CCDS47741.1																																																																																			.	.		0.507	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
GIMAP1	170575	hgsc.bcm.edu	37	7	150417814	150417814	+	Missense_Mutation	SNP	G	G	A	rs537240577	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:150417814G>A	ENST00000307194.5	+	3	862	c.722G>A	c.(721-723)cGg>cAg	p.R241Q		NM_130759.3	NP_570115.1	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	241					B cell differentiation (GO:0030183)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGCGGCTCCGGCGGGTGGCG	0.706													G|||	3	0.000599042	0.0	0.0029	5008	,	,		14481	0.0		0.0	False		,,,				2504	0.001				p.R241Q		Atlas-SNP	.											GIMAP1,NS,carcinoma,0,1	GIMAP1	61	.	0			c.G722A						.						10.0	12.0	11.0					7																	150417814		2123	4150	6273	SO:0001583	missense	170575	exon3			GGCTCCGGCGGGT	AJ306287	CCDS5906.1	7q36.1	2014-04-04			ENSG00000213203	ENSG00000213203		"""GTPases, IMAP"""	23237	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 2"""	608084				15474311, 18701445	Standard	NM_130759		Approved	HIMAP1, IMAP38, IMAP1, IAN2		Q8WWP7	OTTHUMG00000157489	ENST00000307194.5:c.722G>A	chr7.hg19:g.150417814G>A	ENSP00000302833:p.Arg241Gln	65.0	0.0		57.0	6.0	NM_130759	B2RCI3|Q8NAZ0	Missense_Mutation	SNP	ENST00000307194.5	hg19	CCDS5906.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.461332	0.43736	.	.	ENSG00000213203	ENST00000307194	T	0.07021	3.23	4.51	-0.551	0.11822	.	1.927680	0.04097	U	0.312211	T	0.06416	0.0165	L	0.29908	0.895	0.09310	N	1	B	0.22909	0.077	B	0.08055	0.003	T	0.38156	-0.9674	10	0.34782	T	0.22	.	4.3474	0.11139	0.297:0.3023:0.4007:0.0	.	241	Q8WWP7	GIMA1_HUMAN	Q	241	ENSP00000302833:R241Q	ENSP00000302833:R241Q	R	+	2	0	GIMAP1	150048747	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.355000	0.02612	-0.187000	0.10516	-0.145000	0.13849	CGG	.	.		0.706	GIMAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348951.2	NM_130759	
AOC1	26	hgsc.bcm.edu	37	7	150553813	150553813	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:150553813T>C	ENST00000493429.1	+	4	839	c.255T>C	c.(253-255)ttT>ttC	p.F85F	AOC1_ENST00000360937.4_Silent_p.F85F|AOC1_ENST00000467291.1_Silent_p.F85F|AOC1_ENST00000416793.2_Silent_p.F85F			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	85					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	TGCTGAGGTTTCTGGATAAAG	0.567																																					p.F85F		Atlas-SNP	.											.	ABP1	92	.	0			c.T255C						.						153.0	152.0	152.0					7																	150553813		2074	4213	6287	SO:0001819	synonymous_variant	26	exon2			GAGGTTTCTGGAT	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.255T>C	chr7.hg19:g.150553813T>C		121.0	0.0		92.0	4.0	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	hg19	CCDS43679.1																																																																																			.	.		0.567	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
NOS3	4846	hgsc.bcm.edu	37	7	150707785	150707785	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:150707785T>C	ENST00000297494.3	+	22	3143	c.2786T>C	c.(2785-2787)cTc>cCc	p.L929P	NOS3_ENST00000461406.1_Missense_Mutation_p.L723P|ATG9B_ENST00000494791.1_5'Flank|NOS3_ENST00000477227.1_3'UTR	NM_000603.4	NP_000594.2	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCACTGCTCCTCACCCAGCTG	0.657																																					p.L929P		Atlas-SNP	.											.	NOS3	131	.	0			c.T2786C						.						31.0	31.0	31.0					7																	150707785		2202	4300	6502	SO:0001583	missense	4846	exon22			TGCTCCTCACCCA		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"""endothelial nitric oxide synthase"""	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000297494.3:c.2786T>C	chr7.hg19:g.150707785T>C	ENSP00000297494:p.Leu929Pro	133.0	0.0		95.0	4.0	NM_000603	Q495E5	Missense_Mutation	SNP	ENST00000297494.3	hg19	CCDS5912.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.2|28.2	4.897313|4.897313	0.91962|0.91962	.|.	.|.	ENSG00000164867|ENSG00000164867	ENST00000297494;ENST00000461406|ENST00000475017	T;T|.	0.70631|.	-0.5;-0.5|.	4.86|4.86	4.86|4.86	0.63082|0.63082	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);|.	0.000000|.	0.53938|.	D|.	0.000054|.	T|T	0.78880|0.78880	0.4353|0.4353	M|M	0.88640|0.88640	2.97|2.97	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.999|.	T|T	0.82339|0.82339	-0.0506|-0.0506	10|5	0.87932|.	D|.	0|.	3.8375|3.8375	12.443|12.443	0.55635|0.55635	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	723;929|.	E7ESA7;P29474|.	.;NOS3_HUMAN|.	P|P	929;723|223	ENSP00000297494:L929P;ENSP00000417143:L723P|.	ENSP00000297494:L929P|.	L|S	+|+	2|1	0|0	NOS3|NOS3	150338718|150338718	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	7.811000|7.811000	0.86092|0.86092	2.041000|2.041000	0.60428|0.60428	0.402000|0.402000	0.26972|0.26972	CTC|TCA	.	.		0.657	NOS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350750.2	NM_000603	
NCAPG2	54892	hgsc.bcm.edu	37	7	158472756	158472756	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr7:158472756A>G	ENST00000409423.1	-	12	1214	c.1042T>C	c.(1042-1044)Tca>Cca	p.S348P	NCAPG2_ENST00000275830.10_Missense_Mutation_p.S140P|NCAPG2_ENST00000449727.2_Missense_Mutation_p.S348P|NCAPG2_ENST00000356309.3_Missense_Mutation_p.S348P|NCAPG2_ENST00000409339.3_Missense_Mutation_p.S348P	NM_001281932.1	NP_001268861.1	Q86XI2	CNDG2_HUMAN	non-SMC condensin II complex, subunit G2	348					chromosome condensation (GO:0030261)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	39	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)		GCAGCATTTGATCGAACTTCA	0.363																																					p.S348P		Atlas-SNP	.											.	NCAPG2	80	.	0			c.T1042C						.						115.0	106.0	109.0					7																	158472756		1841	4099	5940	SO:0001583	missense	54892	exon11			CATTTGATCGAAC	BC043404	CCDS43686.1, CCDS64816.1	7q36.3	2006-09-04	2006-09-04	2006-09-04	ENSG00000146918	ENSG00000146918			21904	protein-coding gene	gene with protein product		608532	"""leucine zipper protein 5"""	LUZP5		14532007	Standard	NM_001281933		Approved	FLJ20311, MTB, CAP-G2, hCAP-G2	uc003wnv.1	Q86XI2	OTTHUMG00000151438	ENST00000409423.1:c.1042T>C	chr7.hg19:g.158472756A>G	ENSP00000386569:p.Ser348Pro	146.0	0.0		120.0	5.0	NM_017760	A4D228|Q7Z3J9|Q8WUG8|Q9BRX6|Q9H8S2|Q9H9K6	Missense_Mutation	SNP	ENST00000409423.1	hg19	CCDS43686.1	.	.	.	.	.	.	.	.	.	.	A	18.42	3.619619	0.66787	.	.	ENSG00000146918	ENST00000356309;ENST00000409423;ENST00000275830;ENST00000409339;ENST00000449727	T;T;T;T;T	0.48522	1.41;1.41;0.81;1.41;1.41	6.17	5.0	0.66597	Armadillo-like helical (1);Armadillo-type fold (1);	0.063219	0.64402	D	0.000003	T	0.60856	0.2301	L	0.51422	1.61	0.46458	D	0.999057	D;D;D	0.71674	0.997;0.997;0.998	D;D;D	0.66847	0.911;0.939;0.947	T	0.61302	-0.7090	10	0.52906	T	0.07	-10.6941	13.2852	0.60239	0.752:0.248:0.0:0.0	.	348;140;348	Q86XI2-2;E7EUH9;Q86XI2	.;.;CNDG2_HUMAN	P	348;348;140;348;348	ENSP00000348657:S348P;ENSP00000386569:S348P;ENSP00000275830:S140P;ENSP00000387007:S348P;ENSP00000388326:S348P	ENSP00000275830:S140P	S	-	1	0	NCAPG2	158165517	0.998000	0.40836	0.696000	0.30242	0.839000	0.47603	2.303000	0.43646	1.123000	0.41961	0.533000	0.62120	TCA	.	.		0.363	NCAPG2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327111.1	NM_017760	
CSMD1	64478	hgsc.bcm.edu	37	8	2823315	2823315	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:2823315T>C	ENST00000520002.1	-	60	9820	c.9265A>G	c.(9265-9267)Agc>Ggc	p.S3089G	CSMD1_ENST00000537824.1_Missense_Mutation_p.S3088G|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000542608.1_Intron|CSMD1_ENST00000602557.1_Missense_Mutation_p.S3089G			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3089	Sushi 24. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ACAGGTTTGCTCGGATTCCAC	0.418																																					p.S3088G		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A9262G						.						80.0	78.0	78.0					8																	2823315		1988	4181	6169	SO:0001583	missense	64478	exon59			GTTTGCTCGGATT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9265A>G	chr8.hg19:g.2823315T>C	ENSP00000430733:p.Ser3089Gly	145.0	0.0		75.0	4.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.86|11.86	1.765752|1.765752	0.31228|0.31228	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000520002;ENST00000318252;ENST00000537824	.|T;T	.|0.66460	.|-0.21;-0.21	5.42|5.42	5.42|5.42	0.78866|0.78866	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.133108	.|0.50627	.|D	.|0.000113	T|T	0.65154|0.65154	0.2664|0.2664	L|L	0.56199|0.56199	1.76|1.76	0.80722|0.80722	D|D	1|1	.|B;B	.|0.21147	.|0.052;0.018	.|B;B	.|0.29176	.|0.055;0.099	T|T	0.61893|0.61893	-0.6969|-0.6969	5|10	.|0.37606	.|T	.|0.19	.|.	15.475|15.475	0.75471|0.75471	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|3089;3089	.|E5RIG2;Q96PZ7	.|.;CSMD1_HUMAN	G|G	2505|3089;2950;3088	.|ENSP00000430733:S3089G;ENSP00000441462:S3088G	.|ENSP00000320445:S2950G	E|S	-|-	2|1	0|0	CSMD1|CSMD1	2810722|2810722	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.027000|0.027000	0.11550|0.11550	4.845000|4.845000	0.62853|0.62853	2.056000|2.056000	0.61249|0.61249	0.533000|0.533000	0.62120|0.62120	GAG|AGC	.	.		0.418	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
SLC7A2	6542	hgsc.bcm.edu	37	8	17422622	17422622	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:17422622T>C	ENST00000494857.1	+	13	2162	c.1944T>C	c.(1942-1944)ccT>ccC	p.P648P	SLC7A2_ENST00000398090.3_Silent_p.P687P|SLC7A2_ENST00000470360.1_Silent_p.P687P|SLC7A2_ENST00000004531.10_Silent_p.P688P|SLC7A2_ENST00000522656.1_Silent_p.P648P	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	648					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	TCAGTTCACCTTTCATATTCC	0.418																																					p.P688P		Atlas-SNP	.											.	SLC7A2	157	.	0			c.T2064C						.						112.0	89.0	97.0					8																	17422622		2203	4300	6503	SO:0001819	synonymous_variant	6542	exon12			TTCACCTTTCATA	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"""Solute carriers"""	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.1944T>C	chr8.hg19:g.17422622T>C		169.0	0.0		87.0	4.0	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Silent	SNP	ENST00000494857.1	hg19	CCDS34852.1																																																																																			.	.		0.418	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046	
PCM1	5108	hgsc.bcm.edu	37	8	17867212	17867212	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:17867212A>G	ENST00000519253.1	+	31	5346	c.5095A>G	c.(5095-5097)Aaa>Gaa	p.K1699E	PCM1_ENST00000524226.1_Missense_Mutation_p.K1653E|PCM1_ENST00000325083.8_Missense_Mutation_p.K1707E|PCM1_ENST00000327578.8_Missense_Mutation_p.K406E			Q15154	PCM1_HUMAN	pericentriolar material 1	1707	Interaction with HAP1.				centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		ATGCAAAAGGAAAATAGAAGC	0.308			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""																																p.K1707E		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	PCM1	120	.	0			c.A5119G						.						54.0	52.0	52.0					8																	17867212		1830	4074	5904	SO:0001583	missense	5108	exon31			AAAAGGAAAATAG		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.5095A>G	chr8.hg19:g.17867212A>G	ENSP00000431099:p.Lys1699Glu	138.0	0.0		67.0	4.0	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	hg19		.	.	.	.	.	.	.	.	.	.	A	17.25	3.342073	0.61073	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226;ENST00000327578	T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3	4.91	4.91	0.64330	.	0.316425	0.32769	N	0.005662	T	0.71804	0.3383	L	0.50333	1.59	0.39847	D	0.973192	P;P;B;P;P;P;P	0.50272	0.79;0.79;0.379;0.79;0.827;0.933;0.79	P;P;B;P;B;P;P	0.53760	0.561;0.561;0.187;0.561;0.442;0.734;0.561	T	0.76094	-0.3085	10	0.59425	D	0.04	-25.7633	14.8517	0.70300	1.0:0.0:0.0:0.0	.	1699;1707;506;1699;1652;1653;1707	B9EIS5;D3DSQ0;B4DJ00;E7ETA6;Q15154-2;E7EV56;Q15154	.;.;.;.;.;.;PCM1_HUMAN	E	1707;1699;1653;406	ENSP00000327077:K1707E;ENSP00000431099:K1699E;ENSP00000430521:K1653E;ENSP00000328332:K406E	ENSP00000327077:K1707E	K	+	1	0	PCM1	17911492	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.778000	0.75043	1.982000	0.57802	0.377000	0.23210	AAA	.	.		0.308	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
PCM1	5108	hgsc.bcm.edu	37	8	17868140	17868140	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:17868140A>G	ENST00000519253.1	+	32	5410	c.5159A>G	c.(5158-5160)cAt>cGt	p.H1720R	PCM1_ENST00000524226.1_Missense_Mutation_p.H1674R|PCM1_ENST00000325083.8_Missense_Mutation_p.H1728R|PCM1_ENST00000327578.8_Missense_Mutation_p.H427R			Q15154	PCM1_HUMAN	pericentriolar material 1	1728	Interaction with HAP1.				centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		CTTGAAGATCATGGCTCACCT	0.393			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""																																p.H1728R		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	PCM1	120	.	0			c.A5183G						.						128.0	125.0	126.0					8																	17868140		1871	4104	5975	SO:0001583	missense	5108	exon32			AAGATCATGGCTC		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.5159A>G	chr8.hg19:g.17868140A>G	ENSP00000431099:p.His1720Arg	156.0	0.0		71.0	4.0	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.128|6.128	0.391823|0.391823	0.11581|0.11581	.|.	.|.	ENSG00000078674|ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226;ENST00000327578|ENST00000522275	T;T;T;T|.	0.63417|.	-0.04;-0.04;-0.04;-0.04|.	4.85|4.85	-0.802|-0.802	0.10889|0.10889	.|.	0.805653|.	0.11459|.	N|.	0.561977|.	T|T	0.09291|0.09291	0.0229|0.0229	N|N	0.03608|0.03608	-0.345|-0.345	0.22500|0.22500	N|N	0.999041|0.999041	B;B;B;B;B;B;B|.	0.10296|.	0.0;0.0;0.0;0.0;0.0;0.003;0.0|.	B;B;B;B;B;B;B|.	0.15484|.	0.002;0.002;0.001;0.002;0.001;0.013;0.002|.	T|T	0.28870|0.28870	-1.0030|-1.0030	10|5	0.22109|.	T|.	0.4|.	-8.7879|-8.7879	1.8844|1.8844	0.03235|0.03235	0.3329:0.3663:0.0902:0.2106|0.3329:0.3663:0.0902:0.2106	.|.	1720;1728;527;1720;1673;1674;1728|.	B9EIS5;D3DSQ0;B4DJ00;E7ETA6;Q15154-2;E7EV56;Q15154|.	.;.;.;.;.;.;PCM1_HUMAN|.	R|V	1728;1720;1674;427|468	ENSP00000327077:H1728R;ENSP00000431099:H1720R;ENSP00000430521:H1674R;ENSP00000328332:H427R|.	ENSP00000327077:H1728R|.	H|M	+|+	2|1	0|0	PCM1|PCM1	17912420|17912420	0.817000|0.817000	0.29147|0.29147	0.939000|0.939000	0.37840|0.37840	0.951000|0.951000	0.60555|0.60555	0.318000|0.318000	0.19504|0.19504	0.256000|0.256000	0.21614|0.21614	0.459000|0.459000	0.35465|0.35465	CAT|ATG	.	.		0.393	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
LGI3	203190	hgsc.bcm.edu	37	8	22012911	22012911	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:22012911T>C	ENST00000306317.2	-	2	561	c.272A>G	c.(271-273)cAg>cGg	p.Q91R	LGI3_ENST00000424267.2_Missense_Mutation_p.Q91R	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	91					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		ATACAAGAACTGCAGCAGCGG	0.607																																					p.Q91R		Atlas-SNP	.											.	LGI3	44	.	0			c.A272G						.						162.0	157.0	158.0					8																	22012911		2203	4300	6503	SO:0001583	missense	203190	exon2			AAGAACTGCAGCA	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.272A>G	chr8.hg19:g.22012911T>C	ENSP00000302297:p.Gln91Arg	113.0	0.0		32.0	4.0	NM_139278	A5PLP2|Q86TL4|Q8N296	Missense_Mutation	SNP	ENST00000306317.2	hg19	CCDS6025.1	.	.	.	.	.	.	.	.	.	.	T	15.76	2.929034	0.52759	.	.	ENSG00000168481	ENST00000306317;ENST00000424267;ENST00000517694	T;T;D	0.89810	0.35;0.51;-2.57	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	D	0.88822	0.6541	N	0.20445	0.575	0.50467	D	0.999871	D;B	0.59357	0.985;0.192	D;B	0.71414	0.973;0.052	D	0.88685	0.3205	10	0.44086	T	0.13	-27.5892	11.6456	0.51259	0.0:0.0:0.0:1.0	.	91;91	A5PLP2;Q8N145	.;LGI3_HUMAN	R	91;91;52	ENSP00000302297:Q91R;ENSP00000399121:Q91R;ENSP00000427817:Q52R	ENSP00000302297:Q91R	Q	-	2	0	LGI3	22068856	1.000000	0.71417	1.000000	0.80357	0.233000	0.25261	6.856000	0.75450	2.056000	0.61249	0.528000	0.53228	CAG	.	.		0.607	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1		
C8orf58	541565	hgsc.bcm.edu	37	8	22458617	22458617	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:22458617A>G	ENST00000289989.5	+	2	337	c.263A>G	c.(262-264)cAg>cGg	p.Q88R	C8orf58_ENST00000453427.2_3'UTR|C8orf58_ENST00000409586.3_Missense_Mutation_p.Q88R			Q8NAV2	CH058_HUMAN	chromosome 8 open reading frame 58	88										endometrium(1)|lung(1)|ovary(1)|skin(1)	4		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00563)|Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		GGCCTTTCTCAGGACTCCCTG	0.652																																					p.Q88R		Atlas-SNP	.											.	C8orf58	17	.	0			c.A263G						.						25.0	30.0	28.0					8																	22458617		2193	4297	6490	SO:0001583	missense	541565	exon2			TTTCTCAGGACTC	BC012750	CCDS34862.1, CCDS56527.1, CCDS75708.1	8p21.3	2010-08-17			ENSG00000241852	ENSG00000241852			32233	protein-coding gene	gene with protein product							Standard	NM_001013842		Approved	FLJ34715	uc003xce.3	Q8NAV2	OTTHUMG00000154160	ENST00000289989.5:c.263A>G	chr8.hg19:g.22458617A>G	ENSP00000289989:p.Gln88Arg	93.0	0.0		36.0	4.0	NM_001013842	B4DI44	Missense_Mutation	SNP	ENST00000289989.5	hg19	CCDS34862.1	.	.	.	.	.	.	.	.	.	.	a	17.97	3.518831	0.64634	.	.	ENSG00000248235;ENSG00000241852;ENSG00000241852;ENSG00000241852	ENST00000450780;ENST00000409586;ENST00000289989;ENST00000381191	.	.	.	4.1	-0.126	0.13515	.	0.364625	0.19601	N	0.110389	T	0.52256	0.1723	M	0.68317	2.08	0.26117	N	0.980603	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.80764	0.994;0.994;0.994	T	0.38972	-0.9636	9	0.72032	D	0.01	-7.5099	2.9471	0.05849	0.5033:0.0:0.1114:0.3853	.	88;16;88	Q8NAV2-2;E7EQH9;Q8NAV2	.;.;CH058_HUMAN	R	157;88;88;16	.	ENSP00000399696:Q157R	Q	+	2	0	AC037459.4;C8orf58	22514562	0.939000	0.31865	0.997000	0.53966	0.880000	0.50808	1.026000	0.30103	0.205000	0.20568	0.368000	0.22195	CAG	.	.		0.652	C8orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334183.1	NM_001013842	
TNFRSF10D	8793	hgsc.bcm.edu	37	8	22995463	22995463	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:22995463T>C	ENST00000312584.3	-	9	1175	c.1081A>G	c.(1081-1083)Aca>Gca	p.T361A		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	361	Death; truncated.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		TCCTGAATTGTTTCCTTTGCA	0.493																																					p.T361A		Atlas-SNP	.											.	TNFRSF10D	21	.	0			c.A1081G						.						98.0	80.0	86.0					8																	22995463		2203	4300	6503	SO:0001583	missense	8793	exon9			GAATTGTTTCCTT	AF029761	CCDS6038.1	8p21	2006-02-22			ENSG00000173530	ENSG00000173530		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11907	protein-coding gene	gene with protein product		603614				9382840, 9537512	Standard	NM_003840		Approved	DcR2, TRUNDD, TRAILR4, CD264	uc003xcz.2	Q9UBN6	OTTHUMG00000097845	ENST00000312584.3:c.1081A>G	chr8.hg19:g.22995463T>C	ENSP00000310263:p.Thr361Ala	195.0	0.0		98.0	4.0	NM_003840	B2R8W0|Q9Y6Q4	Missense_Mutation	SNP	ENST00000312584.3	hg19	CCDS6038.1	.	.	.	.	.	.	.	.	.	.	T	7.948	0.744320	0.15710	.	.	ENSG00000173530	ENST00000312584	D	0.82619	-1.63	1.96	0.795	0.18643	.	3.827150	0.01571	U	0.020596	T	0.72095	0.3418	L	0.29908	0.895	0.09310	N	1	P	0.36222	0.544	B	0.34873	0.191	T	0.59069	-0.7523	10	0.23302	T	0.38	.	3.4681	0.07557	0.0:0.2172:0.0:0.7828	.	361	Q9UBN6	TR10D_HUMAN	A	361	ENSP00000310263:T361A	ENSP00000310263:T361A	T	-	1	0	TNFRSF10D	23051408	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.540000	0.06106	0.218000	0.20820	0.379000	0.24179	ACA	.	.		0.493	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1		
SCARA3	51435	hgsc.bcm.edu	37	8	27509080	27509080	+	Silent	SNP	G	G	T	rs371890046		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:27509080G>T	ENST00000301904.3	+	3	182	c.162G>T	c.(160-162)tcG>tcT	p.S54S	SCARA3_ENST00000337221.4_Silent_p.S54S	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	54					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)		TGCACACATCGGTGCGGATTC	0.662																																					p.S54S		Atlas-SNP	.											.	SCARA3	93	.	0			c.G162T						.						86.0	83.0	84.0					8																	27509080		2203	4300	6503	SO:0001819	synonymous_variant	51435	exon3			CACATCGGTGCGG	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.162G>T	chr8.hg19:g.27509080G>T		251.0	0.0		79.0	4.0	NM_182826	Q9UM15|Q9UM16	Silent	SNP	ENST00000301904.3	hg19	CCDS34871.1																																																																																			.	.		0.662	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376258.2	NM_016240	
CCDC25	55246	hgsc.bcm.edu	37	8	27605739	27605739	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:27605739T>C	ENST00000356537.4	-	7	499	c.406A>G	c.(406-408)Acc>Gcc	p.T136A	RP11-16P20.3_ENST00000521510.1_RNA|CCDC25_ENST00000539095.1_Missense_Mutation_p.T68A|CCDC25_ENST00000522915.1_Missense_Mutation_p.T68A	NM_018246.2	NP_060716.2	Q86WR0	CCD25_HUMAN	coiled-coil domain containing 25	136						extracellular vesicular exosome (GO:0070062)		p.T136P(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0223)|KIRC - Kidney renal clear cell carcinoma(542;0.11)|Kidney(114;0.131)|Colorectal(74;0.154)		TCGACTTTGGTCTTTTCTAAT	0.388																																					p.T136A		Atlas-SNP	.											CCDC25,NS,carcinoma,0,1	CCDC25	14	.	1	Substitution - Missense(1)	kidney(1)	c.A406G						.						122.0	118.0	119.0					8																	27605739		2203	4300	6503	SO:0001583	missense	55246	exon7			CTTTGGTCTTTTC	AK001715	CCDS6062.2	8p21.1	2006-09-20			ENSG00000147419	ENSG00000147419			25591	protein-coding gene	gene with protein product						12477932	Standard	NM_018246		Approved	FLJ10853	uc003xgc.3	Q86WR0	OTTHUMG00000132173	ENST00000356537.4:c.406A>G	chr8.hg19:g.27605739T>C	ENSP00000348933:p.Thr136Ala	249.0	0.0		110.0	5.0	NM_018246	Q0P663|Q96SI2|Q9NV98	Missense_Mutation	SNP	ENST00000356537.4	hg19	CCDS6062.2	.	.	.	.	.	.	.	.	.	.	T	19.67	3.871617	0.72065	.	.	ENSG00000147419	ENST00000356537;ENST00000539095;ENST00000522915	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.68063	0.2960	M	0.93016	3.37	0.80722	D	1	P	0.41393	0.748	B	0.33339	0.162	T	0.77474	-0.2574	9	0.87932	D	0	-8.3639	13.7503	0.62904	0.0:0.0:0.0:1.0	.	136	Q86WR0	CCD25_HUMAN	A	136;68;68	.	ENSP00000348933:T136A	T	-	1	0	CCDC25	27661658	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.850000	0.75420	2.132000	0.65825	0.533000	0.62120	ACC	.	.		0.388	CCDC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255224.1	NM_018246	
FZD3	7976	hgsc.bcm.edu	37	8	28385289	28385289	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:28385289A>G	ENST00000240093.3	+	5	1490	c.1012A>G	c.(1012-1014)Atc>Gtc	p.I338V	RNA5SP259_ENST00000365541.1_RNA|FZD3_ENST00000537916.1_Missense_Mutation_p.I338V	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	338					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		TGCATGGGGCATCCCCGGAAC	0.438																																					p.I338V		Atlas-SNP	.											.	FZD3	65	.	0			c.A1012G						.						147.0	143.0	145.0					8																	28385289		2203	4300	6503	SO:0001583	missense	7976	exon5			TGGGGCATCCCCG	AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"""GPCR / Class F : Frizzled receptors"""	4041	protein-coding gene	gene with protein product		606143	"""frizzled (Drosophila) homolog 3"", ""frizzled homolog 3 (Drosophila)"", ""frizzled 3, seven transmembrane spanning receptor"", ""frizzled family receptor 3"""			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.1012A>G	chr8.hg19:g.28385289A>G	ENSP00000240093:p.Ile338Val	133.0	0.0		59.0	4.0	NM_017412	A8K615	Missense_Mutation	SNP	ENST00000240093.3	hg19	CCDS6069.1	.	.	.	.	.	.	.	.	.	.	A	2.075	-0.412164	0.04799	.	.	ENSG00000104290	ENST00000537916;ENST00000240093	T;T	0.81330	-1.48;-1.48	5.32	5.32	0.75619	GPCR, family 2-like (1);	0.110358	0.64402	D	0.000011	T	0.63988	0.2558	N	0.13003	0.285	0.45205	D	0.998214	B	0.13594	0.008	B	0.23150	0.044	T	0.59490	-0.7445	10	0.02654	T	1	.	14.0788	0.64907	1.0:0.0:0.0:0.0	.	338	Q9NPG1	FZD3_HUMAN	V	338	ENSP00000437489:I338V;ENSP00000240093:I338V	ENSP00000240093:I338V	I	+	1	0	FZD3	28441208	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.298000	0.43602	2.007000	0.58848	0.460000	0.39030	ATC	.	.		0.438	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866	
FUT10	84750	hgsc.bcm.edu	37	8	33230192	33230192	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:33230192T>C	ENST00000327671.5	-	5	1974	c.1343A>G	c.(1342-1344)gAa>gGa	p.E448G	FUT10_ENST00000524021.1_Missense_Mutation_p.E420G|FUT10_ENST00000518672.1_Missense_Mutation_p.E420G	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	448					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)			cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		CTTGGATTGTTCAAAGCTGGA	0.473																																					p.E448G		Atlas-SNP	.											.	FUT10	62	.	0			c.A1343G						.						93.0	89.0	91.0					8																	33230192		2203	4300	6503	SO:0001583	missense	84750	exon5			GATTGTTCAAAGC	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"""Fucosyltransferases"""	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1343A>G	chr8.hg19:g.33230192T>C	ENSP00000332757:p.Glu448Gly	174.0	0.0		94.0	4.0	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Missense_Mutation	SNP	ENST00000327671.5	hg19	CCDS6088.1	.	.	.	.	.	.	.	.	.	.	T	14.63	2.594131	0.46214	.	.	ENSG00000172728	ENST00000327671;ENST00000380081;ENST00000518672;ENST00000524021	T;T;T	0.39787	1.06;1.07;1.07	5.45	4.26	0.50523	.	0.469911	0.20431	N	0.092465	T	0.38506	0.1043	M	0.72894	2.215	0.80722	D	1	P;B;B	0.40144	0.704;0.181;0.022	B;B;B	0.35182	0.197;0.051;0.04	T	0.14755	-1.0461	10	0.30078	T	0.28	-1.4095	9.6994	0.40178	0.0:0.0839:0.0:0.9161	.	498;448;490	B4E056;Q6P4F1;E7EU36	.;FUT10_HUMAN;.	G	448;490;420;420	ENSP00000332757:E448G;ENSP00000430428:E420G;ENSP00000429870:E420G	ENSP00000332757:E448G	E	-	2	0	FUT10	33349734	1.000000	0.71417	0.935000	0.37517	0.969000	0.65631	4.397000	0.59690	0.875000	0.35847	0.482000	0.46254	GAA	.	.		0.473	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664	
KCNU1	157855	hgsc.bcm.edu	37	8	36693822	36693822	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:36693822C>T	ENST00000399881.3	+	13	1341	c.1304C>T	c.(1303-1305)tCt>tTt	p.S435F		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	435	RCK N-terminal.				multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.S435F(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		AGGGTGCTCTCTATCAAGAAC	0.348																																					p.S435F		Atlas-SNP	.											KCNU1_ENST00000399881,rectum,carcinoma,0,2	KCNU1	359	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1304T						.						140.0	133.0	135.0					8																	36693822		1827	4079	5906	SO:0001583	missense	157855	exon13			TGCTCTCTATCAA	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.1304C>T	chr8.hg19:g.36693822C>T	ENSP00000382770:p.Ser435Phe	89.0	0.0		35.0	2.0	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	hg19	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.049503	0.55218	.	.	ENSG00000215262	ENST00000399881	T	0.70282	-0.47	5.6	4.71	0.59529	NAD(P)-binding domain (1);	0.000000	0.35151	U	0.003416	D	0.84074	0.5392	M	0.77313	2.365	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	D	0.86779	0.1978	10	0.87932	D	0	-4.1264	16.6359	0.85059	0.0:0.87:0.13:0.0	.	435	A8MYU2	KCNU1_HUMAN	F	435	ENSP00000382770:S435F	ENSP00000382770:S435F	S	+	2	0	KCNU1	36812980	0.998000	0.40836	0.929000	0.37066	0.298000	0.27526	4.151000	0.58105	1.466000	0.48025	0.650000	0.86243	TCT	.	.		0.348	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	
HOOK3	84376	hgsc.bcm.edu	37	8	42819473	42819473	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:42819473A>G	ENST00000307602.4	+	9	835	c.635A>G	c.(634-636)gAg>gGg	p.E212G		NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	212					cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			TTGCAGGAAGAGAAAAGTAGT	0.408			T	RET	papillary thyroid																																p.E212G		Atlas-SNP	.		Dom	yes		8	8p11.21	84376	hook homolog 3		E	.	HOOK3	71	.	0			c.A635G						.						121.0	117.0	118.0					8																	42819473		2203	4300	6503	SO:0001583	missense	84376	exon9			AGGAAGAGAAAAG	AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172			23576	protein-coding gene	gene with protein product		607825	"""hook homolog 3 (Drosophila)"""			9927460	Standard	NM_032410		Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.635A>G	chr8.hg19:g.42819473A>G	ENSP00000305699:p.Glu212Gly	86.0	0.0		80.0	5.0	NM_032410	D3DSY8|Q8NBH0|Q9BY13	Missense_Mutation	SNP	ENST00000307602.4	hg19	CCDS6139.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.655876	0.88056	.	.	ENSG00000168172	ENST00000307602	T	0.35236	1.32	5.93	5.93	0.95920	.	0.100609	0.64402	D	0.000003	T	0.65417	0.2689	M	0.84683	2.71	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.69903	-0.5019	10	0.56958	D	0.05	-6.9643	16.418	0.83748	1.0:0.0:0.0:0.0	.	212;212	Q2VJ45;Q86VS8	.;HOOK3_HUMAN	G	212	ENSP00000305699:E212G	ENSP00000305699:E212G	E	+	2	0	HOOK3	42938630	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	8.899000	0.92544	2.281000	0.76405	0.524000	0.50904	GAG	.	.		0.408	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383172.2	NM_032410	
PXDNL	137902	hgsc.bcm.edu	37	8	52321594	52321594	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:52321594G>A	ENST00000356297.4	-	17	2690	c.2590C>T	c.(2590-2592)Cgc>Tgc	p.R864C	PXDNL_ENST00000543296.1_Missense_Mutation_p.R864C	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	864					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.R864C(1)|p.R63C(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GGGCTGGAGCGCGCGAAGAGC	0.662																																					p.R864C		Atlas-SNP	.											PXDNL_ENST00000356297,colon,carcinoma,0,2	PXDNL	414	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2590T						.						22.0	26.0	25.0					8																	52321594		2026	4158	6184	SO:0001583	missense	137902	exon17			TGGAGCGCGCGAA		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2590C>T	chr8.hg19:g.52321594G>A	ENSP00000348645:p.Arg864Cys	87.0	0.0		100.0	6.0	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	10.39	1.336473	0.24253	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	D;D	0.84800	-1.9;-1.9	3.31	0.304	0.15796	.	0.272281	0.26156	N	0.026002	D	0.94128	0.8117	H	0.99286	4.5	0.44123	D	0.996903	D	0.89917	1.0	D	0.91635	0.999	D	0.89382	0.3682	10	0.87932	D	0	.	4.8892	0.13719	0.22:0.1755:0.6045:0.0	.	864	A1KZ92	PXDNL_HUMAN	C	864	ENSP00000348645:R864C;ENSP00000444865:R864C	ENSP00000348645:R864C	R	-	1	0	PXDNL	52484147	1.000000	0.71417	0.029000	0.17559	0.003000	0.03518	2.981000	0.49329	-0.220000	0.09988	-0.898000	0.02899	CGC	.	.		0.662	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
CNBD1	168975	hgsc.bcm.edu	37	8	88218349	88218349	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:88218349G>T	ENST00000518476.1	+	5	611	c.560G>T	c.(559-561)tGg>tTg	p.W187L	CNBD1_ENST00000522427.1_3'UTR	NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	187										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						TCCGAAACCTGGTTGAAAGGC	0.358																																					p.W187L		Atlas-SNP	.											.	CNBD1	206	.	0			c.G560T						.						77.0	72.0	74.0					8																	88218349		1850	4102	5952	SO:0001583	missense	168975	exon5			AAACCTGGTTGAA	AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571			26663	protein-coding gene	gene with protein product							Standard	NM_173538		Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.560G>T	chr8.hg19:g.88218349G>T	ENSP00000430073:p.Trp187Leu	72.0	0.0		98.0	4.0	NM_173538		Missense_Mutation	SNP	ENST00000518476.1	hg19	CCDS55259.1	.	.	.	.	.	.	.	.	.	.	G	11.26	1.586120	0.28268	.	.	ENSG00000176571	ENST00000518476	D	0.95949	-3.86	5.02	5.02	0.67125	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.288280	0.25313	N	0.031579	D	0.96778	0.8948	L	0.58101	1.795	0.30793	N	0.74072	D	0.89917	1.0	D	0.83275	0.996	D	0.94992	0.8135	10	0.52906	T	0.07	-0.3155	13.8978	0.63783	0.0:0.0:1.0:0.0	.	187	Q8NA66	CNBD1_HUMAN	L	187	ENSP00000430073:W187L	ENSP00000430073:W187L	W	+	2	0	CNBD1	88287465	1.000000	0.71417	0.997000	0.53966	0.218000	0.24690	4.489000	0.60309	2.335000	0.79485	0.460000	0.39030	TGG	.	.		0.358	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538	
RIPK2	8767	hgsc.bcm.edu	37	8	90782012	90782012	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:90782012G>T	ENST00000220751.4	+	4	810	c.496G>T	c.(496-498)Ggt>Tgt	p.G166C	RIPK2_ENST00000540020.1_Missense_Mutation_p.G29C	NM_003821.5	NP_003812.1	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	166	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immature T cell proliferation (GO:0033091)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|response to exogenous dsRNA (GO:0043330)|response to interleukin-1 (GO:0070555)|response to interleukin-12 (GO:0070671)|response to interleukin-18 (GO:0070673)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|T cell proliferation (GO:0042098)|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)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|LIM domain binding (GO:0030274)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.G166C(1)		kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	10			BRCA - Breast invasive adenocarcinoma(11;0.0474)			TGCAGATTTTGGTTTATCAAA	0.363																																					p.G166C		Atlas-SNP	.											RIPK2,NS,carcinoma,0,1	RIPK2	37	.	1	Substitution - Missense(1)	lung(1)	c.G496T						.						147.0	153.0	151.0					8																	90782012		2203	4299	6502	SO:0001583	missense	8767	exon4			GATTTTGGTTTAT	AC004003	CCDS6247.1	8q21	2008-05-02			ENSG00000104312	ENSG00000104312			10020	protein-coding gene	gene with protein product		603455				9575181, 9705938	Standard	XM_005251092		Approved	RICK, RIP2, CARDIAK, CARD3	uc003yee.3	O43353	OTTHUMG00000163809	ENST00000220751.4:c.496G>T	chr8.hg19:g.90782012G>T	ENSP00000220751:p.Gly166Cys	56.0	0.0		75.0	3.0	NM_003821	B7Z748|Q6UWF0	Missense_Mutation	SNP	ENST00000220751.4	hg19	CCDS6247.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.601674	0.87055	.	.	ENSG00000104312	ENST00000220751;ENST00000540020	D;D	0.92858	-1.63;-3.12	5.41	5.41	0.78517	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.43747	D	0.000531	D	0.97682	0.9240	H	0.96833	3.89	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98474	1.0602	10	0.87932	D	0	-19.8595	19.3887	0.94570	0.0:0.0:1.0:0.0	.	166	O43353	RIPK2_HUMAN	C	166;29	ENSP00000220751:G166C;ENSP00000441623:G29C	ENSP00000220751:G166C	G	+	1	0	RIPK2	90851149	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	9.350000	0.97070	2.826000	0.97356	0.655000	0.94253	GGT	.	.		0.363	RIPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375686.1		
CALB1	793	hgsc.bcm.edu	37	8	91072909	91072909	+	Missense_Mutation	SNP	T	T	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:91072909T>G	ENST00000265431.3	-	10	801	c.620A>C	c.(619-621)gAt>gCt	p.D207A	CALB1_ENST00000518457.1_Missense_Mutation_p.D150A	NM_004929.2	NP_004920.1	P05937	CALB1_HUMAN	calbindin 1, 28kDa	207	EF-hand 5. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to organic substance (GO:0071310)|cytosolic calcium ion homeostasis (GO:0051480)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|metanephric collecting duct development (GO:0072205)|metanephric connecting tubule development (GO:0072286)|metanephric distal convoluted tubule development (GO:0072221)|metanephric part of ureteric bud development (GO:0035502)|regulation of synaptic plasticity (GO:0048167)|retina layer formation (GO:0010842)|short-term memory (GO:0007614)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|vitamin D binding (GO:0005499)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(8)|pancreas(1)	11			BRCA - Breast invasive adenocarcinoma(11;0.00953)			TTCATTTTCATCTATGTATCC	0.383																																					p.D207A	Melanoma(46;573 1182 27367 39727 48386)	Atlas-SNP	.											.	CALB1	25	.	0			c.A620C						.						199.0	195.0	196.0					8																	91072909		2203	4300	6503	SO:0001583	missense	793	exon10			TTTTCATCTATGT		CCDS6251.1	8q21.3	2013-01-10	2002-08-29		ENSG00000104327	ENSG00000104327		"""EF-hand domain containing"""	1434	protein-coding gene	gene with protein product		114050		CALB			Standard	NM_004929		Approved		uc003yel.1	P05937	OTTHUMG00000134314	ENST00000265431.3:c.620A>C	chr8.hg19:g.91072909T>G	ENSP00000265431:p.Asp207Ala	105.0	0.0		137.0	40.0	NM_004929	B2R696|B7Z9J4	Missense_Mutation	SNP	ENST00000265431.3	hg19	CCDS6251.1	.	.	.	.	.	.	.	.	.	.	T	18.34	3.601966	0.66445	.	.	ENSG00000104327	ENST00000265431;ENST00000518457	T;T	0.73681	-0.77;-0.77	5.8	5.8	0.92144	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.83714	0.5314	L	0.55213	1.73	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.85133	0.0976	10	0.72032	D	0.01	-21.197	16.1606	0.81704	0.0:0.0:0.0:1.0	.	207	P05937	CALB1_HUMAN	A	207;150	ENSP00000265431:D207A;ENSP00000429602:D150A	ENSP00000265431:D207A	D	-	2	0	CALB1	91142085	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.948000	0.75965	2.227000	0.72691	0.460000	0.39030	GAT	.	.		0.383	CALB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259338.2	NM_004929	
RNF139	11236	hgsc.bcm.edu	37	8	125487462	125487462	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:125487462T>C	ENST00000303545.3	+	1	484	c.112T>C	c.(112-114)Ttc>Ctc	p.F38L	RNF139-AS1_ENST00000499418.2_lincRNA	NM_007218.3	NP_009149.2			ring finger protein 139											breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(1)	20	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CGACGCCATCTTCAACTCCTA	0.637																																					p.F38L		Atlas-SNP	.											.	RNF139	57	.	0			c.T112C						.						81.0	84.0	83.0					8																	125487462		2203	4300	6503	SO:0001583	missense	11236	exon1			GCCATCTTCAACT	AF064801	CCDS6350.1	8q24	2013-01-09			ENSG00000170881	ENSG00000170881		"""RING-type (C3HC4) zinc fingers"""	17023	protein-coding gene	gene with protein product		603046				9689122	Standard	NM_007218		Approved	TRC8, RCA1, HRCA1	uc003yrc.3	Q8WU17	OTTHUMG00000165072	ENST00000303545.3:c.112T>C	chr8.hg19:g.125487462T>C	ENSP00000304051:p.Phe38Leu	66.0	0.0		58.0	6.0	NM_007218		Missense_Mutation	SNP	ENST00000303545.3	hg19	CCDS6350.1	.	.	.	.	.	.	.	.	.	.	T	6.611	0.481042	0.12581	.	.	ENSG00000170881	ENST00000303545	T	0.28069	1.63	4.44	3.3	0.37823	.	0.214512	0.40469	N	0.001094	T	0.12220	0.0297	N	0.04090	-0.28	0.37178	D	0.903345	B	0.06786	0.001	B	0.08055	0.003	T	0.13229	-1.0517	10	0.17832	T	0.49	-8.4438	7.4699	0.27342	0.0:0.1002:0.0:0.8998	.	38	Q8WU17	RN139_HUMAN	L	38	ENSP00000304051:F38L	ENSP00000304051:F38L	F	+	1	0	RNF139	125556643	1.000000	0.71417	1.000000	0.80357	0.417000	0.31264	5.377000	0.66184	0.759000	0.33084	0.459000	0.35465	TTC	.	.		0.637	RNF139-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381692.1	NM_007218	
KIAA0196	9897	hgsc.bcm.edu	37	8	126062907	126062907	+	Splice_Site	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:126062907C>T	ENST00000318410.7	-	18	2447	c.2098G>A	c.(2098-2100)Gtg>Atg	p.V700M	KIAA0196_ENST00000517845.1_Splice_Site_p.V552M	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	700					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			TTTGGATCCACCTAAGTGCCA	0.438																																					p.V700M		Atlas-SNP	.											.	KIAA0196	90	.	0			c.G2098A						.						101.0	93.0	96.0					8																	126062907		2203	4300	6503	SO:0001630	splice_region_variant	9897	exon18			GATCCACCTAAGT		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"""strumpellin"""	610657	"""spastic paraplegia 8 (autosomal dominant)"""	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.2098-1G>A	chr8.hg19:g.126062907C>T		77.0	0.0		87.0	4.0	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Missense_Mutation	SNP	ENST00000318410.7	hg19	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.729058	0.89390	.	.	ENSG00000164961	ENST00000318410;ENST00000517845	D;D	0.89810	-2.57;-2.57	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.94739	0.8302	M	0.80616	2.505	0.80722	D	1	D;D	0.67145	0.984;0.996	P;D	0.81914	0.865;0.995	D	0.95079	0.8211	10	0.72032	D	0.01	-19.1397	19.0437	0.93011	0.0:1.0:0.0:0.0	.	552;700	E7EQI7;Q12768	.;STRUM_HUMAN	M	700;552	ENSP00000318016:V700M;ENSP00000429676:V552M	ENSP00000318016:V700M	V	-	1	0	KIAA0196	126132089	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	7.772000	0.85439	2.575000	0.86900	0.655000	0.94253	GTG	.	.		0.438	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	Missense_Mutation
ASAP1	50807	hgsc.bcm.edu	37	8	131130888	131130888	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:131130888A>G	ENST00000518721.1	-	19	1868	c.1641T>C	c.(1639-1641)taT>taC	p.Y547Y	ASAP1_ENST00000357668.1_Silent_p.Y547Y	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	547	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						TATGATCTACATACTTTGCAG	0.333																																					p.Y547Y		Atlas-SNP	.											.	ASAP1	133	.	0			c.T1641C						.						81.0	77.0	78.0					8																	131130888		2203	4300	6503	SO:0001819	synonymous_variant	50807	exon19			ATCTACATACTTT	AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	2720	protein-coding gene	gene with protein product	"""centaurin, beta 4"""	605953	"""development and differentiation enhancing factor 1"""	DDEF1		9819391	Standard	NM_018482		Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.1641T>C	chr8.hg19:g.131130888A>G		177.0	0.0		263.0	72.0	NM_018482	B2RNV3	Silent	SNP	ENST00000518721.1	hg19	CCDS6362.1	.	.	.	.	.	.	.	.	.	.	A	8.808	0.934450	0.18206	.	.	ENSG00000153317	ENST00000524124	.	.	.	5.86	0.792	0.18625	.	.	.	.	.	T	0.57036	0.2026	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48681	-0.9014	4	.	.	.	.	9.2609	0.37612	0.6503:0.0:0.3497:0.0	.	.	.	.	R	368	.	.	C	-	1	0	ASAP1	131200070	1.000000	0.71417	0.935000	0.37517	0.941000	0.58515	1.649000	0.37281	-0.075000	0.12798	-0.261000	0.10672	TGT	.	.		0.333	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380170.1	NM_018482	
ADCY8	114	hgsc.bcm.edu	37	8	131795974	131795974	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:131795974G>T	ENST00000286355.5	-	17	5323	c.3231C>A	c.(3229-3231)atC>atA	p.I1077I	ADCY8_ENST00000377928.3_Silent_p.I946I	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	1077					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)|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)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|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)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.I1077I(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			AATGCTTGTTGATCTCCTGTA	0.502										HNSCC(32;0.087)																											p.I1077I		Atlas-SNP	.											ADCY8,NS,carcinoma,0,1	ADCY8	291	.	1	Substitution - coding silent(1)	lung(1)	c.C3231A						.						163.0	148.0	153.0					8																	131795974		2203	4300	6503	SO:0001819	synonymous_variant	114	exon17			CTTGTTGATCTCC	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"""Adenylate cyclases"""	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.3231C>A	chr8.hg19:g.131795974G>T		115.0	0.0		110.0	6.0	NM_001115		Silent	SNP	ENST00000286355.5	hg19	CCDS6363.1																																																																																			.	.		0.502	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
FAM83H	286077	hgsc.bcm.edu	37	8	144812417	144812417	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:144812417A>G	ENST00000388913.3	-	2	461	c.336T>C	c.(334-336)ccT>ccC	p.P112P	MIR4664_ENST00000583819.1_RNA	NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	112					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)			CGAAGGTCAGAGGCCAGCCCA	0.622																																					p.P112P		Atlas-SNP	.											.	FAM83H	68	.	0			c.T336C						.						46.0	52.0	50.0					8																	144812417		2056	4180	6236	SO:0001819	synonymous_variant	286077	exon2			GGTCAGAGGCCAG	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.336T>C	chr8.hg19:g.144812417A>G		84.0	0.0		72.0	4.0	NM_198488	A0JLS2|Q8N4W0	Silent	SNP	ENST00000388913.3	hg19	CCDS6410.2																																																																																			.	.		0.622	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488	
SCRIB	23513	hgsc.bcm.edu	37	8	144891811	144891811	+	Silent	SNP	G	G	C	rs546935238		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:144891811G>C	ENST00000320476.3	-	14	1614	c.1608C>G	c.(1606-1608)ccC>ccG	p.P536P	SCRIB_ENST00000377533.3_Silent_p.P455P|SCRIB_ENST00000356994.2_Silent_p.P536P	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	536	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-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;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			ACGGGCCCTCGGGCTCAGCCT	0.662																																					p.P536P	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C1608G						.						57.0	55.0	55.0					8																	144891811		2203	4300	6503	SO:0001819	synonymous_variant	23513	exon14			GCCCTCGGGCTCA	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.1608C>G	chr8.hg19:g.144891811G>C		90.0	0.0		93.0	4.0	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	hg19	CCDS6411.1																																																																																			.	.		0.662	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
PLEC	5339	hgsc.bcm.edu	37	8	144990726	144990726	+	Silent	SNP	G	G	T	rs369202116		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:144990726G>T	ENST00000322810.4	-	32	13843	c.13674C>A	c.(13672-13674)acC>acA	p.T4558T	PLEC_ENST00000356346.3_Silent_p.T4407T|PLEC_ENST00000354589.3_Silent_p.T4421T|PLEC_ENST00000398774.2_Silent_p.T4389T|PLEC_ENST00000357649.2_Silent_p.T4425T|PLEC_ENST00000345136.3_Silent_p.T4421T|PLEC_ENST00000527096.1_Silent_p.T4444T|PLEC_ENST00000354958.2_Silent_p.T4399T|PLEC_ENST00000436759.2_Silent_p.T4448T	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4558	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GCTTCTGTGCGGTGCGGGCGT	0.672																																					p.T4558T		Atlas-SNP	.											.	PLEC	1144	.	0			c.C13674A						.						56.0	60.0	59.0					8																	144990726		2002	4131	6133	SO:0001819	synonymous_variant	5339	exon32			CTGTGCGGTGCGG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.13674C>A	chr8.hg19:g.144990726G>T		69.0	0.0		80.0	4.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.		0.672	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
PLEC	5339	hgsc.bcm.edu	37	8	144991010	144991010	+	Missense_Mutation	SNP	C	C	A	rs368027812		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:144991010C>A	ENST00000322810.4	-	32	13559	c.13390G>T	c.(13390-13392)Ggt>Tgt	p.G4464C	PLEC_ENST00000356346.3_Missense_Mutation_p.G4313C|PLEC_ENST00000354589.3_Missense_Mutation_p.G4327C|PLEC_ENST00000398774.2_Missense_Mutation_p.G4295C|PLEC_ENST00000357649.2_Missense_Mutation_p.G4331C|PLEC_ENST00000345136.3_Missense_Mutation_p.G4327C|PLEC_ENST00000527096.1_Missense_Mutation_p.G4350C|PLEC_ENST00000354958.2_Missense_Mutation_p.G4305C|PLEC_ENST00000436759.2_Missense_Mutation_p.G4354C	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4464	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						AAGCGCTCACCGGTGCTGGGG	0.652																																					p.G4464C		Atlas-SNP	.											.	PLEC	1144	.	0			c.G13390T						.						49.0	55.0	53.0					8																	144991010		2123	4226	6349	SO:0001583	missense	5339	exon32			GCTCACCGGTGCT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.13390G>T	chr8.hg19:g.144991010C>A	ENSP00000323856:p.Gly4464Cys	155.0	0.0		138.0	7.0	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	6.324	0.427898	0.11987	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33	5.19	5.19	0.71726	.	0.000000	0.64402	U	0.000006	D	0.91499	0.7316	M	0.88450	2.955	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999;0.999;0.999;0.999	D	0.92759	0.6222	10	0.87932	D	0	.	18.5216	0.90954	0.0:1.0:0.0:0.0	.	4354;4313;4305;4464;4295;4327;4331;4327	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	C	4327;4331;4327;4295;4464;4305;4313;4354;4350	ENSP00000344848:G4327C;ENSP00000350277:G4331C;ENSP00000346602:G4327C;ENSP00000381756:G4295C;ENSP00000323856:G4464C;ENSP00000347044:G4305C;ENSP00000348702:G4313C;ENSP00000388180:G4354C;ENSP00000434583:G4350C	ENSP00000323856:G4464C	G	-	1	0	PLEC	145062998	1.000000	0.71417	0.107000	0.21349	0.025000	0.11179	7.593000	0.82686	2.693000	0.91896	0.643000	0.83706	GGT	.	.		0.652	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
LRRC14	9684	hgsc.bcm.edu	37	8	145740718	145740718	+	5'Flank	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:145740718T>A	ENST00000292524.1	+	0	0				RECQL4_ENST00000428558.2_Missense_Mutation_p.Q461L|RECQL4_ENST00000532237.1_5'UTR|LRRC14_ENST00000529022.1_5'Flank|CTD-2517M22.17_ENST00000580385.1_RNA	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											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)			ACCTGCCAACTGCCCTGAGGG	0.617																																					p.Q461L		Atlas-SNP	.											.	RECQL4	75	.	0			c.A1382T						.						38.0	44.0	42.0					8																	145740718		2050	4208	6258	SO:0001631	upstream_gene_variant	9401	exon7			GCCAACTGCCCTG	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		chr8.hg19:g.145740718T>A	Exception_encountered	154.0	0.0		166.0	10.0	NM_004260	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1																																																																																			.	.		0.617	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
LRRC24	441381	hgsc.bcm.edu	37	8	145749598	145749598	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr8:145749598C>T	ENST00000529415.2	-	4	620	c.503G>A	c.(502-504)gGg>gAg	p.G168E	LRRC14_ENST00000292524.1_3'UTR|LRRC14_ENST00000528528.1_Intron|LRRC24_ENST00000533758.1_Missense_Mutation_p.G165E			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	168						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)			GGAGGACAGCCCCGCTAGAGC	0.612																																					p.G168E		Atlas-SNP	.											.	LRRC24	11	.	0			c.G503A						.						67.0	71.0	70.0					8																	145749598		2203	4300	6503	SO:0001583	missense	441381	exon4			GACAGCCCCGCTA	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.503G>A	chr8.hg19:g.145749598C>T	ENSP00000434849:p.Gly168Glu	76.0	0.0		66.0	4.0	NM_001024678		Missense_Mutation	SNP	ENST00000529415.2	hg19	CCDS34969.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906734	0.92107	.	.	ENSG00000254402	ENST00000529415;ENST00000533758	T;T	0.60548	0.18;0.18	4.55	4.55	0.56014	.	0.057736	0.64402	D	0.000001	T	0.71685	0.3369	M	0.64404	1.975	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.982;0.997	T	0.74411	-0.3674	10	0.72032	D	0.01	.	12.6709	0.56866	0.0:1.0:0.0:0.0	.	165;168	G3V1D8;Q50LG9	.;LRC24_HUMAN	E	168;165	ENSP00000434849:G168E;ENSP00000435653:G165E	ENSP00000434849:G168E	G	-	2	0	LRRC24	145720406	0.998000	0.40836	0.995000	0.50966	0.954000	0.61252	4.090000	0.57693	2.350000	0.79820	0.561000	0.74099	GGG	.	.		0.612	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678	
KCNV2	169522	hgsc.bcm.edu	37	9	2729648	2729648	+	Missense_Mutation	SNP	T	T	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:2729648T>G	ENST00000382082.3	+	2	1797	c.1559T>G	c.(1558-1560)tTc>tGc	p.F520C		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	520					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		GAGGTGAACTTCATGCAGAGA	0.453																																					p.F520C		Atlas-SNP	.											.	KCNV2	72	.	0			c.T1559G						.						113.0	103.0	107.0					9																	2729648		2203	4300	6503	SO:0001583	missense	169522	exon2			TGAACTTCATGCA	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.1559T>G	chr9.hg19:g.2729648T>G	ENSP00000371514:p.Phe520Cys	187.0	0.0		113.0	11.0	NM_133497	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	hg19	CCDS6447.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.352445	0.82132	.	.	ENSG00000168263	ENST00000382082	D	0.96992	-4.2	5.37	5.37	0.77165	.	1.777150	0.03575	N	0.229189	D	0.98261	0.9424	M	0.78916	2.43	0.80722	D	1	D	0.89917	1.0	D	0.67725	0.953	D	0.91921	0.5547	10	0.38643	T	0.18	.	15.6629	0.77203	0.0:0.0:0.0:1.0	.	520	Q8TDN2	KCNV2_HUMAN	C	520	ENSP00000371514:F520C	ENSP00000371514:F520C	F	+	2	0	KCNV2	2719648	1.000000	0.71417	0.990000	0.47175	0.993000	0.82548	7.997000	0.88414	2.165000	0.68154	0.533000	0.62120	TTC	.	.		0.453	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497	
MPDZ	8777	hgsc.bcm.edu	37	9	13193255	13193255	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:13193255T>C	ENST00000319217.7	-	14	1961	c.1714A>G	c.(1714-1716)Aca>Gca	p.T572A	MPDZ_ENST00000546205.1_Missense_Mutation_p.T572A|MPDZ_ENST00000541718.1_Missense_Mutation_p.T572A|MPDZ_ENST00000381022.2_Missense_Mutation_p.T572A|MPDZ_ENST00000536827.1_Missense_Mutation_p.T572A|MPDZ_ENST00000381015.4_Missense_Mutation_p.T572A|MPDZ_ENST00000447879.1_Missense_Mutation_p.T572A	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	572	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)		TGTCCCACTGTCGCTTCCAGG	0.443																																					p.T572A		Atlas-SNP	.											MPDZ_ENST00000541718,NS,carcinoma,0,2	MPDZ	324	.	0			c.A1714G						.						89.0	89.0	89.0					9																	13193255		1925	4123	6048	SO:0001583	missense	8777	exon14			CCACTGTCGCTTC	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.1714A>G	chr9.hg19:g.13193255T>C	ENSP00000320006:p.Thr572Ala	78.0	0.0		60.0	4.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	T	14.32	2.500367	0.44455	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.26518	1.73;1.73;1.73;1.73;1.73;1.73;1.73	5.87	4.73	0.59995	.	0.000000	0.48286	D	0.000187	T	0.21267	0.0512	L	0.41710	1.295	0.80722	D	1	P;P;P	0.44578	0.693;0.644;0.838	P;B;B	0.45660	0.489;0.356;0.356	T	0.07462	-1.0771	10	0.11485	T	0.65	.	6.923	0.24399	0.1329:0.0701:0.0:0.797	.	572;572;572	B7ZMI4;O75970-3;O75970-2	.;.;.	A	572	ENSP00000320006:T572A;ENSP00000439807:T572A;ENSP00000370410:T572A;ENSP00000444151:T572A;ENSP00000415208:T572A;ENSP00000370403:T572A;ENSP00000446358:T572A	ENSP00000320006:T572A	T	-	1	0	MPDZ	13183255	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.685000	0.37659	1.052000	0.40392	0.533000	0.62120	ACA	.	.		0.443	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18829938	18829938	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:18829938A>G	ENST00000380548.4	+	23	4551	c.4212A>G	c.(4210-4212)acA>acG	p.T1404T	ADAMTSL1_ENST00000380545.5_Silent_p.T105T	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1404	Ig-like C2-type 4.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		CTCTGGGAACACAGCTGGTCC	0.562																																					p.T1404T		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.A4212G						.						71.0	72.0	72.0					9																	18829938		2069	4208	6277	SO:0001819	synonymous_variant	92949	exon23			GGGAACACAGCTG	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.4212A>G	chr9.hg19:g.18829938A>G		139.0	0.0		96.0	4.0	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	hg19	CCDS47954.1																																																																																			.	.		0.562	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
DENND4C	55667	hgsc.bcm.edu	37	9	19346681	19346681	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:19346681A>G	ENST00000380432.2	+	18	3092	c.3059A>G	c.(3058-3060)cAc>cGc	p.H1020R	DENND4C_ENST00000602925.1_Missense_Mutation_p.H1256R|DENND4C_ENST00000434457.2_Missense_Mutation_p.H1305R			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1020					cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						ATGGAATTACACAGAGAGGAA	0.398																																					p.H1256R		Atlas-SNP	.											.	DENND4C	120	.	0			c.A3767G						.						75.0	76.0	75.0					9																	19346681		2203	4300	6503	SO:0001583	missense	55667	exon22			AATTACACAGAGA	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.3059A>G	chr9.hg19:g.19346681A>G	ENSP00000369797:p.His1020Arg	146.0	0.0		103.0	5.0	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	hg19		.	.	.	.	.	.	.	.	.	.	A	9.427	1.084460	0.20309	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024	T;T	0.22945	1.94;1.93	5.81	5.81	0.92471	.	0.088740	0.47093	D	0.000251	T	0.20414	0.0491	L	0.44542	1.39	0.35516	D	0.801045	P;P;P;P	0.47910	0.508;0.902;0.508;0.872	B;B;B;B	0.38225	0.135;0.268;0.226;0.213	T	0.28839	-1.0031	10	0.36615	T	0.2	-8.3174	10.5039	0.44821	0.9281:0.0:0.0719:0.0	.	350;1020;202;1020	B7Z660;Q5VZ89-5;Q5VZ89-3;Q5VZ89	.;.;.;DEN4C_HUMAN	R	1020;493;202;350;493;202;17	ENSP00000305795:H493R;ENSP00000443804:H350R	ENSP00000305795:H493R	H	+	2	0	DENND4C	19336681	0.998000	0.40836	0.230000	0.23976	0.231000	0.25187	5.457000	0.66672	2.213000	0.71641	0.528000	0.53228	CAC	.	.		0.398	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
UBAP2	55833	hgsc.bcm.edu	37	9	33996317	33996317	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:33996317T>C	ENST00000379238.1	-	4	309	c.192A>G	c.(190-192)acA>acG	p.T64T	UBAP2_ENST00000480885.1_5'UTR|UBAP2_ENST00000360802.1_Silent_p.T64T|UBAP2_ENST00000379239.4_5'UTR|UBAP2_ENST00000418786.2_Silent_p.T64T|UBAP2_ENST00000449054.1_Silent_p.T64T|UBAP2_ENST00000539807.1_Intron					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		GATTTTTCCCTGTCACTTCCA	0.353																																					p.T64T		Atlas-SNP	.											.	UBAP2	82	.	0			c.A192G						.						178.0	165.0	170.0					9																	33996317		2203	4300	6503	SO:0001819	synonymous_variant	55833	exon4			TTTCCCTGTCACT	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.192A>G	chr9.hg19:g.33996317T>C		168.0	0.0		119.0	5.0	NM_018449		Silent	SNP	ENST00000379238.1	hg19	CCDS6547.1																																																																																			.	.		0.353	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
VCP	7415	hgsc.bcm.edu	37	9	35060881	35060881	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:35060881T>C	ENST00000358901.6	-	12	2294	c.1399A>G	c.(1399-1401)Acc>Gcc	p.T467A		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	467					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TCTACCACGGTTTCCCGCAGT	0.552																																					p.T467A		Atlas-SNP	.											.	VCP	64	.	0			c.A1399G						.						143.0	128.0	133.0					9																	35060881		2203	4300	6503	SO:0001583	missense	7415	exon12			CCACGGTTTCCCG	AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"""ATPases / AAA-type"""	12666	protein-coding gene	gene with protein product		601023	"""valosin-containing protein"""			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.1399A>G	chr9.hg19:g.35060881T>C	ENSP00000351777:p.Thr467Ala	145.0	0.0		119.0	5.0	NM_007126	B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Missense_Mutation	SNP	ENST00000358901.6	hg19	CCDS6573.1	.	.	.	.	.	.	.	.	.	.	T	15.49	2.850296	0.51270	.	.	ENSG00000165280	ENST00000358901	D	0.86627	-2.15	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.87728	0.6250	M	0.77103	2.36	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	D	0.84750	0.0756	10	0.56958	D	0.05	-20.532	15.9966	0.80256	0.0:0.0:0.0:1.0	.	467	P55072	TERA_HUMAN	A	467	ENSP00000351777:T467A	ENSP00000351777:T467A	T	-	1	0	VCP	35050881	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.040000	0.89188	2.179000	0.69175	0.460000	0.39030	ACC	.	.		0.552	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1	NM_007126	
SIT1	27240	hgsc.bcm.edu	37	9	35650500	35650501	+	Splice_Site	DNP	GT	GT	AC	rs199515871		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:35650500_35650501GT>AC	ENST00000259608.3	-	2	320_321	c.234_235AC>GT	c.(232-237)ggACgc>ggGTgc	p.R79C	SIT1_ENST00000474403.1_Intron	NM_014450.2	NP_055265.1	Q9Y3P8	SIT1_HUMAN	signaling threshold regulating transmembrane adaptor 1	79					immune system process (GO:0002376)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	kinase binding (GO:0019900)|SH2 domain binding (GO:0042169)			endometrium(2)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	9			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TTCACCCACCGTCCCTGCCCCG	0.594																																					p.R79C|p.G78G		Atlas-SNP	.											.	SIT1	15	.	0			c.C235T|c.A234G						.																																			SO:0001630	splice_region_variant	27240	exon2			CCCACCGTCCCTG|CCACCGTCCCTGC		CCDS6582.1	9p13-p12	2008-02-05	2005-04-26		ENSG00000137078	ENSG00000137078			17710	protein-coding gene	gene with protein product	"""SHP2 interacting transmembrane adaptor"""	604964	"""suppression inducing transmembrane adaptor 1"""			11491537, 10209036	Standard	NM_014450		Approved	SIT	uc003zxe.1	Q9Y3P8	OTTHUMG00000019867	ENST00000259608.3:c.234_235delinsAC	chr9.hg19:g.35650500_35650501delinsAC		199.0|195.0	0.0		99.0|98.0	4.0	NM_014450	B2RBP9	Missense_Mutation|Silent	SNP	ENST00000259608.3	hg19	CCDS6582.1																																																																																			.	.		0.594	SIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052322.1	NM_014450	Missense_Mutation
TPM2	7169	hgsc.bcm.edu	37	9	35685445	35685445	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:35685445G>T	ENST00000360958.2	-	4	582	c.478C>A	c.(478-480)Cgc>Agc	p.R160S	TPM2_ENST00000378292.3_Missense_Mutation_p.R160S|TPM2_ENST00000329305.2_Missense_Mutation_p.R160S|TPM2_ENST00000378300.5_Missense_Mutation_p.R160S	NM_003289.3	NP_003280.2	P07951	TPM2_HUMAN	tropomyosin 2 (beta)	160					muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)	cytosol (GO:0005829)|muscle thin filament tropomyosin (GO:0005862)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)	p.R160S(2)		NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_epithelial(49;0.121)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TCATATTTGCGGTCTGAATCC	0.542																																					p.R160S		Atlas-SNP	.											.	TPM2	64	.	2	Substitution - Missense(2)	lung(2)	c.C478A						.						193.0	153.0	166.0					9																	35685445		2203	4300	6503	SO:0001583	missense	7169	exon4			ATTTGCGGTCTGA		CCDS6586.1, CCDS6587.1	9p13	2014-09-17	2003-12-02		ENSG00000198467	ENSG00000198467		"""Tropomyosins"""	12011	protein-coding gene	gene with protein product	"""nemaline myopathy type 4"""	190990	"""arthrogryposis multiplex congenital, distal, type 1"""	AMCD1		7606936	Standard	NM_003289		Approved	DA1, NEM4	uc003zxq.3	P07951	OTTHUMG00000019878	ENST00000360958.2:c.478C>A	chr9.hg19:g.35685445G>T	ENSP00000354219:p.Arg160Ser	103.0	0.0		95.0	4.0	NM_213674	A6NM85|P06468|Q13894|Q53FM4|Q5TCU4|Q5TCU7|Q9UH67	Missense_Mutation	SNP	ENST00000360958.2	hg19	CCDS6587.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.080699	0.76528	.	.	ENSG00000198467	ENST00000378300;ENST00000378292;ENST00000329305;ENST00000360958	T;D;D;D	0.97553	1.51;-4.43;-4.43;-4.43	4.92	3.96	0.45880	.	.	.	.	.	D	0.98658	0.9550	M	0.92691	3.335	0.49051	D	0.999741	P;D;D;P;D	0.61697	0.905;0.974;0.987;0.951;0.99	P;D;D;D;D	0.72982	0.897;0.97;0.979;0.914;0.974	D	0.98776	1.0730	9	0.72032	D	0.01	.	15.3262	0.74164	0.0:0.0:0.86:0.14	.	160;160;160;160;160	B4DGC2;A7XZE4;P07951;Q5TCU8;P07951-2	.;.;TPM2_HUMAN;.;.	S	160	ENSP00000367550:R160S;ENSP00000367542:R160S;ENSP00000367541:R160S;ENSP00000354219:R160S	ENSP00000367541:R160S	R	-	1	0	TPM2	35675445	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.411000	0.73298	2.714000	0.92807	0.561000	0.74099	CGC	.	.		0.542	TPM2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052376.1	NM_003289	
MSMP	692094	hgsc.bcm.edu	37	9	35752822	35752822	+	IGR	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:35752822T>C	ENST00000436428.2	-	0	670				RGP1_ENST00000378078.4_Missense_Mutation_p.L376P|MSMP_ENST00000414286.1_5'Flank|GBA2_ENST00000545786.1_5'Flank|RGP1_ENST00000456972.2_Missense_Mutation_p.L416P	NM_001044264.2	NP_001037729.1	Q1L6U9	MSMP_HUMAN	microseminoprotein, prostate associated							cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(2)|kidney(1)|lung(3)|prostate(3)	9						AGCCCCACCCTGGCCTCATAT	0.592																																					p.L376P		Atlas-SNP	.											RGP1_ENST00000378078,colon,carcinoma,0,2	RGP1	60	.	0			c.T1127C						.						36.0	36.0	36.0					9																	35752822		1987	4146	6133	SO:0001628	intergenic_variant	9827	exon9			CCACCCTGGCCTC	DQ012170	CCDS43797.1	9p13.3	2012-10-02			ENSG00000215183	ENSG00000215183			29663	protein-coding gene	gene with protein product		612191				17338636	Standard	NM_001044264		Approved	PC-3, PSMP	uc003zyb.2	Q1L6U9	OTTHUMG00000019882		chr9.hg19:g.35752822T>C		126.0	0.0		91.0	6.0	NM_001080496		Missense_Mutation	SNP	ENST00000436428.2	hg19	CCDS43797.1	.	.	.	.	.	.	.	.	.	.	T	13.42	2.232296	0.39498	.	.	ENSG00000107185	ENST00000456972;ENST00000378078	.	.	.	5.93	4.73	0.59995	.	0.173543	0.43579	D	0.000541	T	0.57548	0.2061	M	0.62723	1.935	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.11329	0.006;0.006	T	0.55585	-0.8118	9	0.34782	T	0.22	-7.8366	11.3719	0.49704	0.1355:0.0:0.0:0.8645	.	376;376	Q92546;A8K0K1	RGP1_HUMAN;.	P	416;376	.	ENSP00000367318:L376P	L	+	2	0	RGP1	35742822	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.073000	0.64395	2.263000	0.75096	0.533000	0.62120	CTG	.	.		0.592	MSMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052384.2	NM_001044264	
TJP2	9414	hgsc.bcm.edu	37	9	71845110	71845110	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:71845110G>T	ENST00000377245.4	+	11	1841	c.1633G>T	c.(1633-1635)Gag>Tag	p.E545*	TJP2_ENST00000265384.7_Nonsense_Mutation_p.E545*|TJP2_ENST00000348208.4_Nonsense_Mutation_p.E545*|TJP2_ENST00000535702.1_Nonsense_Mutation_p.E549*|TJP2_ENST00000453658.2_Nonsense_Mutation_p.E522*|TJP2_ENST00000539225.1_Nonsense_Mutation_p.E576*	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	545	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						GACCTCGGCGGAGCAGGAGGG	0.512																																					p.E576X		Atlas-SNP	.											.	TJP2	120	.	0			c.G1726T						.						73.0	77.0	75.0					9																	71845110		2203	4300	6503	SO:0001587	stop_gained	9414	exon11			TCGGCGGAGCAGG	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1633G>T	chr9.hg19:g.71845110G>T	ENSP00000366453:p.Glu545*	96.0	0.0		83.0	4.0	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Nonsense_Mutation	SNP	ENST00000377245.4	hg19	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	G	41	9.092042	0.99062	.	.	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	.	.	.	5.86	5.86	0.93980	.	0.171732	0.51477	D	0.000100	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	20.5632	0.99335	0.0:0.0:1.0:0.0	.	.	.	.	X	522;545;545;545;549;576	.	ENSP00000265384:E545X	E	+	1	0	TJP2	71034930	1.000000	0.71417	0.949000	0.38748	0.949000	0.60115	9.813000	0.99286	2.937000	0.99478	0.650000	0.86243	GAG	.	.		0.512	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
TLE4	7091	hgsc.bcm.edu	37	9	82337475	82337475	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:82337475T>C	ENST00000376552.2	+	18	3114	c.2096T>C	c.(2095-2097)cTt>cCt	p.L699P	TLE4_ENST00000376537.4_Missense_Mutation_p.L731P|TLE4_ENST00000376534.4_Missense_Mutation_p.L336P|TLE4_ENST00000376520.4_Missense_Mutation_p.L731P|TLE4_ENST00000376544.3_Missense_Mutation_p.L630P|TLE4_ENST00000265284.6_Missense_Mutation_p.L674P	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	699					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						CAACTACATCTTCATGAGAGC	0.498																																					p.L699P		Atlas-SNP	.											.	TLE4	187	.	0			c.T2096C						.						138.0	136.0	137.0					9																	82337475		2031	4221	6252	SO:0001583	missense	7091	exon18			TACATCTTCATGA	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.2096T>C	chr9.hg19:g.82337475T>C	ENSP00000365735:p.Leu699Pro	207.0	0.0		125.0	5.0	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	hg19	CCDS43837.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.883456	0.91740	.	.	ENSG00000106829	ENST00000376552;ENST00000376544;ENST00000376520;ENST00000376537;ENST00000376534;ENST00000265284	T;T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;0.22;0.22	6.17	6.17	0.99709	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	0.73674	0.3617	L	0.58669	1.825	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	0.987;0.999;0.969;1.0	T	0.74435	-0.3666	10	0.56958	D	0.05	-18.4225	16.8222	0.85835	0.0:0.0:0.0:1.0	.	674;630;731;699	F8W6T6;Q04727-2;Q04727-3;Q04727	.;.;.;TLE4_HUMAN	P	699;630;731;731;336;674	ENSP00000365735:L699P;ENSP00000365727:L630P;ENSP00000365703:L731P;ENSP00000365720:L731P;ENSP00000365717:L336P;ENSP00000265284:L674P	ENSP00000265284:L674P	L	+	2	0	TLE4	81527295	1.000000	0.71417	0.968000	0.41197	0.994000	0.84299	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	CTT	.	.		0.498	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84608910	84608910	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:84608910A>G	ENST00000344803.2	+	4	3572	c.3525A>G	c.(3523-3525)aaA>aaG	p.K1175K		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1175					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CAAATGTGAAAGCAAGCACTT	0.398																																					p.K1175K		Atlas-SNP	.											.	.	.	.	0			c.A3525G						.						56.0	54.0	54.0					9																	84608910		1869	4124	5993	SO:0001819	synonymous_variant	389763	exon4			TGTGAAAGCAAGC		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.3525A>G	chr9.hg19:g.84608910A>G		125.0	0.0		82.0	4.0	NM_001001670		Silent	SNP	ENST00000344803.2	hg19	CCDS47986.1																																																																																			.	.		0.398	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
IARS	3376	hgsc.bcm.edu	37	9	95033301	95033301	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:95033301T>C	ENST00000375643.3	-	12	1437	c.1171A>G	c.(1171-1173)Acc>Gcc	p.T391A	IARS_ENST00000443024.2_Missense_Mutation_p.T391A|IARS_ENST00000447699.2_Missense_Mutation_p.T281A|IARS_ENST00000375629.3_5'UTR	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	391					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)	GTGAAGGTGGTGGCAACCAGA	0.388																																					p.T391A		Atlas-SNP	.											.	IARS	74	.	0			c.A1171G						.						178.0	167.0	171.0					9																	95033301		2203	4300	6503	SO:0001583	missense	3376	exon12			AGGTGGTGGCAAC	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.1171A>G	chr9.hg19:g.95033301T>C	ENSP00000364794:p.Thr391Ala	96.0	0.0		65.0	4.0	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	hg19	CCDS6694.1	.	.	.	.	.	.	.	.	.	.	T	10.76	1.439961	0.25900	.	.	ENSG00000196305	ENST00000375643;ENST00000443024;ENST00000447699;ENST00000375660	T;T;T	0.34667	1.35;1.35;1.35	6.08	1.96	0.26148	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (2);Aminoacyl-tRNA synthetase, class Ia (1);	0.208495	0.56097	N	0.000021	T	0.15003	0.0362	N	0.02721	-0.515	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.002	T	0.05305	-1.0893	10	0.32370	T	0.25	-5.9685	10.4604	0.44577	0.0:0.2253:0.0:0.7747	.	391;236	P41252;Q6P0M4	SYIC_HUMAN;.	A	391;391;281;391	ENSP00000364794:T391A;ENSP00000406448:T391A;ENSP00000415020:T281A	ENSP00000364794:T391A	T	-	1	0	IARS	94073122	1.000000	0.71417	0.497000	0.27552	0.369000	0.29798	2.361000	0.44160	0.502000	0.28037	0.533000	0.62120	ACC	.	.		0.388	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161	
FBP2	8789	hgsc.bcm.edu	37	9	97346891	97346891	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:97346891A>G	ENST00000375337.3	-	3	460	c.394T>C	c.(394-396)Tcc>Ccc	p.S132P		NM_003837.2	NP_003828.2	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	132					carbohydrate metabolic process (GO:0005975)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(3)|lung(5)	9		Acute lymphoblastic leukemia(62;0.136)				GTTCCGATGGAGGCCAGGCAG	0.483																																					p.S132P		Atlas-SNP	.											.	FBP2	26	.	0			c.T394C						.						150.0	122.0	132.0					9																	97346891		2203	4300	6503	SO:0001583	missense	8789	exon3			CGATGGAGGCCAG	Y10812	CCDS6711.1	9q22.3	2012-08-13			ENSG00000130957	ENSG00000130957	3.1.3.11		3607	protein-coding gene	gene with protein product		603027				9678974	Standard	NM_003837		Approved		uc004auv.3	O00757	OTTHUMG00000020269	ENST00000375337.3:c.394T>C	chr9.hg19:g.97346891A>G	ENSP00000364486:p.Ser132Pro	151.0	0.0		115.0	5.0	NM_003837	Q17R39|Q6FI53	Missense_Mutation	SNP	ENST00000375337.3	hg19	CCDS6711.1	.	.	.	.	.	.	.	.	.	.	A	14.11	2.437382	0.43224	.	.	ENSG00000130957	ENST00000375337	T	0.79247	-1.25	4.87	4.87	0.63330	.	0.169189	0.53938	D	0.000045	T	0.73426	0.3585	L	0.58354	1.805	0.53005	D	0.999961	B	0.21309	0.054	B	0.25506	0.061	T	0.72782	-0.4189	10	0.66056	D	0.02	-19.1055	9.6905	0.40125	0.9098:0.0:0.0902:0.0	.	132	O00757	F16P2_HUMAN	P	132	ENSP00000364486:S132P	ENSP00000364486:S132P	S	-	1	0	FBP2	96386712	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	3.742000	0.55097	1.941000	0.56285	0.533000	0.62120	TCC	.	.		0.483	FBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053189.1	NM_003837	
FKTN	2218	hgsc.bcm.edu	37	9	108363469	108363469	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:108363469T>C	ENST00000223528.2	+	4	333	c.209T>C	c.(208-210)gTa>gCa	p.V70A	FKTN_ENST00000357998.5_Missense_Mutation_p.V70A|FKTN_ENST00000448551.2_Missense_Mutation_p.V70A|FKTN_ENST00000602661.1_Missense_Mutation_p.V70A|FKTN_ENST00000540160.1_Missense_Mutation_p.V70A	NM_006731.2	NP_006722.2	O75072	FKTN_HUMAN	fukutin	70					muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|nervous system development (GO:0007399)|regulation of protein glycosylation (GO:0060049)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transferase activity (GO:0016740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	25						AACCAAAATGTACCAGTGTTT	0.318																																					p.V70A		Atlas-SNP	.											.	FKTN	47	.	0			c.T209C						.						64.0	64.0	64.0					9																	108363469		2203	4299	6502	SO:0001583	missense	2218	exon4			AAAATGTACCAGT		CCDS6766.1	9q31-q33	2014-09-17	2007-11-21	2007-11-21	ENSG00000106692	ENSG00000106692			3622	protein-coding gene	gene with protein product		607440	"""Fukuyama type congenital muscular dystrophy (fukutin)"""	FCMD		8275093, 17036286, 17044012	Standard	NM_001079802		Approved	LGMD2M	uc004bcs.3	O75072	OTTHUMG00000020425	ENST00000223528.2:c.209T>C	chr9.hg19:g.108363469T>C	ENSP00000223528:p.Val70Ala	108.0	0.0		91.0	5.0	NM_006731	B4DUX9|J3KP13|Q3MIJ1|Q96TE1|Q9P295	Missense_Mutation	SNP	ENST00000223528.2	hg19	CCDS6766.1	.	.	.	.	.	.	.	.	.	.	T	17.68	3.449337	0.63178	.	.	ENSG00000106692	ENST00000223528;ENST00000448551;ENST00000540160;ENST00000357998;ENST00000374705	D;D;D;D;D	0.92199	-2.66;-2.99;-1.84;-2.99;-1.89	5.65	5.65	0.86999	.	0.222664	0.40144	N	0.001170	D	0.88654	0.6495	L	0.44542	1.39	0.40163	D	0.977088	P;P;P	0.41131	0.739;0.495;0.682	B;B;B	0.36464	0.225;0.079;0.079	D	0.90327	0.4349	10	0.87932	D	0	-12.5197	15.0542	0.71901	0.0:0.0:0.0:1.0	.	70;70;70	B4E2W4;B4DUX9;O75072	.;.;FKTN_HUMAN	A	70;70;70;70;47	ENSP00000223528:V70A;ENSP00000399140:V70A;ENSP00000439423:V70A;ENSP00000350687:V70A;ENSP00000363837:V47A	ENSP00000223528:V70A	V	+	2	0	FKTN	107403290	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	4.575000	0.60908	2.155000	0.67459	0.383000	0.25322	GTA	.	.		0.318	FKTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053505.1	NM_006731	
C9orf84	158401	hgsc.bcm.edu	37	9	114454021	114454021	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:114454021A>G	ENST00000318737.4	-	25	4172	c.4044T>C	c.(4042-4044)agT>agC	p.S1348S	C9orf84_ENST00000374287.3_Silent_p.S1348S|C9orf84_ENST00000394779.3_Silent_p.S1309S|C9orf84_ENST00000394777.4_Silent_p.S1274S	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1348										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						CATCTTTTGAACTTTCACATG	0.373																																					p.S1348S		Atlas-SNP	.											.	C9orf84	207	.	0			c.T4044C						.						72.0	74.0	73.0					9																	114454021		2203	4300	6503	SO:0001819	synonymous_variant	158401	exon25			TTTTGAACTTTCA	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.4044T>C	chr9.hg19:g.114454021A>G		118.0	0.0		90.0	4.0	NM_173521	A2A2V3|Q2M1H8|Q96M73	Silent	SNP	ENST00000318737.4	hg19	CCDS6781.3																																																																																			.	.		0.373	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
TTC16	158248	hgsc.bcm.edu	37	9	130482418	130482418	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:130482418C>T	ENST00000373289.3	+	5	568	c.488C>T	c.(487-489)gCt>gTt	p.A163V	TTC16_ENST00000393748.4_5'UTR|PTRH1_ENST00000429848.1_Intron|PTRH1_ENST00000419060.1_Intron	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	163										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						TCACATGCTGCTGAGCTCCAG	0.597																																					p.A163V		Atlas-SNP	.											.	TTC16	55	.	0			c.C488T						.						204.0	157.0	173.0					9																	130482418		2203	4300	6503	SO:0001583	missense	158248	exon5			ATGCTGCTGAGCT	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"""Tetratricopeptide (TTC) repeat domain containing"""	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.488C>T	chr9.hg19:g.130482418C>T	ENSP00000362386:p.Ala163Val	152.0	0.0		96.0	5.0	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	hg19	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	C	3.684	-0.064900	0.07273	.	.	ENSG00000167094	ENST00000373289;ENST00000316259	T	0.50548	0.74	4.84	0.946	0.19549	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.892206	0.09685	N	0.769180	T	0.29158	0.0725	N	0.24115	0.695	0.09310	N	0.999994	B;B;B	0.27450	0.179;0.048;0.179	B;B;B	0.21151	0.033;0.013;0.033	T	0.16867	-1.0388	10	0.33940	T	0.23	-0.4035	6.0062	0.19547	0.0:0.6302:0.1385:0.2313	.	150;115;163	B4DZ42;B4DH05;Q8NEE8	.;.;TTC16_HUMAN	V	163;108	ENSP00000362386:A163V	ENSP00000319048:A108V	A	+	2	0	TTC16	129522239	0.006000	0.16342	0.000000	0.03702	0.391000	0.30476	1.605000	0.36815	0.012000	0.14892	0.195000	0.17529	GCT	.	.		0.597	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	
ZER1	10444	hgsc.bcm.edu	37	9	131515870	131515870	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:131515870C>T	ENST00000291900.2	-	4	725	c.319G>A	c.(319-321)Gag>Aag	p.E107K	ZER1_ENST00000494461.1_5'UTR	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	107					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						AGGTACAGCTCCACCAGGTCC	0.622																																					p.E107K		Atlas-SNP	.											.	ZER1	49	.	0			c.G319A						.						40.0	41.0	40.0					9																	131515870		2203	4300	6503	SO:0001583	missense	10444	exon4			ACAGCTCCACCAG	X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"""ZYG11 cell cycle regulator family"""	30960	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 60"", ""zyg-11 homolog B (C. elegans)-like"", ""zer-1 homolog (C. elegans)"""	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.319G>A	chr9.hg19:g.131515870C>T	ENSP00000291900:p.Glu107Lys	96.0	0.0		62.0	4.0	NM_006336	O00156|Q5T272|Q5T273	Missense_Mutation	SNP	ENST00000291900.2	hg19	CCDS6910.1	.	.	.	.	.	.	.	.	.	.	C	34	5.344655	0.95807	.	.	ENSG00000160445	ENST00000291900;ENST00000414921	T;T	0.18174	2.23;2.23	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.31263	0.0791	L	0.32530	0.975	0.80722	D	1	D	0.63880	0.993	D	0.70935	0.971	T	0.01068	-1.1462	10	0.23302	T	0.38	-35.5407	18.8072	0.92041	0.0:1.0:0.0:0.0	.	107	Q7Z7L7	ZER1_HUMAN	K	107	ENSP00000291900:E107K;ENSP00000393051:E107K	ENSP00000291900:E107K	E	-	1	0	ZER1	130555691	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.374000	0.66167	2.691000	0.91804	0.655000	0.94253	GAG	.	.		0.622	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336	
PHYHD1	254295	hgsc.bcm.edu	37	9	131702690	131702690	+	Missense_Mutation	SNP	T	T	C	rs569532899		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:131702690T>C	ENST00000372592.3	+	10	1433	c.500T>C	c.(499-501)cTg>cCg	p.L167P	RP11-101E3.5_ENST00000482796.1_5'Flank|PHYHD1_ENST00000421063.2_Missense_Mutation_p.L146P|PHYHD1_ENST00000487504.1_3'UTR|PHYHD1_ENST00000353176.5_Missense_Mutation_p.L146P|PHYHD1_ENST00000308941.5_Missense_Mutation_p.W160R	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	167							dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						ACGGAGCCCCTGGGCCGGGTG	0.627													T|||	1	0.000199681	0.0	0.0	5008	,	,		17838	0.0		0.0	False		,,,				2504	0.001				p.L167P		Atlas-SNP	.											.	PHYHD1	29	.	0			c.T500C						.						71.0	77.0	75.0					9																	131702690		2203	4300	6503	SO:0001583	missense	254295	exon10			AGCCCCTGGGCCG	BC051300	CCDS6914.1, CCDS43885.1, CCDS43886.1	9q34.13	2010-08-13			ENSG00000175287	ENSG00000175287			23396	protein-coding gene	gene with protein product						12477932	Standard	NM_174933		Approved	MGC16638	uc004bwp.2	Q5SRE7	OTTHUMG00000020764	ENST00000372592.3:c.500T>C	chr9.hg19:g.131702690T>C	ENSP00000361673:p.Leu167Pro	107.0	0.0		87.0	4.0	NM_001100876	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Missense_Mutation	SNP	ENST00000372592.3	hg19	CCDS43885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.93|18.93	3.726987|3.726987	0.69074|0.69074	.|.	.|.	ENSG00000175287|ENSG00000175287	ENST00000372592;ENST00000353176;ENST00000426694;ENST00000421063|ENST00000308941;ENST00000419872	D;D;D;D|.	0.88664|.	-2.41;-2.41;-2.41;-2.41|.	5.25|5.25	5.25|5.25	0.73442|0.73442	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.78717|0.78717	0.4327|0.4327	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B;B|D	0.19706|0.76494	0.029;0.038|0.999	B;B|D	0.25291|0.74023	0.059;0.027|0.982	T|T	0.81949|0.81949	-0.0699|-0.0699	8|8	0.30078|0.87932	T|D	0.28|0	-3.8361|-3.8361	14.3375|14.3375	0.66600|0.66600	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	146;167|160	Q5SRE7-2;Q5SRE7|Q5SRE7-3	.;PHYD1_HUMAN|.	P|R	167;146;167;146|160;25	ENSP00000361673:L167P;ENSP00000340945:L146P;ENSP00000412377:L167P;ENSP00000409928:L146P|.	ENSP00000340945:L146P|ENSP00000309515:W160R	L|W	+|+	2|1	0|0	PHYHD1|PHYHD1	130742511|130742511	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	5.150000|5.150000	0.64869|0.64869	1.998000|1.998000	0.58463|0.58463	0.454000|0.454000	0.30748|0.30748	CTG|TGG	.	.		0.627	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933	
PRRC2B	84726	hgsc.bcm.edu	37	9	134353913	134353913	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:134353913T>C	ENST00000357304.4	+	17	4720	c.4665T>C	c.(4663-4665)ggT>ggC	p.G1555G	PRRC2B_ENST00000458550.1_Silent_p.G861G|PRRC2B_ENST00000405995.1_Silent_p.G861G|PRRC2B_ENST00000372249.1_5'UTR	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1555							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GTGAGGTGGGTTCTATGGTGG	0.567											OREG0019562	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G1555G		Atlas-SNP	.											.	PRRC2B	266	.	0			c.T4665C						.						134.0	142.0	140.0					9																	134353913		1903	4118	6021	SO:0001819	synonymous_variant	84726	exon17			GGTGGGTTCTATG	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.4665T>C	chr9.hg19:g.134353913T>C		154.0	0.0	1610	96.0	4.0	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	hg19	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	T	6.142	0.394323	0.11638	.	.	ENSG00000130723	ENST00000451855	.	.	.	5.42	0.937	0.19494	.	.	.	.	.	T	0.40839	0.1133	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29181	-1.0020	4	.	.	.	-26.4667	0.8187	0.01107	0.1653:0.2618:0.1618:0.4111	.	.	.	.	L	289	.	.	F	+	1	0	PRRC2B	133343734	0.893000	0.30496	0.804000	0.32291	0.479000	0.33129	0.211000	0.17474	0.643000	0.30638	-0.366000	0.07423	TTC	.	.		0.567	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
GBGT1	26301	hgsc.bcm.edu	37	9	136029497	136029497	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:136029497G>T	ENST00000372040.3	-	7	822	c.511C>A	c.(511-513)Cag>Aag	p.Q171K	GBGT1_ENST00000372038.3_3'UTR|GBGT1_ENST00000372043.3_Silent_p.S164S|RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000540636.1_Missense_Mutation_p.Q154K|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	171					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		GAGTGACCCTGGATGGGGATG	0.627																																					p.Q171K		Atlas-SNP	.											.	GBGT1	25	.	0			c.C511A						.						39.0	35.0	37.0					9																	136029497		2203	4299	6502	SO:0001583	missense	26301	exon7			GACCCTGGATGGG	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.511C>A	chr9.hg19:g.136029497G>T	ENSP00000361110:p.Gln171Lys	90.0	0.0		81.0	4.0	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Missense_Mutation	SNP	ENST00000372040.3	hg19	CCDS6960.1	.	.	.	.	.	.	.	.	.	.	G	0.042	-1.280718	0.01398	.	.	ENSG00000148288	ENST00000372040;ENST00000540636	T;T	0.01099	5.34;5.34	5.38	4.47	0.54385	.	0.981452	0.08357	N	0.958368	T	0.01189	0.0039	N	0.24115	0.695	0.21325	N	0.999724	B;B	0.12013	0.005;0.005	B;B	0.12837	0.008;0.005	T	0.46275	-0.9203	10	0.05525	T	0.97	-0.2384	13.695	0.62572	0.0:0.0:0.7209:0.2791	.	154;171	B7Z8S5;Q8N5D6	.;GBGT1_HUMAN	K	171;154	ENSP00000361110:Q171K;ENSP00000437663:Q154K	ENSP00000361110:Q171K	Q	-	1	0	GBGT1	135019318	0.064000	0.20934	0.818000	0.32626	0.313000	0.28021	0.698000	0.25571	1.237000	0.43756	0.491000	0.48974	CAG	.	.		0.627	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
COL5A1	1289	hgsc.bcm.edu	37	9	137716488	137716488	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:137716488T>C	ENST00000371817.3	+	62	5155	c.4741T>C	c.(4741-4743)Tcc>Ccc	p.S1581P		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1581	Nonhelical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AATCCAGGCATCCAGGACGCG	0.647																																					p.S1581P		Atlas-SNP	.											.	COL5A1	323	.	0			c.T4741C						.						47.0	42.0	44.0					9																	137716488		2203	4300	6503	SO:0001583	missense	1289	exon62			CAGGCATCCAGGA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4741T>C	chr9.hg19:g.137716488T>C	ENSP00000360882:p.Ser1581Pro	168.0	0.0		96.0	6.0	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	T	10.22	1.290693	0.23564	.	.	ENSG00000130635	ENST00000371817;ENST00000355306	D	0.89810	-2.57	4.21	4.21	0.49690	.	0.440276	0.21317	U	0.076538	T	0.79992	0.4542	L	0.27944	0.81	0.34759	D	0.732579	B	0.06786	0.001	B	0.08055	0.003	T	0.76438	-0.2959	10	0.14252	T	0.57	.	10.983	0.47506	0.0:0.0:0.156:0.844	.	1581	P20908	CO5A1_HUMAN	P	1581;118	ENSP00000360882:S1581P	ENSP00000347458:S118P	S	+	1	0	COL5A1	136856309	0.937000	0.31787	0.131000	0.22000	0.957000	0.61999	1.675000	0.37555	1.673000	0.50895	0.363000	0.22086	TCC	.	.		0.647	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
ABCA2	20	hgsc.bcm.edu	37	9	139910924	139910924	+	Splice_Site	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:139910924C>A	ENST00000371605.3	-	20	3068		c.e20-1		ABCA2_ENST00000492260.1_5'Flank|ABCA2_ENST00000265662.5_Splice_Site|ABCA2_ENST00000341511.6_Splice_Site			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2						ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CGGGTCTCCTCTGCACCAGGG	0.642																																					.		Atlas-SNP	.											.	ABCA2	113	.	0			c.3014-1G>T						.						74.0	83.0	80.0					9																	139910924		2095	4202	6297	SO:0001630	splice_region_variant	20	exon22			TCTCCTCTGCACC	U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"""ATP binding cassette transporters / subfamily A"""	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.2921-1G>T	chr9.hg19:g.139910924C>A		144.0	0.0		95.0	4.0	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Splice_Site	SNP	ENST00000371605.3	hg19		.	.	.	.	.	.	.	.	.	.	C	14.15	2.450280	0.43531	.	.	ENSG00000107331	ENST00000265662;ENST00000371605;ENST00000355090;ENST00000341511	.	.	.	4.23	4.23	0.50019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5922	0.84769	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABCA2	139030745	1.000000	0.71417	0.998000	0.56505	0.447000	0.32167	3.667000	0.54547	1.898000	0.54952	0.306000	0.20318	.	.	.		0.642	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606	Intron
RNF208	727800	hgsc.bcm.edu	37	9	140115610	140115610	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr9:140115610A>G	ENST00000392827.1	-	2	223	c.55T>C	c.(55-57)Tcc>Ccc	p.S19P	RNF208_ENST00000391553.1_Missense_Mutation_p.S19P			Q9H0X6	RN208_HUMAN	ring finger protein 208	19					protein autoubiquitination (GO:0051865)		ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			lung(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		TTCAGGCAGGACATGAGGAGG	0.652																																					p.S19P		Atlas-SNP	.											.	RNF208	11	.	0			c.T55C						.						12.0	14.0	14.0					9																	140115610		1928	4112	6040	SO:0001583	missense	727800	exon1			GGCAGGACATGAG	AF416715	CCDS7037.2	9q34.3	2007-01-19				ENSG00000212864		"""RING-type (C3HC4) zinc fingers"""	25420	protein-coding gene	gene with protein product						11230166	Standard	NM_031297		Approved	DKFZP761H1710	uc004clz.2	Q9H0X6		ENST00000392827.1:c.55T>C	chr9.hg19:g.140115610A>G	ENSP00000376572:p.Ser19Pro	146.0	0.0		104.0	5.0	NM_031297	A2BFA0	Missense_Mutation	SNP	ENST00000392827.1	hg19	CCDS7037.2	.	.	.	.	.	.	.	.	.	.	a	13.72	2.321905	0.41096	.	.	ENSG00000212864	ENST00000392827;ENST00000391553	T;T	0.39997	1.05;1.05	3.58	2.39	0.29439	.	.	.	.	.	T	0.31167	0.0788	N	0.19112	0.55	0.40669	D	0.982191	P	0.39250	0.665	B	0.43018	0.405	T	0.13202	-1.0518	9	0.87932	D	0	-5.8566	8.7227	0.34449	0.8074:0.1926:0.0:0.0	.	19	Q9H0X6	RN208_HUMAN	P	19	ENSP00000376572:S19P;ENSP00000375397:S19P	ENSP00000375397:S19P	S	-	1	0	RNF208	139235431	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.163000	0.50763	0.425000	0.26087	0.454000	0.30748	TCC	.	.		0.652	RNF208-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254714.1	NM_031297	
ADARB2	105	hgsc.bcm.edu	37	10	1229197	1229197	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:1229197T>C	ENST00000381312.1	-	10	2481	c.2156A>G	c.(2155-2157)aAg>aGg	p.K719R	ADARB2_ENST00000381305.1_Missense_Mutation_p.K121R|ADARB2_ENST00000381310.3_Missense_Mutation_p.K228R	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	719	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CAGGCCAGCCTTCTGAAAGGC	0.622																																					p.K719R		Atlas-SNP	.											.	ADARB2	95	.	0			c.A2156G						.						61.0	54.0	56.0					10																	1229197		2203	4300	6503	SO:0001583	missense	105	exon10			CCAGCCTTCTGAA	AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"""RED2 homolog (rat)"""	602065	"""adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)"", ""adenosine deaminase, RNA-specific, B2"""			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.2156A>G	chr10.hg19:g.1229197T>C	ENSP00000370713:p.Lys719Arg	176.0	0.0		125.0	5.0	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	hg19	CCDS7058.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077815	0.36662	.	.	ENSG00000185736	ENST00000381312;ENST00000381310;ENST00000381305	D;D;D	0.93859	-3.3;-3.3;-3.3	5.32	5.32	0.75619	Adenosine deaminase/editase (3);	0.093502	0.85682	D	0.000000	D	0.88243	0.6384	L	0.35249	1.045	0.42091	D	0.991298	B;B;B	0.18610	0.004;0.029;0.014	B;B;B	0.22601	0.04;0.039;0.032	D	0.84155	0.0425	10	0.42905	T	0.14	-28.3273	8.6606	0.34091	0.0:0.149:0.0:0.851	.	719;121;228	Q9NS39;Q5VW43;Q5VW42	RED2_HUMAN;.;.	R	719;228;121	ENSP00000370713:K719R;ENSP00000370711:K228R;ENSP00000370706:K121R	ENSP00000370706:K121R	K	-	2	0	ADARB2	1219197	1.000000	0.71417	0.999000	0.59377	0.788000	0.44548	2.792000	0.47837	2.025000	0.59659	0.459000	0.35465	AAG	.	.		0.622	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702	
RBM17	84991	hgsc.bcm.edu	37	10	6143232	6143232	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:6143232A>G	ENST00000446108.1	+	3	767		c.e3-1		RBM17_ENST00000379888.4_Splice_Site	NM_001145547.1	NP_001139019.1	Q96I25	SPF45_HUMAN	RNA binding motif protein 17						alternative mRNA splicing, via spliceosome (GO:0000380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	19						TGATGATTTTAGAGCCAAAGG	0.428																																					.		Atlas-SNP	.											.	RBM17	45	.	0			c.124-2A>G						.						54.0	47.0	50.0					10																	6143232		2203	4300	6503	SO:0001630	splice_region_variant	84991	exon3			GATTTTAGAGCCA	AF083384	CCDS7077.1	10p15.1	2013-01-28			ENSG00000134453	ENSG00000134453		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	16944	protein-coding gene	gene with protein product	"""splicing factor 45kDa"""	606935				9731529	Standard	NM_032905		Approved	SPF45, MGC14439	uc001ijb.3	Q96I25	OTTHUMG00000017618	ENST00000446108.1:c.124-1A>G	chr10.hg19:g.6143232A>G		92.0	0.0		76.0	4.0	NM_032905	Q96GY6	Splice_Site	SNP	ENST00000446108.1	hg19	CCDS7077.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.093478	0.76756	.	.	ENSG00000134453	ENST00000372795;ENST00000379888;ENST00000437845;ENST00000432931;ENST00000446108;ENST00000418631	.	.	.	4.67	4.67	0.58626	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4099	0.67109	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RBM17	6183238	1.000000	0.71417	0.994000	0.49952	0.956000	0.61745	9.014000	0.93635	1.862000	0.54008	0.460000	0.39030	.	.	.		0.428	RBM17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046635.1	NM_032905	Intron
NUDT5	11164	hgsc.bcm.edu	37	10	12215770	12215770	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:12215770C>T	ENST00000491614.1	-	6	727	c.332G>A	c.(331-333)cGg>cAg	p.R111Q	NUDT5_ENST00000378940.3_Missense_Mutation_p.R111Q|NUDT5_ENST00000537776.1_Missense_Mutation_p.R111Q|NUDT5_ENST00000378937.3_Missense_Mutation_p.R124Q|NUDT5_ENST00000378952.3_5'UTR|NUDT5_ENST00000378927.3_Missense_Mutation_p.R111Q			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	111	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				TTCAAGCTCCCGGAGAGCAGC	0.493																																					p.R111Q		Atlas-SNP	.											.	NUDT5	10	.	0			c.G332A						.						174.0	177.0	176.0					10																	12215770		2203	4300	6503	SO:0001583	missense	11164	exon6			AGCTCCCGGAGAG	AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"""Nudix motif containing"""	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.332G>A	chr10.hg19:g.12215770C>T	ENSP00000419628:p.Arg111Gln	149.0	0.0		125.0	5.0	NM_014142	A8K516|Q6IAG0|Q9UH49	Missense_Mutation	SNP	ENST00000491614.1	hg19	CCDS7089.1	.	.	.	.	.	.	.	.	.	.	C	35	5.424703	0.96111	.	.	ENSG00000165609	ENST00000491614;ENST00000378929;ENST00000378937;ENST00000537776;ENST00000378940;ENST00000378927	T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57	5.76	5.76	0.90799	NUDIX hydrolase (1);NUDIX hydrolase domain (3);NUDIX hydrolase, conserved site (1);NUDIX hydrolase domain-like (1);	0.000000	0.85682	D	0.000000	D	0.86041	0.5838	H	0.99379	4.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91491	0.5212	10	0.87932	D	0	-19.7435	20.3242	0.98691	0.0:1.0:0.0:0.0	.	111;111	A6NCQ0;Q9UKK9	.;NUDT5_HUMAN	Q	111;111;124;111;111;111	ENSP00000419628:R111Q;ENSP00000368219:R124Q;ENSP00000445116:R111Q;ENSP00000368222:R111Q;ENSP00000368209:R111Q	ENSP00000368209:R111Q	R	-	2	0	NUDT5	12255776	1.000000	0.71417	0.999000	0.59377	0.869000	0.49853	6.507000	0.73717	2.882000	0.98803	0.655000	0.94253	CGG	.	.		0.493	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1		
MCM10	55388	hgsc.bcm.edu	37	10	13212949	13212949	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:13212949C>T	ENST00000484800.2	+	3	138	c.35C>T	c.(34-36)aCc>aTc	p.T12I	MCM10_ENST00000378694.1_Missense_Mutation_p.T12I|MCM10_ENST00000378714.3_Missense_Mutation_p.T12I			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	12	N-terminal domain. {ECO:0000250}.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						TCTCTGCTGACCGCACTGCTG	0.438																																					p.T12I		Atlas-SNP	.											.	MCM10	76	.	0			c.C35T						.						68.0	70.0	69.0					10																	13212949		2203	4300	6503	SO:0001583	missense	55388	exon3			TGCTGACCGCACT	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"""MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"""			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.35C>T	chr10.hg19:g.13212949C>T	ENSP00000418268:p.Thr12Ile	138.0	0.0		121.0	5.0	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	hg19	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.718569	0.68844	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.19105	2.19;2.18;2.17	5.91	5.91	0.95273	.	0.263978	0.42682	D	0.000671	T	0.33177	0.0854	M	0.64997	1.995	0.45914	D	0.998755	D;D;D	0.58970	0.973;0.984;0.973	P;P;P	0.51266	0.463;0.664;0.463	T	0.00984	-1.1491	10	0.32370	T	0.25	0.7561	15.43	0.75084	0.0:0.9322:0.0:0.0678	.	12;12;12	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	I	12	ENSP00000367986:T12I;ENSP00000418268:T12I;ENSP00000367966:T12I	ENSP00000354945:T12I	T	+	2	0	MCM10	13252955	0.999000	0.42202	0.990000	0.47175	0.936000	0.57629	4.445000	0.60007	2.793000	0.96121	0.655000	0.94253	ACC	.	.		0.438	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
CUBN	8029	hgsc.bcm.edu	37	10	17157511	17157511	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:17157511G>T	ENST00000377833.4	-	7	744	c.679C>A	c.(679-681)Cat>Aat	p.H227N		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	227					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)	CAGATGCCATGGACACAGCGT	0.542																																					p.H227N		Atlas-SNP	.											.	CUBN	515	.	0			c.C679A						.						139.0	117.0	124.0					10																	17157511		2203	4300	6503	SO:0001583	missense	8029	exon7			TGCCATGGACACA	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.679C>A	chr10.hg19:g.17157511G>T	ENSP00000367064:p.His227Asn	91.0	0.0		92.0	4.0	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.478655	0.84747	.	.	ENSG00000107611	ENST00000377833	D	0.86366	-2.11	5.75	5.75	0.90469	Growth factor, receptor (1);Epidermal growth factor-like (1);	0.000000	0.48286	D	0.000198	D	0.94460	0.8217	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94680	0.7864	10	0.87932	D	0	.	19.5261	0.95208	0.0:0.0:1.0:0.0	.	227	O60494	CUBN_HUMAN	N	227	ENSP00000367064:H227N	ENSP00000367064:H227N	H	-	1	0	CUBN	17197517	1.000000	0.71417	0.065000	0.19835	0.739000	0.42172	6.220000	0.72237	2.721000	0.93114	0.655000	0.94253	CAT	.	.		0.542	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
MYO3A	53904	hgsc.bcm.edu	37	10	26312957	26312957	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:26312957A>G	ENST00000265944.5	+	9	904	c.738A>G	c.(736-738)ccA>ccG	p.P246P	MYO3A_ENST00000543632.1_Silent_p.P246P	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	246	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CTAGGAATCCACCCCCAAAAC	0.383																																					p.P246P		Atlas-SNP	.											.	MYO3A	371	.	0			c.A738G						.						133.0	136.0	135.0					10																	26312957		2203	4300	6503	SO:0001819	synonymous_variant	53904	exon9			GAATCCACCCCCA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.738A>G	chr10.hg19:g.26312957A>G		163.0	0.0		124.0	5.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	hg19	CCDS7148.1																																																																																			.	.		0.383	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
ABI1	10006	hgsc.bcm.edu	37	10	27044647	27044647	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:27044647G>T	ENST00000376142.2	-	10	1173	c.1102C>A	c.(1102-1104)Cct>Act	p.P368T	ABI1_ENST00000536334.1_Intron|ABI1_ENST00000355394.4_Missense_Mutation_p.P369T|ABI1_ENST00000376138.3_Intron|ABI1_ENST00000376170.4_Intron|ABI1_ENST00000346832.5_Intron|ABI1_ENST00000376166.1_Intron|ABI1_ENST00000376134.3_Missense_Mutation_p.P342T|ABI1_ENST00000359188.4_Missense_Mutation_p.P340T|ABI1_ENST00000376140.3_Missense_Mutation_p.P341T|ABI1_ENST00000376139.2_Missense_Mutation_p.P336T|ABI1_ENST00000376160.1_Missense_Mutation_p.P335T|ABI1_ENST00000490841.2_Intron|ABI1_ENST00000376137.4_Missense_Mutation_p.P283T	NM_005470.3	NP_005461.2	Q8IZP0	ABI1_HUMAN	abl-interactor 1	368	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium morphogenesis (GO:0072673)|megakaryocyte development (GO:0035855)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|SCAR complex (GO:0031209)	cytoskeletal protein binding (GO:0008092)|protein complex binding (GO:0032403)|protein tyrosine kinase activator activity (GO:0030296)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGAGGCATAGGGGGAGGGGGT	0.458																																					p.P368T		Atlas-SNP	.											.	ABI1	38	.	0			c.C1102A						.						93.0	95.0	94.0					10																	27044647		2203	4300	6503	SO:0001583	missense	10006	exon10			GCATAGGGGGAGG	U87166	CCDS7150.1, CCDS31169.1, CCDS31170.1, CCDS31171.1, CCDS53497.1, CCDS53498.1, CCDS53499.1, CCDS53500.1, CCDS53501.1, CCDS73077.1, CCDS73078.1	10p12.1	2009-05-29	2004-03-17	2004-03-19	ENSG00000136754	ENSG00000136754			11320	protein-coding gene	gene with protein product		603050	"""spectrin SH3 domain binding protein 1"""	SSH3BP1		9593709, 9010225	Standard	NM_005470		Approved	E3B1, ABI-1	uc001isx.3	Q8IZP0	OTTHUMG00000017848	ENST00000376142.2:c.1102C>A	chr10.hg19:g.27044647G>T	ENSP00000365312:p.Pro368Thr	85.0	0.0		84.0	4.0	NM_005470	A9Z1Y6|B3KX62|B4DQ58|H7BXI6|O15147|O76049|O95060|Q5T2R3|Q5T2R4|Q5T2R6|Q5T2R7|Q5T2R9|Q5W070|Q5W072|Q8TB63|Q96S81|Q9NXZ9|Q9NYB8	Missense_Mutation	SNP	ENST00000376142.2	hg19	CCDS7150.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812514	0.70912	.	.	ENSG00000136754	ENST00000376160;ENST00000376142;ENST00000359188;ENST00000376139;ENST00000355394;ENST00000376134;ENST00000376137;ENST00000376140	T;T;T;T;T;T;T;T	0.47528	0.98;0.88;0.94;0.88;1.06;0.84;1.02;0.95	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.65365	0.2684	L	0.50333	1.59	0.80722	D	1	D;P;P;P;B	0.71674	0.998;0.746;0.746;0.746;0.376	D;P;P;P;B	0.73708	0.981;0.557;0.557;0.557;0.164	T	0.65389	-0.6180	10	0.62326	D	0.03	-9.3667	19.6869	0.95982	0.0:0.0:1.0:0.0	.	282;340;336;341;368	B6VEX3;Q8IZP0-6;Q8IZP0-5;Q8IZP0-9;Q8IZP0	.;.;.;.;ABI1_HUMAN	T	335;368;340;336;369;342;283;341	ENSP00000365330:P335T;ENSP00000365312:P368T;ENSP00000352114:P340T;ENSP00000365309:P336T;ENSP00000347555:P369T;ENSP00000365304:P342T;ENSP00000365307:P283T;ENSP00000365310:P341T	ENSP00000347555:P369T	P	-	1	0	ABI1	27084653	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.751000	0.98889	2.726000	0.93360	0.655000	0.94253	CCT	.	.		0.458	ABI1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047287.1	NM_005470	
YME1L1	10730	hgsc.bcm.edu	37	10	27409405	27409405	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:27409405T>C	ENST00000326799.3	-	14	1689	c.1541A>G	c.(1540-1542)gAa>gGa	p.E514G	YME1L1_ENST00000376016.3_Missense_Mutation_p.E457G|YME1L1_ENST00000375972.3_Missense_Mutation_p.E424G	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	514					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						TTTCAAAATTTCTGTTCGACC	0.343																																					p.E514G		Atlas-SNP	.											.	YME1L1	71	.	0			c.A1541G						.						95.0	91.0	92.0					10																	27409405		2203	4300	6503	SO:0001583	missense	10730	exon14			AAAATTTCTGTTC	AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"""ATPases / AAA-type"""	12843	protein-coding gene	gene with protein product		607472	"""YME1 (S.cerevisiae)-like 1"", ""YME1-like 1 (S. cerevisiae)"""			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.1541A>G	chr10.hg19:g.27409405T>C	ENSP00000318480:p.Glu514Gly	117.0	0.0		88.0	4.0	NM_139312	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Missense_Mutation	SNP	ENST00000326799.3	hg19	CCDS7152.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.325619	0.81580	.	.	ENSG00000136758	ENST00000376016;ENST00000326799;ENST00000375969;ENST00000375972;ENST00000546122	T;T;T	0.79845	-1.31;-1.31;-1.31	5.72	5.72	0.89469	Peptidase M41, FtsH (2);	0.000000	0.85682	D	0.000000	D	0.89663	0.6780	M	0.78916	2.43	0.80722	D	1	D;D;D	0.76494	0.999;0.968;0.999	D;P;D	0.75484	0.986;0.852;0.96	D	0.90862	0.4739	10	0.87932	D	0	-30.5238	16.2988	0.82793	0.0:0.0:0.0:1.0	.	424;457;514	B4DNM1;Q96TA2-2;Q96TA2	.;.;YMEL1_HUMAN	G	457;514;514;424;260	ENSP00000365184:E457G;ENSP00000318480:E514G;ENSP00000365139:E424G	ENSP00000318480:E514G	E	-	2	0	YME1L1	27449411	1.000000	0.71417	1.000000	0.80357	0.551000	0.35334	7.954000	0.87848	2.311000	0.77944	0.533000	0.62120	GAA	.	.		0.343	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312	
SVIL	6840	hgsc.bcm.edu	37	10	29820188	29820188	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:29820188A>G	ENST00000355867.4	-	10	2791	c.2039T>C	c.(2038-2040)gTc>gCc	p.V680A	SVIL_ENST00000375398.2_Missense_Mutation_p.V680A|SVIL_ENST00000375400.3_Missense_Mutation_p.V286A	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	680					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)				CTTGCCATCGACAGTTGGCGT	0.353																																					p.V680A		Atlas-SNP	.											.	SVIL	226	.	0			c.T2039C						.						134.0	113.0	120.0					10																	29820188		2203	4300	6503	SO:0001583	missense	6840	exon10			CCATCGACAGTTG	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.2039T>C	chr10.hg19:g.29820188A>G	ENSP00000348128:p.Val680Ala	78.0	0.0		79.0	4.0	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	A	0.349	-0.945961	0.02304	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.52057	0.68;0.68;0.68	5.81	2.71	0.32032	.	1.813340	0.02448	N	0.085221	T	0.21509	0.0518	N	0.01297	-0.9	0.29181	N	0.876508	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.29731	-1.0002	9	.	.	.	-0.9066	6.7409	0.23435	0.3201:0.0:0.6799:0.0	.	286;680	O95425-2;O95425	.;SVIL_HUMAN	A	286;680;680	ENSP00000364549:V286A;ENSP00000364547:V680A;ENSP00000348128:V680A	.	V	-	2	0	SVIL	29860194	0.004000	0.15560	0.009000	0.14445	0.002000	0.02628	0.960000	0.29253	0.622000	0.30249	0.533000	0.62120	GTC	.	.		0.353	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
ZNF33A	7581	hgsc.bcm.edu	37	10	38344489	38344489	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:38344489T>C	ENST00000458705.2	+	5	1592	c.1434T>C	c.(1432-1434)agT>agC	p.S478S	ZNF33A_ENST00000307441.9_Silent_p.S478S|ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Silent_p.S485S|ZNF33A_ENST00000374618.3_Silent_p.S479S			Q06730	ZN33A_HUMAN	zinc finger protein 33A	478					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)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						AATCCTTTAGTGAAAAGTCAA	0.388																																					p.S479S		Atlas-SNP	.											.	ZNF33A	103	.	0			c.T1437C						.						60.0	59.0	59.0					10																	38344489		2202	4300	6502	SO:0001819	synonymous_variant	7581	exon5			CTTTAGTGAAAAG	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.1434T>C	chr10.hg19:g.38344489T>C		91.0	0.0		97.0	4.0	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Silent	SNP	ENST00000458705.2	hg19	CCDS31182.1																																																																																			.	.		0.388	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
ARHGAP22	58504	hgsc.bcm.edu	37	10	49667827	49667827	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:49667827C>T	ENST00000249601.4	-	5	855	c.559G>A	c.(559-561)Ggg>Agg	p.G187R	ARHGAP22_ENST00000417912.2_Missense_Mutation_p.G203R|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.G78R|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.G193R|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.G97R|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.G97R	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	187	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TCAGTGAGCCCGCGCTCCCGG	0.647																																					p.G203R		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.G607A						.						101.0	94.0	96.0					10																	49667827		2203	4300	6503	SO:0001583	missense	58504	exon5			TGAGCCCGCGCTC	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.559G>A	chr10.hg19:g.49667827C>T	ENSP00000249601:p.Gly187Arg	120.0	0.0		97.0	4.0	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	hg19	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.745759	0.89663	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T	0.57752	2.25;0.38;2.25;2.25;2.25;0.38	4.9	4.9	0.64082	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.80523	0.4639	H	0.94264	3.515	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;1.0;1.0;1.0;0.991	D	0.86287	0.1671	10	0.87932	D	0	.	17.2419	0.87015	0.0:1.0:0.0:0.0	.	193;187;203;187;97	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3	.;.;.;RHG22_HUMAN;.	R	187;78;97;97;193;203	ENSP00000249601:G187R;ENSP00000363287:G78R;ENSP00000363285:G97R;ENSP00000410054:G97R;ENSP00000416701:G193R;ENSP00000412461:G203R	ENSP00000249601:G187R	G	-	1	0	ARHGAP22	49337833	1.000000	0.71417	0.942000	0.38095	0.639000	0.38242	7.564000	0.82326	2.565000	0.86533	0.313000	0.20887	GGG	.	.		0.647	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226	
WDFY4	57705	hgsc.bcm.edu	37	10	49939422	49939422	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:49939422T>C	ENST00000325239.5	+	8	1424	c.1397T>C	c.(1396-1398)aTc>aCc	p.I466T	WDFY4_ENST00000413659.2_Missense_Mutation_p.I466T|WDFY4_ENST00000360890.2_Missense_Mutation_p.I466T	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	466						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						CCTCATGAGATCCTGCGAAAG	0.592																																					p.I466T		Atlas-SNP	.											.	WDFY4	205	.	0			c.T1397C						.						71.0	68.0	69.0					10																	49939422		692	1591	2283	SO:0001583	missense	57705	exon9			ATGAGATCCTGCG	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.1397T>C	chr10.hg19:g.49939422T>C	ENSP00000320563:p.Ile466Thr	68.0	0.0		69.0	5.0	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	hg19	CCDS44385.1	.	.	.	.	.	.	.	.	.	.	T	14.23	2.472782	0.43942	.	.	ENSG00000128815	ENST00000360890;ENST00000454161;ENST00000426033;ENST00000325239;ENST00000413659	T;T;T	0.41400	1.0;3.27;3.27	5.58	5.58	0.84498	Armadillo-like helical (1);	.	.	.	.	T	0.39835	0.1093	L	0.46157	1.445	0.23765	N	0.996902	B;B	0.20988	0.016;0.05	B;B	0.20955	0.009;0.032	T	0.23868	-1.0176	9	0.35671	T	0.21	.	14.9432	0.71009	0.0:0.0:0.0:1.0	.	466;466	Q6ZS81;Q6ZS81-2	WDFY4_HUMAN;.	T	466;475;466;466;466	ENSP00000354141:I466T;ENSP00000320563:I466T;ENSP00000403789:I466T	ENSP00000320563:I466T	I	+	2	0	WDFY4	49609428	0.999000	0.42202	0.998000	0.56505	0.714000	0.41099	3.157000	0.50716	2.134000	0.65973	0.460000	0.39030	ATC	.	.		0.592	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
JMJD1C	221037	hgsc.bcm.edu	37	10	64946064	64946064	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:64946064T>C	ENST00000399262.2	-	19	6868	c.6650A>G	c.(6649-6651)gAc>gGc	p.D2217G	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000542921.1_Missense_Mutation_p.D2035G|JMJD1C_ENST00000402544.1_Missense_Mutation_p.D1980G	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2217					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					AGCTTGGTGGTCTCCAAAATC	0.368																																					p.D2217G		Atlas-SNP	.											.	JMJD1C	347	.	0			c.A6650G						.						109.0	103.0	105.0					10																	64946064		1861	4098	5959	SO:0001583	missense	221037	exon19			TGGTGGTCTCCAA	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.6650A>G	chr10.hg19:g.64946064T>C	ENSP00000382204:p.Asp2217Gly	132.0	0.0		94.0	4.0	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.67|19.67	3.871796|3.871796	0.72180|0.72180	.|.	.|.	ENSG00000171988|ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921|ENST00000327520	T;T;T|.	0.74002|.	-0.8;-0.8;-0.8|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.047245|.	0.85682|.	D|.	0.000000|.	T|T	0.69495|0.69495	0.3117|0.3117	L|L	0.53617|0.53617	1.68|1.68	0.80722|0.80722	D|D	1|1	P;P;B|.	0.48294|.	0.908;0.908;0.004|.	B;B;B|.	0.43950|.	0.437;0.437;0.027|.	T|T	0.67337|0.67337	-0.5696|-0.5696	10|5	0.72032|.	D|.	0.01|.	-13.429|-13.429	15.8601|15.8601	0.79014|0.79014	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2035;2217;2035|.	B7ZLC8;Q15652;A0T124|.	.;JHD2C_HUMAN;.|.	G|A	2217;1980;2035|764	ENSP00000382204:D2217G;ENSP00000384990:D1980G;ENSP00000444682:D2035G|.	ENSP00000382204:D2217G|.	D|T	-|-	2|1	0|0	JMJD1C|JMJD1C	64616070|64616070	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	4.773000|4.773000	0.62331|0.62331	2.284000|2.284000	0.76573|0.76573	0.528000|0.528000	0.53228|0.53228	GAC|ACC	.	.		0.368	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
LRRTM3	347731	hgsc.bcm.edu	37	10	68857536	68857536	+	Missense_Mutation	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:68857536T>A	ENST00000361320.4	+	3	2306	c.1728T>A	c.(1726-1728)caT>caA	p.H576Q	CTNNA3_ENST00000433211.2_Intron|CTNNA3_ENST00000373744.4_Intron|LRRTM3_ENST00000485868.1_3'UTR	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	576					positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						TCAGTGACCATAAACAGCAGC	0.458																																					p.H576Q		Atlas-SNP	.											.	LRRTM3	241	.	0			c.T1728A						.						125.0	108.0	114.0					10																	68857536		2203	4300	6503	SO:0001583	missense	347731	exon3			TGACCATAAACAG	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.1728T>A	chr10.hg19:g.68857536T>A	ENSP00000355187:p.His576Gln	93.0	0.0		91.0	4.0	NM_178011	A8K2A3|Q2NKX7|Q6N0A3	Missense_Mutation	SNP	ENST00000361320.4	hg19	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.069775	0.36566	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	T	0.41758	0.99	5.62	3.26	0.37387	.	0.000000	0.49305	D	0.000149	T	0.21145	0.0509	N	0.08118	0	0.29259	N	0.871486	B	0.17852	0.024	B	0.06405	0.002	T	0.12630	-1.0540	10	0.87932	D	0	.	7.2321	0.26049	0.0:0.235:0.0:0.7649	.	576	Q86VH5	LRRT3_HUMAN	Q	576	ENSP00000355187:H576Q	ENSP00000355187:H576Q	H	+	3	2	LRRTM3	68527542	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.183000	0.16919	1.074000	0.40909	0.528000	0.53228	CAT	.	.		0.458	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011	
MYPN	84665	hgsc.bcm.edu	37	10	69925542	69925542	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:69925542A>G	ENST00000358913.5	+	9	2055	c.1567A>G	c.(1567-1569)Aca>Gca	p.T523A	MYPN_ENST00000540630.1_Missense_Mutation_p.T523A|MYPN_ENST00000354393.2_Missense_Mutation_p.T248A	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	523	Ig-like 2.				sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						CAAATACGGCACAGTGTCAAG	0.438																																					p.T523A		Atlas-SNP	.											.	MYPN	189	.	0			c.A1567G						.						169.0	136.0	147.0					10																	69925542		2203	4300	6503	SO:0001583	missense	84665	exon9			TACGGCACAGTGT	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1567A>G	chr10.hg19:g.69925542A>G	ENSP00000351790:p.Thr523Ala	85.0	0.0		76.0	4.0	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	hg19	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.172926	0.78452	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.66638	-0.22;-0.22;-0.22	5.23	4.06	0.47325	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.72542	0.3473	L	0.39566	1.225	0.58432	D	0.999991	D;D;D	0.76494	0.996;0.999;0.999	D;D;D	0.83275	0.987;0.978;0.996	T	0.69250	-0.5194	9	.	.	.	.	11.1945	0.48704	0.8623:0.0:0.0:0.1377	.	523;248;523	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	A	248;248;523;523	ENSP00000346369:T248A;ENSP00000351790:T523A;ENSP00000441668:T523A	.	T	+	1	0	MYPN	69595548	1.000000	0.71417	0.908000	0.35775	0.884000	0.51177	8.923000	0.92808	0.779000	0.33543	0.459000	0.35465	ACA	.	.		0.438	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
DDX21	9188	hgsc.bcm.edu	37	10	70723119	70723119	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:70723119T>C	ENST00000354185.4	+	4	778	c.680T>C	c.(679-681)aTt>aCt	p.I227T	RN7SL373P_ENST00000577512.1_RNA	NM_001256910.1|NM_004728.3	NP_001243839.1|NP_004719.2	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 21	227	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|osteoblast differentiation (GO:0001649)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	20						AAGGACTTAATTGCACAGGCA	0.463																																					p.I227T		Atlas-SNP	.											.	DDX21	57	.	0			c.T680C						.						143.0	125.0	131.0					10																	70723119		2203	4300	6503	SO:0001583	missense	9188	exon4			ACTTAATTGCACA	U41387	CCDS31211.1, CCDS73144.1	10q21	2013-05-13	2012-02-23		ENSG00000165732	ENSG00000165732		"""DEAD-boxes"""	2744	protein-coding gene	gene with protein product		606357	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 21"""			8614622, 18180292	Standard	NM_004728		Approved	RH-II/GU, GURDB	uc001jov.2	Q9NR30	OTTHUMG00000018366	ENST00000354185.4:c.680T>C	chr10.hg19:g.70723119T>C	ENSP00000346120:p.Ile227Thr	95.0	0.0		100.0	4.0	NM_004728	B2RDL0|Q13436|Q5VX41|Q68D35	Missense_Mutation	SNP	ENST00000354185.4	hg19	CCDS31211.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.979987	0.74360	.	.	ENSG00000165732	ENST00000354185	T	0.58060	0.36	5.4	4.27	0.50696	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.204155	0.52532	N	0.000080	T	0.72439	0.3460	M	0.84683	2.71	0.51012	D	0.999905	D	0.71674	0.998	D	0.71870	0.975	T	0.75752	-0.3207	10	0.72032	D	0.01	-4.9461	11.1026	0.48184	0.0:0.0721:0.0:0.9279	.	227	Q9NR30	DDX21_HUMAN	T	227	ENSP00000346120:I227T	ENSP00000346120:I227T	I	+	2	0	DDX21	70393125	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	7.655000	0.83696	1.004000	0.39156	0.533000	0.62120	ATT	.	.		0.463	DDX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048374.1	NM_004728	
CDH23	64072	hgsc.bcm.edu	37	10	73375297	73375297	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:73375297G>T	ENST00000224721.6	+	9	889	c.884G>T	c.(883-885)aGc>aTc	p.S295I	CDH23_ENST00000398809.4_Missense_Mutation_p.S290I|CDH23_ENST00000461841.3_Missense_Mutation_p.S335I|CDH23_ENST00000299366.7_Missense_Mutation_p.S335I|CDH23_ENST00000398842.3_Missense_Mutation_p.S290I	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	290	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GACTACATCAGCGGAGTGCTG	0.592																																					p.S290I		Atlas-SNP	.											.	CDH23	365	.	0			c.G869T						.						86.0	89.0	88.0					10																	73375297		2034	4178	6212	SO:0001583	missense	64072	exon10			ACATCAGCGGAGT	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.884G>T	chr10.hg19:g.73375297G>T	ENSP00000224721:p.Ser295Ile	130.0	0.0		79.0	4.0	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	G	19.76	3.888389	0.72524	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000398809;ENST00000398842;ENST00000299366;ENST00000224721;ENST00000416060	T;T	0.63744	-0.06;-0.06	4.22	4.22	0.49857	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.82033	0.4949	M	0.88979	2.995	0.80722	D	1	D;D;D	0.69078	0.973;0.997;0.997	P;D;D	0.80764	0.677;0.988;0.994	D	0.86633	0.1887	10	0.87932	D	0	.	16.7626	0.85516	0.0:0.0:1.0:0.0	.	290;290;290	A5D6V9;Q9H251;Q9H251-5	.;CAD23_HUMAN;.	I	297;290;290;290;290;295;295;207	ENSP00000381789:S290I;ENSP00000381822:S290I	ENSP00000224721:S297I	S	+	2	0	CDH23	73045303	1.000000	0.71417	0.985000	0.45067	0.604000	0.37047	7.210000	0.77924	2.182000	0.69389	0.557000	0.71058	AGC	.	.		0.592	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
C10orf54	64115	hgsc.bcm.edu	37	10	73511594	73511594	+	Silent	SNP	G	G	T	rs201880754		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:73511594G>T	ENST00000394957.3	-	6	787	c.729C>A	c.(727-729)ccC>ccA	p.P243P	CDH23_ENST00000224721.6_Intron	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	243					BMP signaling pathway (GO:0030509)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of T cell cytokine production (GO:0002725)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of stem cell differentiation (GO:2000738)|stem cell differentiation (GO:0048863)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						CTTCAAAGCCGGGGTTTTCAA	0.602																																					p.P243P		Atlas-SNP	.											.	C10orf54	29	.	0			c.C729A						.						48.0	49.0	49.0					10																	73511594		2203	4300	6503	SO:0001819	synonymous_variant	64115	exon6			AAAGCCGGGGTTT	AF193048	CCDS31218.1	10q22.1	2013-11-28			ENSG00000107738	ENSG00000107738		"""Immunoglobulin superfamily / V-set domain containing"""	30085	protein-coding gene	gene with protein product	"""stress induced secreted protein 1"""	615608				12975309	Standard	NM_022153		Approved	SISP1, GI24, B7-H5, B7H5	uc001jsd.3	Q9H7M9	OTTHUMG00000018426	ENST00000394957.3:c.729C>A	chr10.hg19:g.73511594G>T		125.0	0.0		110.0	5.0	NM_022153	A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Silent	SNP	ENST00000394957.3	hg19	CCDS31218.1																																																																																			.	G|1.000;A|0.000		0.602	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153	
MCU	90550	hgsc.bcm.edu	37	10	74631338	74631338	+	Splice_Site	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:74631338G>T	ENST00000373053.3	+	6	882	c.861G>T	c.(859-861)caG>caT	p.Q287H	MCU_ENST00000357157.6_Splice_Site_p.Q266H|MCU_ENST00000605416.1_3'UTR|MCU_ENST00000536019.1_Splice_Site_p.Q238H	NM_138357.2	NP_612366.1	Q8NE86	MCU_HUMAN	mitochondrial calcium uniporter	287					calcium ion transmembrane import into mitochondrion (GO:0036444)|calcium-mediated signaling (GO:0019722)|glucose homeostasis (GO:0042593)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein complex oligomerization (GO:0035786)	calcium channel complex (GO:0034704)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|uniplex complex (GO:1990246)	calcium channel activity (GO:0005262)|uniporter activity (GO:0015292)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(1)	14						TGACACGCCAGGTAAGAATTC	0.358																																					p.Q287H		Atlas-SNP	.											.	MCU	29	.	0			c.G861T						.						75.0	73.0	74.0					10																	74631338		2203	4300	6503	SO:0001630	splice_region_variant	90550	exon6			ACGCCAGGTAAGA	BC034235	CCDS7317.1, CCDS59218.1, CCDS59219.1	10q22.2	2011-06-23	2011-06-23	2011-06-23	ENSG00000156026	ENSG00000156026			23526	protein-coding gene	gene with protein product		614197	"""coiled-coil domain containing 109A"""	C10orf42, CCDC109A		21685886, 21685888	Standard	NM_138357		Approved	FLJ46135	uc001jtc.3	Q8NE86	OTTHUMG00000018443	ENST00000373053.3:c.861+1G>T	chr10.hg19:g.74631338G>T		52.0	0.0		82.0	4.0	NM_138357	B2RDF3|B3KXV7|Q96FL3	Missense_Mutation	SNP	ENST00000373053.3	hg19	CCDS7317.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577859	0.86645	.	.	ENSG00000156026	ENST00000373053;ENST00000357157;ENST00000536019	T;T;T	0.32272	1.46;1.46;1.46	5.92	5.0	0.66597	Coiled-coil domain containing protein 109, C-terminal (1);	0.050514	0.85682	N	0.000000	T	0.59959	0.2232	M	0.82517	2.595	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.74674	0.973;0.951;0.984	T	0.67929	-0.5543	10	0.87932	D	0	-11.0743	16.9087	0.86135	0.0:0.1281:0.8719:0.0	.	266;238;287	Q8NE86-2;Q8NE86-3;Q8NE86	.;.;MCU_HUMAN	H	287;266;238	ENSP00000362144:Q287H;ENSP00000349680:Q266H;ENSP00000440913:Q238H	ENSP00000349680:Q266H	Q	+	3	2	MCU	74301344	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.869000	0.99810	1.439000	0.47511	0.650000	0.86243	CAG	.	.		0.358	MCU-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048594.1	NM_138357	Missense_Mutation
SEC24C	9632	hgsc.bcm.edu	37	10	75525917	75525917	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:75525917T>C	ENST00000339365.2	+	12	1718	c.1556T>C	c.(1555-1557)cTt>cCt	p.L519P	SEC24C_ENST00000411652.2_Missense_Mutation_p.L400P|SEC24C_ENST00000546025.1_Intron|SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000345254.4_Missense_Mutation_p.L519P	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	519					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)	p.L519H(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					AGGACTGGTCTTGTTAGGCTC	0.468																																					p.L519P		Atlas-SNP	.											SEC24C,NS,carcinoma,0,1	SEC24C	86	.	1	Substitution - Missense(1)	endometrium(1)	c.T1556C						.						123.0	123.0	123.0					10																	75525917		2203	4300	6503	SO:0001583	missense	9632	exon11			CTGGTCTTGTTAG	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"""SEC24 (S. cerevisiae) related gene family, member C"", ""SEC24 family, member C (S. cerevisiae)"""			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.1556T>C	chr10.hg19:g.75525917T>C	ENSP00000343405:p.Leu519Pro	57.0	0.0		50.0	3.0	NM_198597	B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	hg19	CCDS7332.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.968865	0.74131	.	.	ENSG00000176986	ENST00000345254;ENST00000339365;ENST00000411652	T;T;T	0.49432	0.78;0.78;0.78	5.71	5.71	0.89125	Sec23/Sec24, trunk domain (1);	0.109254	0.64402	D	0.000015	T	0.74107	0.3673	M	0.88377	2.95	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	0.79914	-0.1602	10	0.87932	D	0	-17.1134	15.9812	0.80111	0.0:0.0:0.0:1.0	.	400;519;519	E7EP00;G5EA31;P53992	.;.;SC24C_HUMAN	P	519;519;400	ENSP00000321845:L519P;ENSP00000343405:L519P;ENSP00000402913:L400P	ENSP00000343405:L519P	L	+	2	0	SEC24C	75195923	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.178000	0.69098	0.533000	0.62120	CTT	.	.		0.468	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1		
VCL	7414	hgsc.bcm.edu	37	10	75854142	75854142	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:75854142C>T	ENST00000211998.4	+	11	1560	c.1466C>T	c.(1465-1467)gCa>gTa	p.A489V	VCL_ENST00000478896.2_Intron|VCL_ENST00000417648.2_Intron|VCL_ENST00000372755.3_Missense_Mutation_p.A489V	NM_014000.2	NP_054706.1	P18206	VINC_HUMAN	vinculin	489	3 X 112 AA tandem repeats.|N-terminal globular head.				adherens junction assembly (GO:0034333)|apical junction assembly (GO:0043297)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|epithelial cell-cell adhesion (GO:0090136)|lamellipodium assembly (GO:0030032)|morphogenesis of an epithelium (GO:0002009)|muscle contraction (GO:0006936)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|protein localization to cell surface (GO:0034394)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cell-substrate junction (GO:0030055)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	actin binding (GO:0003779)|alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)		VCL/ALK(4)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Prostate(51;0.0112)					CCGGCCAAAGCAGCTGTACAC	0.577																																					p.A489V		Atlas-SNP	.											.	VCL	77	.	0			c.C1466T						.						65.0	54.0	58.0					10																	75854142		2203	4300	6503	SO:0001583	missense	7414	exon11			CCAAAGCAGCTGT	M33308	CCDS7340.1, CCDS7341.1	10q22.1-q23	2014-09-17			ENSG00000035403	ENSG00000035403			12665	protein-coding gene	gene with protein product	"""metavinculin"""	193065				1339348	Standard	NM_014000		Approved		uc001jwd.3	P18206	OTTHUMG00000018498	ENST00000211998.4:c.1466C>T	chr10.hg19:g.75854142C>T	ENSP00000211998:p.Ala489Val	258.0	0.0		239.0	11.0	NM_003373	Q16450|Q5SWX2|Q7Z3B8|Q8IXU7	Missense_Mutation	SNP	ENST00000211998.4	hg19	CCDS7341.1	.	.	.	.	.	.	.	.	.	.	C	32	5.111533	0.94339	.	.	ENSG00000035403	ENST00000372755;ENST00000211998;ENST00000415462;ENST00000537043;ENST00000436396	T;T;T	0.39229	1.09;1.09;1.09	5.47	5.47	0.80525	.	0.056220	0.64402	D	0.000001	T	0.35799	0.0944	L	0.47716	1.5	0.80722	D	1	P;B;B	0.42993	0.797;0.097;0.134	B;B;B	0.34038	0.101;0.042;0.174	T	0.15321	-1.0441	10	0.24483	T	0.36	.	19.378	0.94519	0.0:1.0:0.0:0.0	.	416;489;489	F5H7T3;P18206-2;P18206	.;.;VINC_HUMAN	V	489;489;396;416;161	ENSP00000361841:A489V;ENSP00000211998:A489V;ENSP00000415489:A161V	ENSP00000211998:A489V	A	+	2	0	VCL	75524148	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.441000	0.80485	2.583000	0.87209	0.585000	0.79938	GCA	.	.		0.577	VCL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003373, NM_014000	
KAT6B	23522	hgsc.bcm.edu	37	10	76788578	76788578	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:76788578T>C	ENST00000287239.4	+	18	4485	c.3996T>C	c.(3994-3996)ccT>ccC	p.P1332P	KAT6B_ENST00000372724.1_Silent_p.P1040P|KAT6B_ENST00000372714.1_Silent_p.P1040P|KAT6B_ENST00000372711.1_Silent_p.P1149P|KAT6B_ENST00000372725.1_Silent_p.P1040P	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1332					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)										CATGTGCCCCTGTAAGTCCAA	0.502																																					p.P1332P		Atlas-SNP	.											.	.	.	.	0			c.T3996C						.						73.0	71.0	72.0					10																	76788578		2203	4300	6503	SO:0001819	synonymous_variant	23522	exon18			TGCCCCTGTAAGT	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.3996T>C	chr10.hg19:g.76788578T>C		114.0	0.0		103.0	5.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.		0.502	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	
GRID1	2894	hgsc.bcm.edu	37	10	87628897	87628897	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:87628897G>T	ENST00000327946.7	-	6	906	c.821C>A	c.(820-822)gCc>gAc	p.A274D		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	274					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						CCTTCCAAGGGCACTATGGAC	0.517										Multiple Myeloma(13;0.14)																											p.A274D		Atlas-SNP	.											.	GRID1	204	.	0			c.C821A						.						157.0	136.0	143.0					10																	87628897		2203	4300	6503	SO:0001583	missense	2894	exon6			CCAAGGGCACTAT	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.821C>A	chr10.hg19:g.87628897G>T	ENSP00000330148:p.Ala274Asp	146.0	0.0		107.0	5.0	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	hg19	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.488424	0.84854	.	.	ENSG00000182771	ENST00000327946	D	0.85556	-2.0	5.82	5.82	0.92795	Extracellular ligand-binding receptor (1);	0.097857	0.64402	D	0.000001	D	0.87030	0.6076	L	0.44542	1.39	0.80722	D	1	D	0.58268	0.982	P	0.52159	0.691	D	0.87980	0.2742	10	0.87932	D	0	.	19.0974	0.93258	0.0:0.0:1.0:0.0	.	274	Q9ULK0	GRID1_HUMAN	D	274	ENSP00000330148:A274D	ENSP00000330148:A274D	A	-	2	0	GRID1	87618877	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.848000	0.99507	2.745000	0.94114	0.655000	0.94253	GCC	.	.		0.517	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	
PPP1R3C	5507	hgsc.bcm.edu	37	10	93390552	93390552	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:93390552C>A	ENST00000238994.5	-	2	170	c.86G>T	c.(85-87)tGc>tTc	p.C29F		NM_005398.5	NP_005389.1			protein phosphatase 1, regulatory subunit 3C											breast(1)|endometrium(1)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(1)	12		Colorectal(252;0.235)				ATGTGCCAAGCAAAGCCTCAT	0.453																																					p.C29F		Atlas-SNP	.											.	PPP1R3C	30	.	0			c.G86T						.						81.0	83.0	82.0					10																	93390552		2203	4300	6503	SO:0001583	missense	5507	exon2			GCCAAGCAAAGCC	Y18207	CCDS7416.1	10q23-q24	2012-04-17	2011-10-04	2001-08-01	ENSG00000119938	ENSG00000119938		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9293	protein-coding gene	gene with protein product	"""Phosphatase 1, regulatory inhibitor subunit 5"", ""protein targeting to glycogen"""	602999	"""protein phosphatase 1, regulatory (inhibitor) subunit 3C"""	PPP1R5		8985175	Standard	NM_005398		Approved	PTG	uc001kho.3	Q9UQK1	OTTHUMG00000018745	ENST00000238994.5:c.86G>T	chr10.hg19:g.93390552C>A	ENSP00000238994:p.Cys29Phe	96.0	0.0		79.0	4.0	NM_005398		Missense_Mutation	SNP	ENST00000238994.5	hg19	CCDS7416.1	.	.	.	.	.	.	.	.	.	.	C	9.503	1.103720	0.20632	.	.	ENSG00000119938	ENST00000238994;ENST00000438999	T	0.41400	1.0	5.68	5.68	0.88126	.	0.104848	0.64402	D	0.000002	T	0.41050	0.1142	L	0.56769	1.78	0.52099	D	0.999943	B	0.30889	0.299	B	0.26517	0.07	T	0.26087	-1.0113	10	0.15499	T	0.54	-13.9965	19.7888	0.96450	0.0:1.0:0.0:0.0	.	29	Q9UQK1	PPR3C_HUMAN	F	29	ENSP00000238994:C29F	ENSP00000238994:C29F	C	-	2	0	PPP1R3C	93380532	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.173000	0.50839	2.662000	0.90505	0.655000	0.94253	TGC	.	.		0.453	PPP1R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049372.1	NM_005398	
CEP55	55165	hgsc.bcm.edu	37	10	95279490	95279490	+	Missense_Mutation	SNP	G	G	A	rs542873829		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:95279490G>A	ENST00000371485.3	+	8	1421	c.1117G>A	c.(1117-1119)Gtg>Atg	p.V373M	CEP55_ENST00000496302.1_3'UTR	NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	373	Required for localization to the interphase centrosome and to the midbody during cytokinesis.				establishment of protein localization (GO:0045184)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|midbody (GO:0030496)				kidney(1)|large_intestine(5)|lung(6)|stomach(1)	13		Colorectal(252;0.207)				CCGTCAACATGTGCAGCATCA	0.393													g|||	1	0.000199681	0.0008	0.0	5008	,	,		20466	0.0		0.0	False		,,,				2504	0.0				p.V373M		Atlas-SNP	.											.	CEP55	35	.	0			c.G1117A						.						117.0	102.0	107.0					10																	95279490		2203	4300	6503	SO:0001583	missense	55165	exon8			CAACATGTGCAGC	AK001402	CCDS7428.1	10q24.1	2014-02-20	2005-12-01	2005-12-01	ENSG00000138180	ENSG00000138180			1161	protein-coding gene	gene with protein product	"""cancer/testis antigen 111"""	610000	"""chromosome 10 open reading frame 3"""	C10orf3		16198290	Standard	NM_018131		Approved	FLJ10540, CT111	uc009xug.3	Q53EZ4	OTTHUMG00000018774	ENST00000371485.3:c.1117G>A	chr10.hg19:g.95279490G>A	ENSP00000360540:p.Val373Met	93.0	0.0		84.0	4.0	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Missense_Mutation	SNP	ENST00000371485.3	hg19	CCDS7428.1	.	.	.	.	.	.	.	.	.	.	g	1.489	-0.555262	0.03967	.	.	ENSG00000138180	ENST00000371485;ENST00000358339	T	0.15952	2.38	5.79	3.46	0.39613	.	0.262502	0.46758	N	0.000267	T	0.02727	0.0082	N	0.00289	-1.7	0.22096	N	0.999361	B	0.02656	0.0	B	0.04013	0.001	T	0.41645	-0.9497	10	0.02654	T	1	-10.0504	4.4531	0.11630	0.6671:0.0:0.1569:0.1761	.	373	Q53EZ4	CEP55_HUMAN	M	373	ENSP00000360540:V373M	ENSP00000351102:V373M	V	+	1	0	CEP55	95269480	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.307000	0.33516	0.455000	0.26910	-0.405000	0.06341	GTG	.	.		0.393	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131	
PLCE1	51196	hgsc.bcm.edu	37	10	96076352	96076352	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:96076352T>C	ENST00000371380.3	+	28	6416	c.6181T>C	c.(6181-6183)Ttg>Ctg	p.L2061L	RP11-76P2.4_ENST00000609123.1_RNA|NOC3L_ENST00000543788.1_Intron|PLCE1_ENST00000371385.3_Silent_p.L1753L|PLCE1_ENST00000260766.3_Silent_p.L2061L|PLCE1_ENST00000371375.1_Silent_p.L1753L			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	2061	Ras-associating 1. {ECO:0000255|PROSITE- ProRule:PRU00166}.				activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				AGACTATTTTTTGATGGAAGA	0.333																																					p.L2061L		Atlas-SNP	.											PLCE1_ENST00000371375,NS,carcinoma,0,3	PLCE1	543	.	0			c.T6181C						.						46.0	45.0	45.0					10																	96076352		1793	4065	5858	SO:0001819	synonymous_variant	51196	exon29			TATTTTTTGATGG		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"""nephrosis type 3"""	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.6181T>C	chr10.hg19:g.96076352T>C		56.0	0.0		38.0	2.0	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	hg19	CCDS41552.1																																																																																			.	.		0.333	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
MMS19	64210	hgsc.bcm.edu	37	10	99220678	99220678	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:99220678T>C	ENST00000438925.2	-	24	2733	c.2398A>G	c.(2398-2400)Act>Gct	p.T800A	MMS19_ENST00000370782.2_Missense_Mutation_p.T800A|MMS19_ENST00000355839.6_Missense_Mutation_p.T757A|MMS19_ENST00000327238.10_Missense_Mutation_p.T702A|MMS19_ENST00000327277.7_3'UTR	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	800					cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		AGAAGAAGAGTGAAGGCCTGA	0.498								Direct reversal of damage																													p.T800A		Atlas-SNP	.											.	MMS19	36	.	0			c.A2398G						.						37.0	35.0	36.0					10																	99220678		2203	4297	6500	SO:0001583	missense	64210	exon24			GAAGAGTGAAGGC	AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229			13824	protein-coding gene	gene with protein product	"""MET18 homolog (S. cerevisiae)"""	614777		MMS19L		11071939	Standard	NM_022362		Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.2398A>G	chr10.hg19:g.99220678T>C	ENSP00000412698:p.Thr800Ala	86.0	0.0		98.0	4.0	NM_022362	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	Missense_Mutation	SNP	ENST00000438925.2	hg19	CCDS7464.1	.	.	.	.	.	.	.	.	.	.	T	15.46	2.839897	0.51057	.	.	ENSG00000155229	ENST00000438925;ENST00000370782;ENST00000327238;ENST00000422291;ENST00000355839	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.66	5.66	0.87406	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.46502	0.1396	M	0.61703	1.905	0.80722	D	1	P;D;D;B;D	0.71674	0.911;0.996;0.998;0.138;0.966	B;P;P;B;P	0.62560	0.288;0.834;0.904;0.082;0.493	T	0.38134	-0.9675	10	0.08837	T	0.75	.	15.5432	0.76074	0.0:0.0:0.0:1.0	.	821;702;757;800;757	B4DQX2;Q96T76-5;F8W9Y2;Q96T76;B4E2I3	.;.;.;MMS19_HUMAN;.	A	800;800;702;779;757	ENSP00000412698:T800A;ENSP00000359818:T800A;ENSP00000320059:T702A;ENSP00000348097:T757A	ENSP00000320059:T702A	T	-	1	0	MMS19	99210668	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	3.458000	0.53014	2.154000	0.67381	0.397000	0.26171	ACT	.	.		0.498	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049706.2		
ERLIN1	10613	hgsc.bcm.edu	37	10	101937926	101937926	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:101937926G>T	ENST00000421367.2	-	4	2975	c.268C>A	c.(268-270)Cga>Aga	p.R90R	ERLIN1_ENST00000407654.3_Silent_p.R90R	NM_001100626.1|NM_006459.3	NP_001094096.1|NP_006450.2	O75477	ERLN1_HUMAN	ER lipid raft associated 1	88					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)							Colorectal(252;0.234)		Epithelial(162;3.85e-10)|all cancers(201;3.25e-08)		ACTTCTATTCGGTCAATATAG	0.373																																					p.R90R		Atlas-SNP	.											.	.	.	.	0			c.C268A						.						64.0	54.0	57.0					10																	101937926		2199	4296	6495	SO:0001819	synonymous_variant	10613	exon4			CTATTCGGTCAAT	AF064093	CCDS7487.2	10q24.31	2014-03-03	2007-01-26	2007-01-26	ENSG00000107566	ENSG00000107566			16947	protein-coding gene	gene with protein product	"""Band_7 23-211 Keo4 (Interim) similar to C.elegans protein C42C1.9"""	611604	"""chromosome 10 open reading frame 69"", ""SPFH domain family, member 1"""	C10orf69, SPFH1		11118313, 16835267, 24482476	Standard	NM_006459		Approved	KE04, Erlin-1, SPG62	uc001kqo.4	O75477	OTTHUMG00000018900	ENST00000421367.2:c.268C>A	chr10.hg19:g.101937926G>T		62.0	0.0		72.0	4.0	NM_006459	B0QZ42|Q53HV0	Silent	SNP	ENST00000421367.2	hg19	CCDS7487.2																																																																																			.	.		0.373	ERLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049840.2	NM_006459	
ELOVL3	83401	hgsc.bcm.edu	37	10	103988767	103988767	+	Missense_Mutation	SNP	A	A	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:103988767A>T	ENST00000370005.3	+	4	792	c.571A>T	c.(571-573)Aac>Tac	p.N191Y		NM_152310.1	NP_689523.1	Q9HB03	ELOV3_HUMAN	ELOVL fatty acid elongase 3	191					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity (GO:0016740)			breast(2)|lung(10)|ovary(2)|prostate(1)|skin(1)	16		Colorectal(252;0.207)		Epithelial(162;4.47e-08)|all cancers(201;7.96e-07)		GAAGGCTGCCAACGTGAAGCC	0.517																																					p.N191Y		Atlas-SNP	.											.	ELOVL3	39	.	0			c.A571T						.						128.0	118.0	121.0					10																	103988767		2203	4300	6503	SO:0001583	missense	83401	exon4			GCTGCCAACGTGA	AF292387	CCDS7531.1	10q24	2011-05-25	2011-05-25		ENSG00000119915	ENSG00000119915			18047	protein-coding gene	gene with protein product		611815	"""elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 3"""				Standard	NM_152310		Approved	CIG-30	uc001kut.3	Q9HB03	OTTHUMG00000018951	ENST00000370005.3:c.571A>T	chr10.hg19:g.103988767A>T	ENSP00000359022:p.Asn191Tyr	149.0	0.0		122.0	5.0	NM_152310	Q5VZL3|Q8N180	Missense_Mutation	SNP	ENST00000370005.3	hg19	CCDS7531.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.067863	0.55539	.	.	ENSG00000119915	ENST00000370005	T	0.22336	1.96	5.57	1.96	0.26148	.	0.684456	0.13693	N	0.369386	T	0.19005	0.0456	L	0.33339	1.005	0.26067	N	0.981271	B	0.16603	0.018	B	0.35073	0.195	T	0.35400	-0.9790	10	0.87932	D	0	-15.7707	6.2622	0.20907	0.4996:0.0:0.5004:0.0	.	191	Q9HB03	ELOV3_HUMAN	Y	191	ENSP00000359022:N191Y	ENSP00000359022:N191Y	N	+	1	0	ELOVL3	103978757	0.998000	0.40836	0.462000	0.27118	0.979000	0.70002	3.902000	0.56310	0.410000	0.25675	0.528000	0.53228	AAC	.	.		0.517	ELOVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050030.1	NM_152310	
SFXN2	118980	hgsc.bcm.edu	37	10	104486433	104486433	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:104486433C>A	ENST00000369893.5	+	2	207	c.40C>A	c.(40-42)Cgt>Agt	p.R14S	SFXN2_ENST00000602785.1_3'UTR	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	14					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		CGATGCCCCCCGTTGGGACCA	0.542																																					p.R14S		Atlas-SNP	.											.	SFXN2	40	.	0			c.C40A						.						113.0	112.0	113.0					10																	104486433		2203	4300	6503	SO:0001583	missense	118980	exon2			GCCCCCCGTTGGG	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"""Sideroflexins"""	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.40C>A	chr10.hg19:g.104486433C>A	ENSP00000358909:p.Arg14Ser	99.0	0.0		64.0	4.0	NM_178858	Q5JSM6	Missense_Mutation	SNP	ENST00000369893.5	hg19	CCDS7539.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.357748	0.82243	.	.	ENSG00000156398	ENST00000369893	T	0.36340	1.26	5.49	5.49	0.81192	.	0.052777	0.85682	D	0.000000	T	0.55130	0.1901	M	0.90082	3.085	0.80722	D	1	P	0.43287	0.802	B	0.43445	0.42	T	0.66834	-0.5823	10	0.72032	D	0.01	0.0231	19.3785	0.94521	0.0:1.0:0.0:0.0	.	14	Q96NB2	SFXN2_HUMAN	S	14	ENSP00000358909:R14S	ENSP00000358909:R14S	R	+	1	0	SFXN2	104476423	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	4.918000	0.63376	2.566000	0.86566	0.561000	0.74099	CGT	.	.		0.542	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359	
PDCD11	22984	hgsc.bcm.edu	37	10	105184772	105184772	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:105184772T>C	ENST00000369797.3	+	20	2889	c.2795T>C	c.(2794-2796)gTg>gCg	p.V932A	PDCD11_ENST00000490787.1_3'UTR	NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	932					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)		CAGGCGATTGTGCAGCACTTG	0.552																																					p.V932A		Atlas-SNP	.											.	PDCD11	160	.	0			c.T2795C						.						125.0	112.0	117.0					10																	105184772		2203	4300	6503	SO:0001583	missense	22984	exon20			CGATTGTGCAGCA	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.2795T>C	chr10.hg19:g.105184772T>C	ENSP00000358812:p.Val932Ala	91.0	0.0		77.0	4.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	hg19	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	T	31	5.078234	0.94000	.	.	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.15372	2.43	5.74	5.74	0.90152	.	0.057567	0.64402	D	0.000001	T	0.35158	0.0922	M	0.65498	2.005	0.80722	D	1	D	0.58268	0.982	P	0.55112	0.769	T	0.07849	-1.0751	10	0.87932	D	0	-20.9168	16.3305	0.83010	0.0:0.0:0.0:1.0	.	932	Q14690	RRP5_HUMAN	A	932	ENSP00000358812:V932A	ENSP00000358812:V932A	V	+	2	0	PDCD11	105174762	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	7.310000	0.78947	2.317000	0.78254	0.459000	0.35465	GTG	.	.		0.552	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
SLK	9748	hgsc.bcm.edu	37	10	105762224	105762224	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:105762224C>T	ENST00000369755.3	+	9	1833	c.1288C>T	c.(1288-1290)Ctt>Ttt	p.L430F	SLK_ENST00000335753.4_Missense_Mutation_p.L430F	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	430	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)		GAGGCCCAAGCTTGAAAATCT	0.363																																					p.L430F	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.C1288T						.						109.0	120.0	117.0					10																	105762224		2203	4300	6503	SO:0001583	missense	9748	exon9			CCCAAGCTTGAAA		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.1288C>T	chr10.hg19:g.105762224C>T	ENSP00000358770:p.Leu430Phe	104.0	0.0		97.0	4.0	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	hg19	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	C	9.783	1.175873	0.21704	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.69685	-0.42;-0.41	5.62	0.391	0.16282	Protein kinase-like domain (1);	1.163690	0.06371	N	0.713543	T	0.53818	0.1820	L	0.54323	1.7	0.09310	N	1	P;P	0.43701	0.815;0.718	B;B	0.40228	0.323;0.172	T	0.41233	-0.9520	10	0.14252	T	0.57	.	1.1987	0.01880	0.1395:0.3639:0.1506:0.3459	.	430;430	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	F	430	ENSP00000336824:L430F;ENSP00000358770:L430F	ENSP00000336824:L430F	L	+	1	0	SLK	105752214	0.000000	0.05858	0.661000	0.29709	0.652000	0.38707	-0.707000	0.05041	0.332000	0.23536	-0.300000	0.09419	CTT	.	.		0.363	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720	
KIAA1598	57698	hgsc.bcm.edu	37	10	118719735	118719735	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:118719735T>C	ENST00000355371.4	-	4	676	c.179A>G	c.(178-180)cAc>cGc	p.H60R	KIAA1598_ENST00000392901.4_5'UTR|KIAA1598_ENST00000392903.2_Missense_Mutation_p.H60R|KIAA1598_ENST00000260777.10_Missense_Mutation_p.H60R|KIAA1598_ENST00000497044.1_5'UTR	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	60					axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)				endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		TATGACCATGTGAGAAACTAG	0.403																																					p.H60R		Atlas-SNP	.											.	KIAA1598	74	.	0			c.A179G						.						67.0	66.0	66.0					10																	118719735		2203	4300	6503	SO:0001583	missense	57698	exon4			ACCATGTGAGAAA	BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.179A>G	chr10.hg19:g.118719735T>C	ENSP00000347532:p.His60Arg	78.0	0.0		76.0	4.0	NM_001258299	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Missense_Mutation	SNP	ENST00000355371.4	hg19	CCDS44482.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.399350	0.83120	.	.	ENSG00000187164	ENST00000392903;ENST00000260777;ENST00000355371	D;D;D	0.91843	-2.92;-2.92;-2.92	5.98	5.98	0.97165	.	0.045076	0.85682	D	0.000000	D	0.93612	0.7960	L	0.41710	1.295	0.80722	D	1	D;D;D	0.89917	1.0;0.989;0.974	D;D;P	0.83275	0.996;0.985;0.796	D	0.91555	0.5260	10	0.19147	T	0.46	-15.2069	16.4728	0.84119	0.0:0.0:0.0:1.0	.	60;60;30	A0MZ66;A0MZ66-2;A0MZ66-6	SHOT1_HUMAN;.;.	R	60	ENSP00000376636:H60R;ENSP00000260777:H60R;ENSP00000347532:H60R	ENSP00000260777:H60R	H	-	2	0	KIAA1598	118709725	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.257000	0.78362	2.296000	0.77279	0.482000	0.46254	CAC	.	.		0.403	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330	
SLC18A2	6571	hgsc.bcm.edu	37	10	119003656	119003656	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:119003656A>G	ENST00000298472.5	+	3	439	c.296A>G	c.(295-297)cAt>cGt	p.H99R	SLC18A2_ENST00000497497.1_3'UTR|RP11-501J20.5_ENST00000425264.1_RNA	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	99					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	CTGACACTTCATCAGACCGCC	0.517																																					p.H99R		Atlas-SNP	.											.	SLC18A2	58	.	0			c.A296G						.						119.0	103.0	108.0					10																	119003656		2203	4300	6503	SO:0001583	missense	6571	exon3			CACTTCATCAGAC	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"""Solute carriers"""	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.296A>G	chr10.hg19:g.119003656A>G	ENSP00000298472:p.His99Arg	92.0	0.0		83.0	4.0	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Missense_Mutation	SNP	ENST00000298472.5	hg19	CCDS7599.1	.	.	.	.	.	.	.	.	.	.	A	1.201	-0.632442	0.03584	.	.	ENSG00000165646	ENST00000298472	T	0.03524	3.9	5.58	-8.56	0.00904	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	2.472560	0.01099	N	0.005329	T	0.01695	0.0054	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43163	-0.9408	10	0.23302	T	0.38	6.9713	2.3047	0.04171	0.4916:0.2249:0.121:0.1625	.	99	Q05940	VMAT2_HUMAN	R	99	ENSP00000298472:H99R	ENSP00000298472:H99R	H	+	2	0	SLC18A2	118993646	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.241000	0.02911	-2.053000	0.00901	-0.376000	0.06991	CAT	.	.		0.517	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054	
C10orf90	118611	hgsc.bcm.edu	37	10	128114440	128114440	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:128114440G>T	ENST00000284694.7	-	9	2213	c.2093C>A	c.(2092-2094)gCg>gAg	p.A698E	C10orf90_ENST00000356858.3_3'UTR|C10orf90_ENST00000544758.1_Missense_Mutation_p.A795E|C10orf90_ENST00000480379.1_Missense_Mutation_p.A102E|C10orf90_ENST00000454341.1_Missense_Mutation_p.A601E	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	698	ALMS motif. {ECO:0000250}.				mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.A698V(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		TGGTTAGACCGCATTCCTTTG	0.483																																					p.A698E		Atlas-SNP	.											C10orf90,NS,carcinoma,0,1	C10orf90	121	.	1	Substitution - Missense(1)	prostate(1)	c.C2093A						.						105.0	98.0	100.0					10																	128114440		2203	4300	6503	SO:0001583	missense	118611	exon9			TAGACCGCATTCC	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"""fragile-site associated tumor suppressor"""					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.2093C>A	chr10.hg19:g.128114440G>T	ENSP00000284694:p.Ala698Glu	80.0	0.0		74.0	4.0	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	hg19	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.135846	0.77662	.	.	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758	T;T;T	0.22539	1.95;2.04;1.97	5.58	4.63	0.57726	.	0.000000	0.43919	D	0.000505	T	0.24275	0.0588	N	0.08118	0	0.38645	D	0.951701	D;D;D	0.76494	0.997;0.999;0.997	P;D;P	0.65323	0.851;0.934;0.89	T	0.21827	-1.0234	10	0.72032	D	0.01	-21.9319	13.9111	0.63866	0.0:0.0:0.8492:0.1508	.	795;698;601	F5GZL2;Q96M02;Q96M02-2	.;CJ090_HUMAN;.	E	651;698;601;795	ENSP00000284694:A698E;ENSP00000398786:A601E;ENSP00000444369:A795E	ENSP00000284694:A698E	A	-	2	0	C10orf90	128104430	0.993000	0.37304	0.072000	0.20136	0.343000	0.28985	4.314000	0.59166	2.782000	0.95742	0.655000	0.94253	GCG	.	.		0.483	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298	
ZNF511	118472	hgsc.bcm.edu	37	10	135123793	135123793	+	Splice_Site	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:135123793G>A	ENST00000359035.3	+	4	557		c.e4+1		TUBGCP2_ENST00000470829.1_5'Flank|TUBGCP2_ENST00000368563.2_5'Flank|ZNF511_ENST00000361518.5_Splice_Site|ZNF511_ENST00000368554.4_Splice_Site|ZNF511_ENST00000463816.2_Splice_Site|TUBGCP2_ENST00000417178.2_5'Flank			Q8NB15	ZN511_HUMAN	zinc finger protein 511						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(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	8		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		all cancers(32;7.56e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.15e-06)|Epithelial(32;9.99e-06)		AAAGCAGAAGGTAGGGAGCCG	0.502																																					.		Atlas-SNP	.											.	ZNF511	17	.	0			c.554+1G>A						.						58.0	63.0	61.0					10																	135123793		2203	4300	6503	SO:0001630	splice_region_variant	118472	exon4			CAGAAGGTAGGGA	AK091711	CCDS7677.1	10q26.3	2010-04-12			ENSG00000198546	ENSG00000198546		"""Zinc fingers, C2H2-type"""	28445	protein-coding gene	gene with protein product						12477932	Standard	NM_145806		Approved	MGC30006	uc001lmj.1	Q8NB15	OTTHUMG00000019317	ENST00000359035.3:c.554+1G>A	chr10.hg19:g.135123793G>A		34.0	0.0		44.0	16.0	NM_145806	A8K8L5|Q8WUP1|Q96BV2	Splice_Site	SNP	ENST00000359035.3	hg19		.	.	.	.	.	.	.	.	.	.	G	15.68	2.905908	0.52333	.	.	ENSG00000198546	ENST00000361518;ENST00000359035;ENST00000368554	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0977	0.86639	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF511	134973783	1.000000	0.71417	0.971000	0.41717	0.426000	0.31534	8.496000	0.90485	2.475000	0.83589	0.655000	0.94253	.	.	.		0.502	ZNF511-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051143.1	NM_145806	Intron
MTG1	92170	hgsc.bcm.edu	37	10	135215725	135215725	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr10:135215725A>G	ENST00000317502.6	+	8	696	c.646A>G	c.(646-648)Aca>Gca	p.T216A	RP11-108K14.8_ENST00000468317.2_Missense_Mutation_p.T221A|MTG1_ENST00000477902.2_Missense_Mutation_p.T175A	NM_138384.2	NP_612393.2	Q9BT17	MTG1_HUMAN	mitochondrial ribosome-associated GTPase 1	216					GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|all cancers(32;1.69e-06)|Epithelial(32;1.94e-06)		AAGTGTGGAGACAGGCCTGAA	0.662																																					p.T216A		Atlas-SNP	.											.	MTG1	38	.	0			c.A646G						.						74.0	76.0	75.0					10																	135215725		2203	4300	6503	SO:0001583	missense	92170	exon8			GTGGAGACAGGCC		CCDS31320.1	10q26.3	2013-05-24	2013-05-24	2006-01-09	ENSG00000148824	ENSG00000148824			32159	protein-coding gene	gene with protein product			"""GTP-binding protein 7"", ""GTP-binding protein 7 (putative)"", ""mitochondrial GTPase 1 homolog (S. cerevisiae)"""	GTPBP7		12808030, 23396448	Standard	NM_138384		Approved		uc001lnd.3	Q9BT17	OTTHUMG00000166564	ENST00000317502.6:c.646A>G	chr10.hg19:g.135215725A>G	ENSP00000323047:p.Thr216Ala	113.0	0.0		89.0	4.0	NM_138384	Q5VWX8|Q6PIY9|Q8IYJ4|Q8NC48|Q9BVU8	Missense_Mutation	SNP	ENST00000317502.6	hg19	CCDS31320.1	.	.	.	.	.	.	.	.	.	.	a	15.59	2.879426	0.51801	.	.	ENSG00000254536;ENSG00000148824;ENSG00000148824	ENST00000468317;ENST00000317502;ENST00000432508	T;T;T	0.13657	2.57;2.57;2.57	5.59	5.59	0.84812	GTP-binding protein, orthogonal bundle domain (1);	0.141126	0.64402	N	0.000005	T	0.13329	0.0323	L	0.33245	0.995	0.50813	D	0.999896	B;B	0.18610	0.029;0.011	B;B	0.26310	0.06;0.068	T	0.05716	-1.0868	10	0.40728	T	0.16	-3.6768	13.7015	0.62611	1.0:0.0:0.0:0.0	.	165;216	E7EVK2;Q9BT17	.;MTG1_HUMAN	A	221;216;165	ENSP00000436767:T221A;ENSP00000323047:T216A;ENSP00000393480:T165A	ENSP00000323047:T216A	T	+	1	0	AL360181.1;MTG1	135065715	1.000000	0.71417	0.978000	0.43139	0.819000	0.46315	4.693000	0.61753	2.126000	0.65437	0.366000	0.22137	ACA	.	.		0.662	MTG1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051166.1	NM_138384	
B4GALNT4	338707	hgsc.bcm.edu	37	11	377213	377213	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:377213G>T	ENST00000329962.6	+	14	2090	c.2090G>T	c.(2089-2091)cGc>cTc	p.R697L		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	697					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAGCTGCTGCGCTCGGACTGG	0.697																																					p.R697L		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.G2090T						.						17.0	12.0	14.0					11																	377213		2143	4203	6346	SO:0001583	missense	338707	exon14			TGCTGCGCTCGGA	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2090G>T	chr11.hg19:g.377213G>T	ENSP00000328277:p.Arg697Leu	148.0	0.0		90.0	4.0	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	hg19	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	g	23.6	4.439040	0.83885	.	.	ENSG00000182272	ENST00000329962	T	0.21932	1.98	3.12	3.12	0.35913	.	0.000000	0.85682	D	0.000000	T	0.38878	0.1057	L	0.52126	1.63	0.54753	D	0.999988	D	0.61697	0.99	D	0.71414	0.973	T	0.38887	-0.9640	10	0.87932	D	0	-23.6486	14.7266	0.69349	0.0:0.0:1.0:0.0	.	697	Q76KP1	B4GN4_HUMAN	L	697	ENSP00000328277:R697L	ENSP00000328277:R697L	R	+	2	0	B4GALNT4	367213	1.000000	0.71417	1.000000	0.80357	0.657000	0.38888	9.511000	0.98006	1.764000	0.52075	0.205000	0.17691	CGC	.	.		0.697	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
MUC2	4583	hgsc.bcm.edu	37	11	1092653	1092653	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:1092653C>A	ENST00000441003.2	+	30	4499	c.4472C>A	c.(4471-4473)aCa>aAa	p.T1491K	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1492K	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4226	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACAaccaccacaaccacccct	0.627																																					p.T1491K		Atlas-SNP	.											.	MUC2	614	.	0			c.C4472A						.						331.0	486.0	432.0					11																	1092653		1708	3175	4883	SO:0001583	missense	4583	exon30			CCACCACAACCAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4472C>A	chr11.hg19:g.1092653C>A	ENSP00000415183:p.Thr1491Lys	3967.0	2.0		2125.0	392.0	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	-	3.506	-0.100813	0.06967	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13778	2.59;2.56	0.924	0.924	0.19418	.	260.082000	0.01025	U	0.004044	T	0.04634	0.0126	.	.	.	0.21473	N	0.999671	P	0.45531	0.86	B	0.33890	0.172	T	0.32161	-0.9917	9	0.06365	T	0.9	.	5.0734	0.14618	0.0:0.7871:0.0:0.2129	.	1491	E7EUV1	.	K	1491;1492	ENSP00000415183:T1491K;ENSP00000351956:T1492K	ENSP00000351956:T1492K	T	+	2	0	MUC2	1082653	0.003000	0.15002	0.024000	0.17045	0.000000	0.00434	0.330000	0.19715	0.935000	0.37341	0.000000	0.15137	ACA	.	.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR52M1	119772	hgsc.bcm.edu	37	11	4566442	4566442	+	Missense_Mutation	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:4566442T>A	ENST00000360213.1	+	1	22	c.22T>A	c.(22-24)Tgc>Agc	p.C8S		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCATAATGTCTGCTCAGTACC	0.478																																					p.C8S		Atlas-SNP	.											.	OR52M1	53	.	0			c.T22A						.						90.0	82.0	85.0					11																	4566442		2201	4298	6499	SO:0001583	missense	119772	exon1			AATGTCTGCTCAG	AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790		"""GPCR / Class A : Olfactory receptors"""	15225	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily M, member 1 pseudogene"""	OR52M1P			Standard	NM_001004137		Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.22T>A	chr11.hg19:g.4566442T>A	ENSP00000353343:p.Cys8Ser	139.0	0.0		125.0	6.0	NM_001004137		Missense_Mutation	SNP	ENST00000360213.1	hg19	CCDS31353.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.207980	0.39003	.	.	ENSG00000197790	ENST00000360213	T	0.01092	5.35	4.12	4.12	0.48240	.	0.000000	0.51477	D	0.000084	T	0.00906	0.0030	N	0.00385	-1.57	0.26071	N	0.981229	D	0.76494	0.999	D	0.80764	0.994	T	0.58411	-0.7641	10	0.02654	T	1	.	11.7384	0.51778	0.0:0.0:0.0:1.0	.	8	Q8NGK5	O52M1_HUMAN	S	8	ENSP00000353343:C8S	ENSP00000353343:C8S	C	+	1	0	OR52M1	4523018	0.969000	0.33509	0.153000	0.22517	0.954000	0.61252	2.059000	0.41384	2.085000	0.62840	0.533000	0.62120	TGC	.	.		0.478	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137	
OR52I1	390037	hgsc.bcm.edu	37	11	4616131	4616131	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:4616131T>C	ENST00000530443.2	+	1	863	c.863T>C	c.(862-864)aTc>aCc	p.I288T	OR52I1_ENST00000450052.2_Missense_Mutation_p.I312T	NM_001005169.1	NP_001005169.1	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I, member 1	288						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	15		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;7.98e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TACGTGATCATCCCAGCCACT	0.498																																					p.I288T		Atlas-SNP	.											OR52I1,NS,carcinoma,0,1	OR52I1	29	.	0			c.T863C						.						135.0	133.0	134.0					11																	4616131		2201	4298	6499	SO:0001583	missense	390037	exon1			TGATCATCCCAGC	BK004371	CCDS59223.1	11p15.4	2012-08-09				ENSG00000232268		"""GPCR / Class A : Olfactory receptors"""	15220	protein-coding gene	gene with protein product							Standard	NM_001005169		Approved		uc010qyi.2	Q8NGK6		ENST00000530443.2:c.863T>C	chr11.hg19:g.4616131T>C	ENSP00000436453:p.Ile288Thr	262.0	2.0		186.0	10.0	NM_001005169	Q6IF91	Missense_Mutation	SNP	ENST00000530443.2	hg19	CCDS59223.1	.	.	.	.	.	.	.	.	.	.	T	10.14	1.267162	0.23136	.	.	ENSG00000232268	ENST00000450052;ENST00000530443	T;T	0.38722	1.12;1.12	4.96	3.82	0.43975	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45361	D	0.000366	T	0.58481	0.2125	M	0.77103	2.36	0.29564	N	0.850419	D	0.61080	0.989	P	0.58077	0.832	T	0.71052	-0.4704	9	0.87932	D	0	-7.1178	11.4104	0.49923	0.0:0.0807:0.0:0.9193	.	288	Q8NGK6	O52I1_HUMAN	T	312;288	ENSP00000409094:I312T;ENSP00000436453:I288T	ENSP00000409094:I312T	I	+	2	0	OR52I1	4572707	0.901000	0.30685	0.961000	0.40146	0.002000	0.02628	5.915000	0.69973	0.449000	0.26747	-1.477000	0.00996	ATC	.	.		0.498	OR52I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385947.2	NM_001005169	
OR51V1	283111	hgsc.bcm.edu	37	11	5221456	5221456	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:5221456C>A	ENST00000321255.1	-	1	474	c.475G>T	c.(475-477)Ggt>Tgt	p.G159C		NM_001004760.2	NP_001004760.2	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V, member 1	159					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(13)|lung(19)|skin(2)|upper_aerodigestive_tract(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAACTCCTACCTATTATAGTG	0.393																																					p.G159C		Atlas-SNP	.											.	OR51V1	77	.	0			c.G475T						.						48.0	54.0	52.0					11																	5221456		2200	4298	6498	SO:0001583	missense	283111	exon1			TCCTACCTATTAT	BK004432	CCDS31375.1	11p15.4	2012-08-09			ENSG00000176742	ENSG00000176742		"""GPCR / Class A : Olfactory receptors"""	19597	protein-coding gene	gene with protein product				OR51A12			Standard	NM_001004760		Approved		uc010qyz.2	Q9H2C8	OTTHUMG00000066671	ENST00000321255.1:c.475G>T	chr11.hg19:g.5221456C>A	ENSP00000321729:p.Gly159Cys	89.0	0.0		88.0	4.0	NM_001004760		Missense_Mutation	SNP	ENST00000321255.1	hg19	CCDS31375.1	.	.	.	.	.	.	.	.	.	.	C	2.357	-0.347590	0.05208	.	.	ENSG00000176742	ENST00000321255	T	0.37915	1.17	5.27	-5.05	0.02955	GPCR, rhodopsin-like superfamily (1);	1.346060	0.05003	N	0.469573	T	0.27489	0.0675	L	0.39085	1.19	0.09310	N	1	B	0.11235	0.004	B	0.17979	0.02	T	0.39901	-0.9591	10	0.48119	T	0.1	.	9.0537	0.36392	0.7026:0.1152:0.0:0.1822	.	159	Q9H2C8	O51V1_HUMAN	C	159	ENSP00000321729:G159C	ENSP00000321729:G159C	G	-	1	0	OR51V1	5178032	0.000000	0.05858	0.002000	0.10522	0.032000	0.12392	-2.274000	0.01163	-0.745000	0.04772	-0.182000	0.12963	GGT	.	.		0.393	OR51V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142965.1	NM_001004760	
OR56B4	196335	hgsc.bcm.edu	37	11	6129433	6129433	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:6129433T>C	ENST00000316529.3	+	1	520	c.425T>C	c.(424-426)gTc>gCc	p.V142A	RP11-290F24.3_ENST00000529961.1_RNA	NM_001005181.1	NP_001005181.1	Q8NH76	O56B4_HUMAN	olfactory receptor, family 56, subfamily B, member 4	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(1)|lung(10)|skin(6)|urinary_tract(2)	21		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.31e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCCTCCATAGTCACTAAAGCT	0.502																																					p.V142A		Atlas-SNP	.											.	OR56B4	50	.	0			c.T425C						.						127.0	112.0	117.0					11																	6129433		2201	4296	6497	SO:0001583	missense	196335	exon1			CCATAGTCACTAA	AB065513	CCDS31406.1	11p15.4	2012-08-09			ENSG00000180919	ENSG00000180919		"""GPCR / Class A : Olfactory receptors"""	15248	protein-coding gene	gene with protein product							Standard	NM_001005181		Approved		uc010qzx.2	Q8NH76	OTTHUMG00000165531	ENST00000316529.3:c.425T>C	chr11.hg19:g.6129433T>C	ENSP00000321196:p.Val142Ala	167.0	0.0		97.0	4.0	NM_001005181	Q6IFD7	Missense_Mutation	SNP	ENST00000316529.3	hg19	CCDS31406.1	.	.	.	.	.	.	.	.	.	.	T	16.10	3.026492	0.54683	.	.	ENSG00000180919	ENST00000316529	T	0.20598	2.06	4.06	4.06	0.47325	GPCR, rhodopsin-like superfamily (1);	0.257961	0.20024	U	0.100857	T	0.39784	0.1091	M	0.64997	1.995	0.27968	N	0.936522	D	0.53619	0.961	P	0.61328	0.887	T	0.18967	-1.0320	10	0.87932	D	0	.	12.9386	0.58329	0.0:0.0:0.0:1.0	.	142	Q8NH76	O56B4_HUMAN	A	142	ENSP00000321196:V142A	ENSP00000321196:V142A	V	+	2	0	OR56B4	6086009	0.991000	0.36638	0.998000	0.56505	0.058000	0.15608	7.628000	0.83189	1.804000	0.52760	0.454000	0.30748	GTC	.	.		0.502	OR56B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384668.1	NM_001005181	
TRIM3	10612	hgsc.bcm.edu	37	11	6472512	6472512	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:6472512C>T	ENST00000525074.1	-	8	2084	c.1690G>A	c.(1690-1692)Ggc>Agc	p.G564S	TRIM3_ENST00000536344.1_Missense_Mutation_p.G445S|TRIM3_ENST00000359518.3_Missense_Mutation_p.G564S|TRIM3_ENST00000345851.3_Missense_Mutation_p.G564S|TRIM3_ENST00000537602.1_Missense_Mutation_p.G486S	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	564					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGAACTTGCCCTCAGGGGAG	0.557																																					p.G564S	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.G1690A						.						110.0	87.0	95.0					11																	6472512		2201	4296	6497	SO:0001583	missense	10612	exon8			ACTTGCCCTCAGG	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10064	protein-coding gene	gene with protein product	"""ring finger protein 22"", ""brain expressed ring finger"", ""tripartite motif protein TRIM3"""	605493	"""tripartite motif-containing 3"""	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.1690G>A	chr11.hg19:g.6472512C>T	ENSP00000433102:p.Gly564Ser	85.0	0.0		53.0	4.0	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Missense_Mutation	SNP	ENST00000525074.1	hg19	CCDS7764.1	.	.	.	.	.	.	.	.	.	.	C	32	5.110732	0.94292	.	.	ENSG00000110171	ENST00000530899;ENST00000525074;ENST00000545029;ENST00000345851;ENST00000336043;ENST00000537602;ENST00000359518;ENST00000536344	D;D;D;D;D	0.91894	-2.93;-2.93;-2.93;-2.93;-2.93	5.25	5.25	0.73442	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.96667	0.8912	M	0.88775	2.98	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97137	0.9822	10	0.62326	D	0.03	-21.2117	17.4604	0.87619	0.0:1.0:0.0:0.0	.	445;564	F5H2Q8;O75382	.;TRIM3_HUMAN	S	564;564;564;564;553;486;564;445	ENSP00000433102:G564S;ENSP00000340797:G564S;ENSP00000441091:G486S;ENSP00000352508:G564S;ENSP00000445460:G445S	ENSP00000337094:G553S	G	-	1	0	TRIM3	6429088	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.446000	0.82766	0.563000	0.77884	GGC	.	.		0.557	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
ARFIP2	23647	hgsc.bcm.edu	37	11	6501223	6501223	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:6501223C>A	ENST00000254584.2	-	3	258	c.175G>T	c.(175-177)Ggt>Tgt	p.G59C	ARFIP2_ENST00000445086.2_Silent_p.L13L|TIMM10B_ENST00000254616.6_5'Flank|ARFIP2_ENST00000396777.3_Missense_Mutation_p.G59C|TIMM10B_ENST00000472836.1_5'Flank|ARFIP2_ENST00000423813.2_Missense_Mutation_p.G21C|TIMM10B_ENST00000530751.1_5'Flank|ARFIP2_ENST00000525235.1_Missense_Mutation_p.G59C	NM_012402.3	NP_036534.1	P53365	ARFP2_HUMAN	ADP-ribosylation factor interacting protein 2	59					actin cytoskeleton organization (GO:0030036)|cellular component movement (GO:0006928)|lamellipodium assembly (GO:0030032)|ruffle organization (GO:0031529)|small GTPase mediated signal transduction (GO:0007264)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|Rac GTPase binding (GO:0048365)			endometrium(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(2)	15		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;3.41e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGTCCATCACCAGAGCCCCCA	0.527																																					p.G59C	Melanoma(119;796 1674 9049 20480 24794)	Atlas-SNP	.											ARFIP2,right_upper_lobe,carcinoma,0,1	ARFIP2	23	.	0			c.G175T						.						188.0	181.0	184.0					11																	6501223		2201	4296	6497	SO:0001583	missense	23647	exon3			CATCACCAGAGCC	BC000392	CCDS7765.1, CCDS55739.1, CCDS55740.1, CCDS73250.1	11p15	2008-08-01	2008-08-01		ENSG00000132254	ENSG00000132254			17160	protein-coding gene	gene with protein product	"""arfaptin 2"""	601638				8670882, 9038142	Standard	NM_012402		Approved	POR1	uc010ran.2	P53365	OTTHUMG00000133406	ENST00000254584.2:c.175G>T	chr11.hg19:g.6501223C>A	ENSP00000254584:p.Gly59Cys	76.0	0.0		41.0	3.0	NM_012402	B4DX86|B4E306|D3DQT5	Missense_Mutation	SNP	ENST00000254584.2	hg19	CCDS7765.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.446162	0.63178	.	.	ENSG00000132254	ENST00000254584;ENST00000396777;ENST00000423813;ENST00000525235	T;T;T	0.78364	-1.09;-1.09;-1.17	5.12	5.12	0.69794	.	0.102417	0.64402	D	0.000003	T	0.78978	0.4369	.	.	.	0.80722	D	1	P;P;P	0.48998	0.918;0.877;0.8	P;B;B	0.46076	0.503;0.436;0.436	T	0.81604	-0.0857	9	0.56958	D	0.05	.	17.125	0.86711	0.0:1.0:0.0:0.0	.	59;59;59	B4DUZ3;E9PPY7;P53365	.;.;ARFP2_HUMAN	C	59;59;21;59	ENSP00000254584:G59C;ENSP00000379998:G59C;ENSP00000398375:G21C	ENSP00000254584:G59C	G	-	1	0	ARFIP2	6457799	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.026000	0.64103	2.373000	0.80994	0.563000	0.77884	GGT	.	.		0.527	ARFIP2-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387044.1	NM_012402	
DNHD1	144132	hgsc.bcm.edu	37	11	6561171	6561171	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:6561171G>T	ENST00000527990.2	+	16	3486	c.3486G>T	c.(3484-3486)tgG>tgT	p.W1162C	DNHD1_ENST00000254579.6_Missense_Mutation_p.W1162C			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1162					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		AGCGGTACTGGGAAGCGCGCC	0.592																																					p.W1162C		Atlas-SNP	.											.	DNHD1	198	.	0			c.G3486T						.						57.0	60.0	59.0					11																	6561171		692	1591	2283	SO:0001583	missense	144132	exon18			GTACTGGGAAGCG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.3486G>T	chr11.hg19:g.6561171G>T	ENSP00000436180:p.Trp1162Cys	122.0	0.0		87.0	4.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.769358	0.49680	.	.	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.68765	-0.35;-0.35	5.57	5.57	0.84162	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.68622	0.3021	N	0.08118	0	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.76528	-0.2926	9	0.87932	D	0	.	18.3162	0.90221	0.0:0.0:1.0:0.0	.	1162	Q96M86	DNHD1_HUMAN	C	1162	ENSP00000254579:W1162C;ENSP00000436180:W1162C	ENSP00000254579:W1162C	W	+	3	0	DNHD1	6517747	1.000000	0.71417	1.000000	0.80357	0.088000	0.18126	5.613000	0.67688	2.611000	0.88343	0.561000	0.74099	TGG	.	.		0.592	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
PPFIBP2	8495	hgsc.bcm.edu	37	11	7670813	7670813	+	Missense_Mutation	SNP	C	C	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:7670813C>G	ENST00000299492.4	+	21	2437	c.2049C>G	c.(2047-2049)atC>atG	p.I683M	PPFIBP2_ENST00000528883.1_Missense_Mutation_p.I571M|PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000533792.1_Missense_Mutation_p.I525M|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.I540M	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	683	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		ATCTCAGCATCAAATGTGCCA	0.453																																					p.I683M		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.C2049G						.						246.0	247.0	246.0					11																	7670813		2201	4296	6497	SO:0001583	missense	8495	exon21			CAGCATCAAATGT	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.2049C>G	chr11.hg19:g.7670813C>G	ENSP00000299492:p.Ile683Met	303.0	0.0		199.0	67.0	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	hg19	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.555140	0.65425	.	.	ENSG00000166387	ENST00000299492;ENST00000537211;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	5.2	3.25	0.37280	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.64402	D	0.000001	T	0.72285	0.3441	L	0.50993	1.605	0.45930	D	0.998769	D;D;D;D;D;D	0.89917	1.0;0.973;1.0;0.998;1.0;1.0	D;D;D;D;D;D	0.97110	0.998;0.949;0.995;0.998;0.999;1.0	T	0.72286	-0.4338	10	0.72032	D	0.01	-16.1897	5.3238	0.15895	0.1765:0.6576:0.0:0.1659	.	571;571;606;525;540;683	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.;.;.;.;.;LIPB2_HUMAN	M	683;24;525;606;571;540	ENSP00000299492:I683M;ENSP00000436498:I525M;ENSP00000435469:I571M;ENSP00000437321:I540M	ENSP00000299492:I683M	I	+	3	3	PPFIBP2	7627389	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.503000	0.35715	1.269000	0.44280	0.563000	0.77884	ATC	.	.		0.453	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
OVCH2	341277	hgsc.bcm.edu	37	11	7718054	7718054	+	RNA	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:7718054G>T	ENST00000533663.1	-	0	0				OVCH2_ENST00000534193.2_RNA|OVCH2_ENST00000454689.1_RNA			Q7RTZ1	OVCH2_HUMAN	ovochymase 2 (gene/pseudogene)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(2)	15				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		AGGTAACTGTGGTGACAAGAC	0.473																																					p.H367N		Atlas-SNP	.											.	OVCH2	47	.	0			c.C1099A						.						105.0	100.0	102.0					11																	7718054		1958	4148	6106			341277	exon10			AACTGTGGTGACA	BN000120	CCDS73251.1	11p15.4	2012-10-02	2010-06-08		ENSG00000183378	ENSG00000183378			29970	protein-coding gene	gene with protein product			"""ovochymase 2"""			12838346	Standard	XM_006718221		Approved	OVTN	uc031pyw.1	Q7RTZ1	OTTHUMG00000165418		chr11.hg19:g.7718054G>T		72.0	0.0		54.0	4.0	NM_198185		Missense_Mutation	SNP	ENST00000533663.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.08	3.022077	0.54576	.	.	ENSG00000183378	ENST00000454689	T	0.16897	2.31	5.69	5.69	0.88448	CUB (5);	0.172702	0.29015	N	0.013415	T	0.20901	0.0503	L	0.35341	1.055	0.24520	N	0.994167	P	0.48589	0.912	P	0.50049	0.629	T	0.10291	-1.0636	10	0.24483	T	0.36	-15.649	15.3063	0.73995	0.0:0.0:1.0:0.0	.	367	Q7RTZ1	OVCH2_HUMAN	N	367	ENSP00000407158:H367N	ENSP00000407158:H367N	H	-	1	0	OVCH2	7674630	1.000000	0.71417	0.978000	0.43139	0.641000	0.38312	4.061000	0.57485	2.679000	0.91253	0.655000	0.94253	CAC	.	.		0.473	OVCH2-002	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000383928.1	NM_198185	
SCUBE2	57758	hgsc.bcm.edu	37	11	9069079	9069079	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:9069079C>A	ENST00000309263.3	-	15	1811	c.1739G>T	c.(1738-1740)cGa>cTa	p.R580L	SCUBE2_ENST00000457346.2_Missense_Mutation_p.R609L|SCUBE2_ENST00000450649.2_Missense_Mutation_p.R454L|RP11-467K18.2_ENST00000531592.1_RNA|SCUBE2_ENST00000520467.1_Missense_Mutation_p.R609L			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	580						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		CTTCTCGGTTCGCTTTACGAT	0.572																																					p.R609L		Atlas-SNP	.											SCUBE2,NS,carcinoma,0,1	SCUBE2	102	.	0			c.G1826T						.						69.0	56.0	60.0					11																	9069079		2201	4296	6497	SO:0001583	missense	57758	exon16			TCGGTTCGCTTTA	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.1739G>T	chr11.hg19:g.9069079C>A	ENSP00000310658:p.Arg580Leu	228.0	0.0		174.0	17.0	NM_020974	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	hg19		.	.	.	.	.	.	.	.	.	.	C	15.36	2.810857	0.50421	.	.	ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	D;D;D;D	0.84370	-1.55;-1.65;-1.84;-1.81	5.21	4.28	0.50868	.	0.163887	0.49916	D	0.000133	D	0.85566	0.5726	M	0.73962	2.25	0.43959	D	0.996634	P;P;P	0.51537	0.946;0.664;0.534	P;B;B	0.47118	0.538;0.307;0.228	D	0.86791	0.1985	10	0.87932	D	0	.	9.3048	0.37867	0.0:0.7914:0.0:0.2086	.	454;609;580	Q9NQ36-3;Q9NQ36-2;Q9NQ36	.;.;SCUB2_HUMAN	L	609;580;454;609	ENSP00000390481:R609L;ENSP00000310658:R580L;ENSP00000415187:R454L;ENSP00000429969:R609L	ENSP00000310658:R580L	R	-	2	0	SCUBE2	9025655	0.932000	0.31603	0.974000	0.42286	0.772000	0.43724	1.679000	0.37597	2.603000	0.88011	0.655000	0.94253	CGA	.	.		0.572	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974	
INSC	387755	hgsc.bcm.edu	37	11	15247245	15247245	+	Silent	SNP	G	G	T	rs111784838		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:15247245G>T	ENST00000379554.3	+	9	1228	c.1182G>T	c.(1180-1182)gcG>gcT	p.A394A	INSC_ENST00000424273.1_Silent_p.A305A|INSC_ENST00000525218.1_Silent_p.A305A|INSC_ENST00000447214.2_3'UTR|INSC_ENST00000530161.1_Silent_p.A347A|INSC_ENST00000379556.3_Silent_p.A347A|INSC_ENST00000528567.1_Silent_p.A347A	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	394					establishment of mitotic spindle orientation (GO:0000132)|lung epithelial cell differentiation (GO:0060487)|nervous system development (GO:0007399)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(3)|lung(24)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						TGGCCTCTGCGGCCCTTGCCA	0.512																																					p.A394A		Atlas-SNP	.											.	INSC	104	.	0			c.G1182T						.						67.0	66.0	66.0					11																	15247245		1951	4142	6093	SO:0001819	synonymous_variant	387755	exon9			CTCTGCGGCCCTT	AB231744	CCDS41621.1, CCDS41622.1, CCDS60735.1, CCDS60736.1	11p15.2	2014-02-05			ENSG00000188487	ENSG00000188487			33116	protein-coding gene	gene with protein product	"""inscuteable spindle orientation adaptor protein"""	610668				16458856	Standard	NM_001031853		Approved		uc001mly.4	Q1MX18	OTTHUMG00000165838	ENST00000379554.3:c.1182G>T	chr11.hg19:g.15247245G>T		96.0	0.0		66.0	4.0	NM_001031853	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Silent	SNP	ENST00000379554.3	hg19	CCDS41621.1																																																																																			.	G|0.999;A|0.001		0.512	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853	
INSC	387755	hgsc.bcm.edu	37	11	15262003	15262003	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:15262003T>C	ENST00000379554.3	+	12	1591	c.1545T>C	c.(1543-1545)cgT>cgC	p.R515R	INSC_ENST00000424273.1_Silent_p.R426R|INSC_ENST00000525218.1_Silent_p.R426R|INSC_ENST00000447214.2_3'UTR|INSC_ENST00000530161.1_Silent_p.R468R|INSC_ENST00000379556.3_Silent_p.R468R|INSC_ENST00000528567.1_Silent_p.R468R	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	515					establishment of mitotic spindle orientation (GO:0000132)|lung epithelial cell differentiation (GO:0060487)|nervous system development (GO:0007399)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(3)|lung(24)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						GCATGTCCCGTCTCATCGAGC	0.622																																					p.R515R		Atlas-SNP	.											.	INSC	104	.	0			c.T1545C						.						57.0	60.0	59.0					11																	15262003		2022	4177	6199	SO:0001819	synonymous_variant	387755	exon12			GTCCCGTCTCATC	AB231744	CCDS41621.1, CCDS41622.1, CCDS60735.1, CCDS60736.1	11p15.2	2014-02-05			ENSG00000188487	ENSG00000188487			33116	protein-coding gene	gene with protein product	"""inscuteable spindle orientation adaptor protein"""	610668				16458856	Standard	NM_001031853		Approved		uc001mly.4	Q1MX18	OTTHUMG00000165838	ENST00000379554.3:c.1545T>C	chr11.hg19:g.15262003T>C		165.0	0.0		111.0	5.0	NM_001031853	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Silent	SNP	ENST00000379554.3	hg19	CCDS41621.1																																																																																			.	.		0.622	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853	
HPS5	11234	hgsc.bcm.edu	37	11	18317630	18317630	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:18317630T>C	ENST00000349215.3	-	13	1827	c.1550A>G	c.(1549-1551)aAg>aGg	p.K517R	HPS5_ENST00000396253.3_Missense_Mutation_p.K403R|HPS5_ENST00000438420.2_Missense_Mutation_p.K403R|HPS5_ENST00000352460.3_5'UTR	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	517					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						AGTTTCATTCTTATCTGTCTC	0.378									Hermansky-Pudlak syndrome																												p.K517R		Atlas-SNP	.											HPS5,NS,carcinoma,0,1	HPS5	70	.	0			c.A1550G						.						132.0	127.0	129.0					11																	18317630		2199	4293	6492	SO:0001583	missense	11234	exon13	Familial Cancer Database	HPS, HPS1-8	TCATTCTTATCTG	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.1550A>G	chr11.hg19:g.18317630T>C	ENSP00000265967:p.Lys517Arg	97.0	0.0		72.0	4.0	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	hg19	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	T	5.721	0.317550	0.10845	.	.	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215	T;T;T	0.49720	0.78;0.78;0.77	5.35	4.23	0.50019	.	0.059785	0.64402	D	0.000002	T	0.19967	0.0480	N	0.11560	0.145	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	T	0.16012	-1.0417	10	0.07030	T	0.85	.	3.1692	0.06546	0.0:0.3692:0.0:0.6308	.	517	Q9UPZ3	HPS5_HUMAN	R	403;403;517	ENSP00000379552:K403R;ENSP00000399590:K403R;ENSP00000265967:K517R	ENSP00000265967:K517R	K	-	2	0	HPS5	18274206	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.466000	0.53071	2.035000	0.60131	0.528000	0.53228	AAG	.	.		0.378	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	
TSG101	7251	hgsc.bcm.edu	37	11	18502150	18502150	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:18502150C>T	ENST00000251968.3	-	10	1531	c.1116G>A	c.(1114-1116)caG>caA	p.Q372Q	TSG101_ENST00000536719.1_Intron|TSG101_ENST00000357193.3_Silent_p.Q267Q	NM_006292.3	NP_006283.1	Q99816	TS101_HUMAN	tumor susceptibility 101	372	SB. {ECO:0000255|PROSITE- ProRule:PRU00644}.				cell cycle arrest (GO:0007050)|cell division (GO:0051301)|cellular protein modification process (GO:0006464)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|keratinocyte differentiation (GO:0030216)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell growth (GO:0001558)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral budding (GO:0046755)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transcription corepressor activity (GO:0003714)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	22						GTGCCCTCAGCTGGAACTGTT	0.443																																					p.Q372Q	GBM(99;1348 1396 8611 26475 50572)	Atlas-SNP	.											.	TSG101	43	.	0			c.G1116A						.						91.0	86.0	88.0					11																	18502150		2199	4293	6492	SO:0001819	synonymous_variant	7251	exon10			CCTCAGCTGGAAC	U82130	CCDS7842.1	11p15	2013-08-22	2013-08-22		ENSG00000074319	ENSG00000074319			15971	protein-coding gene	gene with protein product		601387	"""tumor susceptibility gene 10"", ""tumor susceptibility gene 101"""	TSG10		9019400, 9241264	Standard	NM_006292		Approved	VPS23	uc001mor.3	Q99816	OTTHUMG00000167725	ENST00000251968.3:c.1116G>A	chr11.hg19:g.18502150C>T		215.0	0.0		127.0	50.0	NM_006292	Q9BUM5	Silent	SNP	ENST00000251968.3	hg19	CCDS7842.1																																																																																			.	.		0.443	TSG101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395906.1	NM_006292	
SPTY2D1	144108	hgsc.bcm.edu	37	11	18655797	18655797	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:18655797A>G	ENST00000336349.5	-	1	243	c.8T>C	c.(7-9)tTc>tCc	p.F3S	SPTY2D1_ENST00000543776.1_Intron	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	3										breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						AATTTCTCTGAAGTCCATGTT	0.567																																					p.F3S		Atlas-SNP	.											.	SPTY2D1	72	.	0			c.T8C						.						154.0	141.0	146.0					11																	18655797		2199	4293	6492	SO:0001583	missense	144108	exon1			TCTCTGAAGTCCA	BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.8T>C	chr11.hg19:g.18655797A>G	ENSP00000337991:p.Phe3Ser	95.0	0.0		80.0	4.0	NM_194285	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Missense_Mutation	SNP	ENST00000336349.5	hg19	CCDS31441.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.067782	0.76301	.	.	ENSG00000179119	ENST00000336349;ENST00000333429	T	0.38722	1.12	5.65	5.65	0.86999	.	0.160682	0.56097	D	0.000029	T	0.57388	0.2050	L	0.49778	1.585	0.52501	D	0.999957	D	0.71674	0.998	D	0.78314	0.991	T	0.59773	-0.7391	10	0.87932	D	0	-9.5335	12.1892	0.54261	1.0:0.0:0.0:0.0	.	3	Q68D10	SPT2_HUMAN	S	3	ENSP00000337991:F3S	ENSP00000331447:F3S	F	-	2	0	SPTY2D1	18612373	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.944000	0.56629	2.371000	0.80710	0.533000	0.62120	TTC	.	.		0.567	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	NM_194285	
IGSF22	283284	hgsc.bcm.edu	37	11	18735929	18735929	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:18735929C>A	ENST00000513874.1	-	13	1832	c.1693G>T	c.(1693-1695)Ggt>Tgt	p.G565C	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	565										NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						TGCACTGCACCCTGCTTCACA	0.582																																					p.G565C		Atlas-SNP	.											.	IGSF22	211	.	0			c.G1693T						.						101.0	106.0	105.0					11																	18735929		2082	4200	6282	SO:0001583	missense	283284	exon13			CTGCACCCTGCTT	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.1693G>T	chr11.hg19:g.18735929C>A	ENSP00000421191:p.Gly565Cys	98.0	0.0		99.0	4.0	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	hg19	CCDS41625.2	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319693	0.60524	.	.	ENSG00000179057	ENST00000513874	T	0.51817	0.69	4.42	3.51	0.40186	.	0.000000	0.37437	U	0.002097	T	0.64034	0.2562	M	0.72479	2.2	0.31587	N	0.654372	D	0.89917	1.0	D	0.87578	0.998	T	0.69243	-0.5196	10	0.87932	D	0	.	9.3646	0.38217	0.0:0.8962:0.0:0.1038	.	565	D6RGV7	.	C	565	ENSP00000421191:G565C	ENSP00000322422:G565C	G	-	1	0	IGSF22	18692505	1.000000	0.71417	0.971000	0.41717	0.811000	0.45836	3.997000	0.57016	0.861000	0.35504	0.551000	0.68910	GGT	.	.		0.582	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
PTPN5	84867	hgsc.bcm.edu	37	11	18754887	18754887	+	Silent	SNP	G	G	A	rs144666949		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:18754887G>A	ENST00000358540.2	-	11	1543	c.1113C>T	c.(1111-1113)gcC>gcT	p.A371A	PTPN5_ENST00000477854.1_Silent_p.A175A|PTPN5_ENST00000396168.1_Silent_p.A347A|PTPN5_ENST00000396166.3_5'Flank|RP11-1081L13.4_ENST00000527285.1_RNA|PTPN5_ENST00000396167.2_Silent_p.A339A|PTPN5_ENST00000396171.4_Silent_p.A371A|PTPN5_ENST00000396170.1_Silent_p.A339A	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	371	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						GTCCCTGAGTGGCGATGTACA	0.612																																					p.A371A		Atlas-SNP	.											.	PTPN5	163	.	0			c.C1113T						.	G	,,	1,4397	2.1+/-5.4	0,1,2198	180.0	143.0	155.0		1017,1113,1113	4.5	1.0	11	dbSNP_134	155	0,8586		0,0,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPN5	NM_001039970.1,NM_006906.1,NM_032781.3	,,	0,1,6491	AA,AG,GG		0.0,0.0227,0.0077	,,	339/534,371/566,371/566	18754887	1,12983	2199	4293	6492	SO:0001819	synonymous_variant	84867	exon11			CTGAGTGGCGATG	BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.1113C>T	chr11.hg19:g.18754887G>A		95.0	0.0		86.0	27.0	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Silent	SNP	ENST00000358540.2	hg19	CCDS7845.1																																																																																			.	G|1.000;A|0.000		0.612	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970	
FBXO3	26273	hgsc.bcm.edu	37	11	33763518	33763518	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:33763518T>C	ENST00000265651.3	-	11	1370	c.1352A>G	c.(1351-1353)gAg>gGg	p.E451G	FBXO3_ENST00000526785.1_Missense_Mutation_p.E338G|FBXO3_ENST00000532057.1_Missense_Mutation_p.E138G|FBXO3_ENST00000531080.1_Missense_Mutation_p.E138G|FBXO3_ENST00000530401.1_3'UTR	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	451	Asp/Glu-rich (highly acidic).				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		CCGTCTCTCCTCTTCATCATC	0.473																																					p.E451G		Atlas-SNP	.											.	FBXO3	37	.	0			c.A1352G						.						228.0	173.0	192.0					11																	33763518		2202	4298	6500	SO:0001583	missense	26273	exon11			CTCTCCTCTTCAT	AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"""F-boxes /  ""other"""""	13582	protein-coding gene	gene with protein product		609089	"""F-box only protein 3"""			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.1352A>G	chr11.hg19:g.33763518T>C	ENSP00000265651:p.Glu451Gly	113.0	0.0		78.0	4.0	NM_012175	B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Missense_Mutation	SNP	ENST00000265651.3	hg19	CCDS7887.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.151073	0.38021	.	.	ENSG00000110429	ENST00000526785;ENST00000265651;ENST00000531080;ENST00000532057	T;T;T;T	0.33865	1.39;1.39;1.39;1.39	3.69	3.69	0.42338	.	0.135863	0.34067	N	0.004282	T	0.35451	0.0932	N	0.14661	0.345	0.80722	D	1	P	0.39094	0.659	P	0.55391	0.775	T	0.20907	-1.0261	10	0.48119	T	0.1	-14.3224	9.0552	0.36401	0.0:0.0:0.0:1.0	.	451	Q9UK99	FBX3_HUMAN	G	338;451;138;138	ENSP00000435680:E338G;ENSP00000265651:E451G;ENSP00000435165:E138G;ENSP00000434001:E138G	ENSP00000265651:E451G	E	-	2	0	FBXO3	33720094	0.975000	0.34042	0.979000	0.43373	0.830000	0.47004	1.729000	0.38115	1.897000	0.54924	0.459000	0.35465	GAG	.	.		0.473	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1	NM_012175	
NAT10	55226	hgsc.bcm.edu	37	11	34152409	34152409	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:34152409C>A	ENST00000257829.3	+	13	1500	c.1294C>A	c.(1294-1296)Cgt>Agt	p.R432S	NAT10_ENST00000527971.1_Intron|NAT10_ENST00000531159.2_Missense_Mutation_p.R360S	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	432						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				TCAGCAGCTCCGTCAACAGAG	0.557																																					p.R432S		Atlas-SNP	.											.	NAT10	78	.	0			c.C1294A						.						109.0	100.0	103.0					11																	34152409		2202	4298	6500	SO:0001583	missense	55226	exon13			CAGCTCCGTCAAC	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"""N-acetyltransferase 10"""			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.1294C>A	chr11.hg19:g.34152409C>A	ENSP00000257829:p.Arg432Ser	100.0	0.0		94.0	5.0	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Missense_Mutation	SNP	ENST00000257829.3	hg19	CCDS7889.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.442045	0.83993	.	.	ENSG00000135372	ENST00000257829;ENST00000531159	T;T	0.44083	0.93;0.93	5.53	5.53	0.82687	Domain of unknown function DUF699, exodeoxyribonuclease V alpha chain (1);	0.000000	0.85682	D	0.000000	T	0.68220	0.2977	M	0.79805	2.47	0.80722	D	1	D	0.76494	0.999	D	0.74348	0.983	T	0.69235	-0.5198	10	0.52906	T	0.07	-14.4578	19.8251	0.96614	0.0:1.0:0.0:0.0	.	432	Q9H0A0	NAT10_HUMAN	S	432;360	ENSP00000257829:R432S;ENSP00000433011:R360S	ENSP00000257829:R432S	R	+	1	0	NAT10	34108985	0.998000	0.40836	0.994000	0.49952	0.997000	0.91878	3.745000	0.55119	2.763000	0.94921	0.561000	0.74099	CGT	.	.		0.557	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662	
CD82	3732	hgsc.bcm.edu	37	11	44639811	44639811	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:44639811G>T	ENST00000227155.4	+	8	786	c.538G>T	c.(538-540)Ggg>Tgg	p.G180W	CD82_ENST00000530931.1_3'UTR|CD82_ENST00000342935.3_Missense_Mutation_p.G155W	NM_002231.3	NP_002222.1	P27701	CD82_HUMAN	CD82 molecule	180						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				large_intestine(1)|ovary(1)	2						CGAAGTCAAGGGGGAAGAGGA	0.597																																					p.G180W		Atlas-SNP	.											.	CD82	27	.	0			c.G538T						.						68.0	60.0	63.0					11																	44639811		2203	4299	6502	SO:0001583	missense	3732	exon8			GTCAAGGGGGAAG	U20770	CCDS7909.1, CCDS31469.1	11p11.2	2013-02-14	2006-03-28	2005-03-03		ENSG00000085117		"""CD molecules"", ""Tetraspanins"""	6210	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 6"", ""R2 leukocyte antigen"""	600623	"""kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4))"", ""CD82 antigen"""	ST6, KAI1			Standard	XM_006718222		Approved	R2, IA4, TSPAN27	uc001myc.3	P27701		ENST00000227155.4:c.538G>T	chr11.hg19:g.44639811G>T	ENSP00000227155:p.Gly180Trp	115.0	0.0		91.0	4.0	NM_002231	D3DQN6|E9PC70|Q7Z2D4|Q7Z5N2	Missense_Mutation	SNP	ENST00000227155.4	hg19	CCDS7909.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.967788	0.53507	.	.	ENSG00000085117	ENST00000227155;ENST00000342935	T;T	0.51325	0.96;0.71	4.86	-5.09	0.02920	Tetraspanin, EC2 domain (1);	.	.	.	.	T	0.40522	0.1120	N	0.24115	0.695	0.09310	N	1	P;D	0.59767	0.733;0.986	P;P	0.58520	0.84;0.799	T	0.38672	-0.9650	9	0.72032	D	0.01	.	4.489	0.11805	0.5078:0.0:0.2271:0.2651	.	155;180	E9PC70;P27701	.;CD82_HUMAN	W	180;155	ENSP00000227155:G180W;ENSP00000339686:G155W	ENSP00000227155:G180W	G	+	1	0	CD82	44596387	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-2.311000	0.01128	-0.657000	0.05373	-0.258000	0.10820	GGG	.	.		0.597	CD82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389886.1		
AMBRA1	55626	hgsc.bcm.edu	37	11	46569854	46569854	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:46569854T>C	ENST00000458649.2	-	2	495	c.77A>G	c.(76-78)cAg>cGg	p.Q26R	AMBRA1_ENST00000534300.1_Missense_Mutation_p.Q26R|AMBRA1_ENST00000426438.1_Missense_Mutation_p.Q26R|AMBRA1_ENST00000533727.1_Missense_Mutation_p.Q26R|AMBRA1_ENST00000528950.1_Missense_Mutation_p.Q26R|AMBRA1_ENST00000298834.3_Missense_Mutation_p.Q26R|AMBRA1_ENST00000314845.3_Missense_Mutation_p.Q26R			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	26					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		CAGAAGCCGCTGAGCTCCCAT	0.537																																					p.Q26R		Atlas-SNP	.											.	AMBRA1	201	.	0			c.A77G						.						172.0	187.0	182.0					11																	46569854		2201	4299	6500	SO:0001583	missense	55626	exon2			AGCCGCTGAGCTC	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.77A>G	chr11.hg19:g.46569854T>C	ENSP00000415327:p.Gln26Arg	160.0	0.0		97.0	5.0	NM_001267783	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	hg19		.	.	.	.	.	.	.	.	.	.	T	21.0	4.075037	0.76415	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000314823;ENST00000458649;ENST00000528950	T;T;T;T;T;T;T	0.70282	-0.31;-0.47;-0.19;-0.31;-0.19;-0.29;-0.31	6.08	6.08	0.98989	.	0.104010	0.64402	D	0.000002	T	0.75547	0.3864	N	0.22421	0.69	0.58432	D	0.999998	D;D;D;D;D;D	0.63046	0.987;0.992;0.992;0.992;0.992;0.992	D;D;D;D;D;D	0.72982	0.953;0.979;0.979;0.979;0.979;0.979	T	0.77239	-0.2661	10	0.49607	T	0.09	.	16.6512	0.85203	0.0:0.0:0.0:1.0	.	26;26;26;26;26;26	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	R	26	ENSP00000318313:Q26R;ENSP00000433372:Q26R;ENSP00000431926:Q26R;ENSP00000410899:Q26R;ENSP00000298834:Q26R;ENSP00000415327:Q26R;ENSP00000433945:Q26R	ENSP00000298834:Q26R	Q	-	2	0	AMBRA1	46526430	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.331000	0.79192	2.333000	0.79357	0.482000	0.46254	CAG	.	.		0.537	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749	
FNBP4	23360	hgsc.bcm.edu	37	11	47755663	47755663	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:47755663C>T	ENST00000263773.5	-	10	1612	c.1600G>A	c.(1600-1602)Gca>Aca	p.A534T	FNBP4_ENST00000534003.1_5'UTR	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	534						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						AGGGTATTTGCCAGTTCTCCA	0.323																																					p.A534T		Atlas-SNP	.											.	FNBP4	99	.	0			c.G1600A						.						107.0	101.0	103.0					11																	47755663		1827	4084	5911	SO:0001583	missense	23360	exon10			TATTTGCCAGTTC	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.1600G>A	chr11.hg19:g.47755663C>T	ENSP00000263773:p.Ala534Thr	73.0	0.0		74.0	4.0	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Missense_Mutation	SNP	ENST00000263773.5	hg19	CCDS41644.1	.	.	.	.	.	.	.	.	.	.	C	36	5.658373	0.96734	.	.	ENSG00000109920	ENST00000263773	T	0.11063	2.81	6.02	6.02	0.97574	.	0.089636	0.85682	D	0.000000	T	0.24812	0.0602	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.00613	-1.1644	10	0.54805	T	0.06	-24.6893	20.5373	0.99239	0.0:1.0:0.0:0.0	.	534	Q8N3X1	FNBP4_HUMAN	T	534	ENSP00000263773:A534T	ENSP00000263773:A534T	A	-	1	0	FNBP4	47712239	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.796000	0.85898	2.857000	0.98124	0.650000	0.86243	GCA	.	.		0.323	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3		
TRIM51	84767	hgsc.bcm.edu	37	11	55653258	55653258	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:55653258T>C	ENST00000449290.2	+	2	446	c.354T>C	c.(352-354)tcT>tcC	p.S118S	TRIM51_ENST00000244891.3_5'Flank	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	118						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										GCTCCAACTCTCAGGAGCACC	0.498																																					p.S118S		Atlas-SNP	.											.	.	.	.	0			c.T354C						.						18.0	17.0	17.0					11																	55653258		692	1591	2283	SO:0001819	synonymous_variant	84767	exon2			CAACTCTCAGGAG	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19023	protein-coding gene	gene with protein product			"""SPRY domain containing 5"""	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.354T>C	chr11.hg19:g.55653258T>C		158.0	0.0		96.0	5.0	NM_032681	A6NMG2	Silent	SNP	ENST00000449290.2	hg19																																																																																				.	.		0.498	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681	
OR8J1	219477	hgsc.bcm.edu	37	11	56128618	56128618	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:56128618A>G	ENST00000303039.3	+	1	928	c.896A>G	c.(895-897)aAg>aGg	p.K299R		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	299						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(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					AAGGATGTGAAGACTGCTCTA	0.373																																					p.K299R		Atlas-SNP	.											.	OR8J1	87	.	0			c.A896G						.						81.0	73.0	76.0					11																	56128618		2201	4296	6497	SO:0001583	missense	219477	exon1			ATGTGAAGACTGC	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"""GPCR / Class A : Olfactory receptors"""	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.896A>G	chr11.hg19:g.56128618A>G	ENSP00000304060:p.Lys299Arg	119.0	0.0		86.0	4.0	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	hg19	CCDS31529.1	.	.	.	.	.	.	.	.	.	.	A	7.016	0.557679	0.13436	.	.	ENSG00000172487	ENST00000303039	T	0.23552	1.9	3.76	3.76	0.43208	.	0.087193	0.49305	D	0.000141	T	0.17534	0.0421	L	0.31526	0.94	0.21604	N	0.999628	B	0.10296	0.003	B	0.16722	0.016	T	0.14671	-1.0464	10	0.72032	D	0.01	.	6.8501	0.24010	0.8904:0.0:0.1096:0.0	.	299	Q8NGP2	OR8J1_HUMAN	R	299	ENSP00000304060:K299R	ENSP00000304060:K299R	K	+	2	0	OR8J1	55885194	0.852000	0.29690	0.990000	0.47175	0.045000	0.14185	1.513000	0.35823	1.707000	0.51288	0.448000	0.29417	AAG	.	.		0.373	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
OR5M11	219487	hgsc.bcm.edu	37	11	56310189	56310189	+	Missense_Mutation	SNP	G	G	T	rs200285217		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:56310189G>T	ENST00000528616.2	-	1	568	c.545C>A	c.(544-546)cCg>cAg	p.P182Q		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11	182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)	18						CTTAATGAGCGGCGGGTCAGC	0.502																																					p.P182Q		Atlas-SNP	.											OR5M11,caecum,carcinoma,0,2	OR5M11	60	.	0			c.C545A						.						46.0	48.0	48.0					11																	56310189		2063	4220	6283	SO:0001583	missense	219487	exon1			ATGAGCGGCGGGT	AP002517	CCDS53629.1	11q11	2012-08-09				ENSG00000255223		"""GPCR / Class A : Olfactory receptors"""	15291	protein-coding gene	gene with protein product							Standard	NM_001005245		Approved	OR11-199	uc010rjl.2	Q96RB7		ENST00000528616.2:c.545C>A	chr11.hg19:g.56310189G>T	ENSP00000432417:p.Pro182Gln	146.0	0.0		100.0	4.0	NM_001005245	B2RNL5|B2RNL7	Missense_Mutation	SNP	ENST00000528616.2	hg19	CCDS53629.1	.	.	.	.	.	.	.	.	.	.	A	10.50	1.366503	0.24771	.	.	ENSG00000255223	ENST00000528616	T	0.00137	8.68	4.89	1.97	0.26223	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00328	0.0010	L	0.58969	1.84	0.09310	N	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.51679	-0.8675	9	0.87932	D	0	.	7.6395	0.28286	0.1337:0.0:0.6314:0.2349	.	182	Q96RB7	OR5MB_HUMAN	Q	182	ENSP00000432417:P182Q	ENSP00000432417:P182Q	P	-	2	0	OR5M11	56066765	0.003000	0.15002	0.493000	0.27502	0.234000	0.25298	1.152000	0.31663	0.040000	0.15660	-1.789000	0.00628	CCG	.	.		0.502	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	NM_001005245	
YPEL4	219539	hgsc.bcm.edu	37	11	57413535	57413535	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:57413535A>G	ENST00000524669.1	-	5	3025	c.303T>C	c.(301-303)gcT>gcC	p.A101A	AP000662.4_ENST00000530595.1_RNA|YPEL4_ENST00000300022.3_Silent_p.A101A|YPEL4_ENST00000531442.1_5'Flank|YPEL4_ENST00000534711.1_Silent_p.A101A|YPEL4_ENST00000544993.1_Silent_p.A101A			Q96NS1	YPEL4_HUMAN	yippee-like 4 (Drosophila)	101						nucleus (GO:0005634)				lung(2)|skin(1)	3						TCGTCTCAAAAGCTTGCTCCT	0.532																																					p.A101A		Atlas-SNP	.											.	YPEL4	5	.	0			c.T303C						.						149.0	111.0	124.0					11																	57413535		2201	4296	6497	SO:0001819	synonymous_variant	219539	exon5			CTCAAAAGCTTGC	AK054775	CCDS7963.1	11q12	2008-02-05				ENSG00000166793			18328	protein-coding gene	gene with protein product		609725					Standard	NM_145008		Approved	FLJ30213	uc001nkv.4	Q96NS1		ENST00000524669.1:c.303T>C	chr11.hg19:g.57413535A>G		93.0	0.0		79.0	5.0	NM_145008	B3KW92|Q2M3U7|Q65Z98	Silent	SNP	ENST00000524669.1	hg19	CCDS7963.1																																																																																			.	.		0.532	YPEL4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393370.1	NM_145008	
BTBD18	643376	hgsc.bcm.edu	37	11	57511709	57511709	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:57511709A>G	ENST00000436147.3	-	2	2223	c.2036T>C	c.(2035-2037)gTg>gCg	p.V679A	RP11-691N7.6_ENST00000531074.1_Intron|TMX2-CTNND1_ENST00000528395.1_Intron|BTBD18_ENST00000422652.1_Missense_Mutation_p.V679A			B2RXH4	BTBDI_HUMAN	BTB (POZ) domain containing 18	679										endometrium(3)|kidney(1)	4						CCAGTCCACCACATCAATCTC	0.517																																					p.V679A		Atlas-SNP	.											.	BTBD18	26	.	0			c.T2036C						.						112.0	103.0	106.0					11																	57511709		692	1591	2283	SO:0001583	missense	643376	exon3			TCCACCACATCAA		CCDS44603.1	11q12.1	2013-01-08			ENSG00000233436	ENSG00000233436		"""BTB/POZ domain containing"""	37214	protein-coding gene	gene with protein product							Standard	NM_001145101		Approved		uc010rjy.2	B2RXH4	OTTHUMG00000167203	ENST00000436147.3:c.2036T>C	chr11.hg19:g.57511709A>G	ENSP00000397020:p.Val679Ala	153.0	0.0		90.0	4.0	NM_001145101		Missense_Mutation	SNP	ENST00000436147.3	hg19	CCDS44603.1	.	.	.	.	.	.	.	.	.	.	A	17.25	3.342952	0.61073	.	.	ENSG00000233436	ENST00000422652;ENST00000436147	D;D	0.84800	-1.9;-1.9	5.53	5.53	0.82687	.	.	.	.	.	D	0.87541	0.6203	L	0.27053	0.805	0.27237	N	0.959242	D	0.76494	0.999	D	0.76071	0.987	T	0.81457	-0.0924	9	0.87932	D	0	.	13.4753	0.61306	1.0:0.0:0.0:0.0	.	679	B2RXH4	BTBDI_HUMAN	A	679	ENSP00000394472:V679A;ENSP00000397020:V679A	ENSP00000394472:V679A	V	-	2	0	BTBD18	57268285	0.994000	0.37717	0.999000	0.59377	0.823000	0.46562	3.919000	0.56439	2.227000	0.72691	0.459000	0.35465	GTG	.	.		0.517	BTBD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393718.2	NM_001145101	
MS4A4A	51338	hgsc.bcm.edu	37	11	60073590	60073590	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:60073590G>A	ENST00000337908.4	+	6	654	c.564G>A	c.(562-564)gtG>gtA	p.V188V	MS4A4A_ENST00000355131.3_Silent_p.V169V|MS4A4A_ENST00000532114.1_Silent_p.V135V|MS4A4A_ENST00000395016.3_Silent_p.V169V	NM_148975.2	NP_683876.1	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member 4A	188						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(12)|prostate(1)|skin(4)	23						ATGGCATGGTGCTCCTCCTAA	0.463																																					p.V188V		Atlas-SNP	.											.	MS4A4A	76	.	0			c.G564A						.						281.0	239.0	253.0					11																	60073590		2203	4300	6503	SO:0001819	synonymous_variant	51338	exon6			CATGGTGCTCCTC	AB013102	CCDS7982.1, CCDS58135.1	11q12	2012-02-28	2012-02-28		ENSG00000110079	ENSG00000110079			13371	protein-coding gene	gene with protein product		606547	"""membrane-spanning 4-domains, subfamily A, member 4"""	MS4A4		11245982, 11401424	Standard	NM_148975		Approved	CD20L1, MS4A7	uc001noz.3	Q96JQ5	OTTHUMG00000154949	ENST00000337908.4:c.564G>A	chr11.hg19:g.60073590G>A		675.0	0.0		458.0	95.0	NM_148975	Q8TEZ6|Q96PG7|Q9BY18|Q9H3V3|Q9P1S3	Silent	SNP	ENST00000337908.4	hg19	CCDS7982.1																																																																																			.	.		0.463	MS4A4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337774.2		
MS4A8	83661	hgsc.bcm.edu	37	11	60476245	60476245	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:60476245C>A	ENST00000300226.2	+	5	728	c.525C>A	c.(523-525)gcC>gcA	p.A175A		NM_031457.1	NP_113645.1	Q9BY19	M4A8_HUMAN	membrane-spanning 4-domains, subfamily A, member 8	175						integral component of membrane (GO:0016021)											ATCCTTACGCCTGGGGTGTGG	0.463																																					p.A175A		Atlas-SNP	.											.	.	.	.	0			c.C525A						.						125.0	112.0	116.0					11																	60476245		2203	4300	6503	SO:0001819	synonymous_variant	83661	exon5			TTACGCCTGGGGT	AF237905	CCDS7990.1	11q12	2013-03-01	2013-03-01	2013-03-01	ENSG00000166959	ENSG00000166959			13380	protein-coding gene	gene with protein product		606549	"""membrane-spanning 4-domains, subfamily A, member 8B"""	MS4A8B		11245982, 11401424	Standard	NM_031457		Approved	MS4A4, CD20L5	uc001npv.3	Q9BY19	OTTHUMG00000167686	ENST00000300226.2:c.525C>A	chr11.hg19:g.60476245C>A		238.0	0.0		151.0	56.0	NM_031457	Q8TCA5	Silent	SNP	ENST00000300226.2	hg19	CCDS7990.1	.	.	.	.	.	.	.	.	.	.	C	3.417	-0.118946	0.06838	.	.	ENSG00000166959	ENST00000525458	.	.	.	4.0	2.07	0.26955	.	.	.	.	.	T	0.31827	0.0809	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.20107	-1.0285	4	.	.	.	3.6068	6.33	0.21264	0.0:0.7636:0.0:0.2364	.	.	.	.	H	157	.	.	P	+	2	0	MS4A8B	60232821	0.002000	0.14202	0.004000	0.12327	0.097000	0.18754	0.687000	0.25407	0.903000	0.36546	-0.218000	0.12543	CCT	.	.		0.463	MS4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395605.1		
PRPF19	27339	hgsc.bcm.edu	37	11	60670241	60670241	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:60670241A>G	ENST00000227524.4	-	4	564	c.359T>C	c.(358-360)cTc>cCc	p.L120P		NM_014502.4	NP_055317.1			pre-mRNA processing factor 19											haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						TTCCTTGGTGAGACGGGCAAT	0.592																																					p.L120P		Atlas-SNP	.											.	PRPF19	62	.	0			c.T359C						.						63.0	55.0	58.0					11																	60670241		2203	4299	6502	SO:0001583	missense	27339	exon4			TTGGTGAGACGGG	BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"""WD repeat domain containing"", ""U-box domain containing"""	17896	protein-coding gene	gene with protein product	"""nuclear matrix protein NMP200 related to splicing factor PRP19"", ""psoralen 4"""	608330	"""PRP19/PSO4 homolog (S. cerevisiae)"", ""PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"""	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.359T>C	chr11.hg19:g.60670241A>G	ENSP00000227524:p.Leu120Pro	121.0	0.0		97.0	4.0	NM_014502		Missense_Mutation	SNP	ENST00000227524.4	hg19	CCDS7995.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.392617	0.83011	.	.	ENSG00000110107	ENST00000227524;ENST00000541371;ENST00000546152	T	0.70749	-0.51	4.62	4.62	0.57501	Pre-mRNA-splicing factor 19 (1);	0.131926	0.52532	D	0.000075	D	0.87083	0.6089	M	0.92367	3.3	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90297	0.4327	10	0.87932	D	0	-22.4155	14.1796	0.65564	1.0:0.0:0.0:0.0	.	120	Q9UMS4	PRP19_HUMAN	P	120;120;35	ENSP00000227524:L120P	ENSP00000227524:L120P	L	-	2	0	PRPF19	60426817	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.547000	0.90665	2.064000	0.61679	0.533000	0.62120	CTC	.	.		0.592	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1	NM_014502	
CD6	923	hgsc.bcm.edu	37	11	60785418	60785418	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:60785418A>G	ENST00000313421.7	+	11	1956	c.1770A>G	c.(1768-1770)tcA>tcG	p.S590S	CD6_ENST00000352009.5_Silent_p.S558S|CD6_ENST00000452451.2_Silent_p.S549S|CD6_ENST00000346437.4_Silent_p.S517S|CD6_ENST00000344028.5_Silent_p.S558S	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	590					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						TGTTTTCTTCAGAGAGGAGTT	0.577																																					p.S590S	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.A1770G						.						59.0	63.0	62.0					11																	60785418		2203	4299	6502	SO:0001819	synonymous_variant	923	exon11			TTCTTCAGAGAGG		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1770A>G	chr11.hg19:g.60785418A>G		81.0	0.0		58.0	4.0	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Silent	SNP	ENST00000313421.7	hg19	CCDS7999.1																																																																																			.	.		0.577	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
AHNAK	79026	hgsc.bcm.edu	37	11	62300901	62300901	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:62300901T>C	ENST00000378024.4	-	5	1262	c.988A>G	c.(988-990)Agg>Ggg	p.R330G	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	330					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)				GCAGAAACCCTCAGCCCTGCC	0.542																																					p.R330G		Atlas-SNP	.											.	AHNAK	532	.	0			c.A988G						.						61.0	65.0	63.0					11																	62300901		2202	4299	6501	SO:0001583	missense	79026	exon5			AAACCCTCAGCCC	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.988A>G	chr11.hg19:g.62300901T>C	ENSP00000367263:p.Arg330Gly	106.0	0.0		76.0	4.0	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	T	6.865	0.529006	0.13127	.	.	ENSG00000124942	ENST00000378024	T	0.00730	5.77	5.05	2.36	0.29203	.	1.083490	0.07313	U	0.876171	T	0.00580	0.0019	N	0.03608	-0.345	0.09310	N	1	B	0.24132	0.098	B	0.23716	0.048	T	0.47459	-0.9116	10	0.39692	T	0.17	-0.5385	8.1366	0.31058	0.0:0.1978:0.0:0.8022	.	330	Q09666	AHNK_HUMAN	G	330	ENSP00000367263:R330G	ENSP00000367263:R330G	R	-	1	2	AHNAK	62057477	0.004000	0.15560	0.636000	0.29352	0.484000	0.33280	0.859000	0.27858	0.770000	0.33336	0.528000	0.53228	AGG	.	.		0.542	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
ZBTB3	79842	hgsc.bcm.edu	37	11	62520653	62520653	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:62520653T>C	ENST00000394807.3	-	2	759	c.634A>G	c.(634-636)Aca>Gca	p.T212A		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	212					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)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						TGGCCTGATGTCTCAGCAGAT	0.542																																					p.T212A		Atlas-SNP	.											.	ZBTB3	47	.	0			c.A634G						.						99.0	84.0	89.0					11																	62520653		2202	4299	6501	SO:0001583	missense	79842	exon2			CTGATGTCTCAGC	AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.634A>G	chr11.hg19:g.62520653T>C	ENSP00000378286:p.Thr212Ala	93.0	0.0		94.0	4.0	NM_024784		Missense_Mutation	SNP	ENST00000394807.3	hg19	CCDS8034.1	.	.	.	.	.	.	.	.	.	.	T	0.039	-1.291688	0.01375	.	.	ENSG00000185670	ENST00000394807	T	0.11495	2.77	5.22	2.7	0.31948	.	0.893105	0.09879	N	0.743895	T	0.05547	0.0146	N	0.14661	0.345	0.19945	N	0.999942	B	0.22800	0.075	B	0.19946	0.027	T	0.45264	-0.9273	10	0.07644	T	0.81	.	6.4125	0.21698	0.1467:0.0:0.4211:0.4322	.	212	Q9H5J0	ZBTB3_HUMAN	A	212	ENSP00000378286:T212A	ENSP00000378286:T212A	T	-	1	0	ZBTB3	62277229	0.004000	0.15560	0.996000	0.52242	0.480000	0.33159	0.285000	0.18883	0.334000	0.23590	0.459000	0.35465	ACA	.	.		0.542	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784	
RCOR2	283248	hgsc.bcm.edu	37	11	63680389	63680389	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:63680389G>A	ENST00000301459.4	-	9	1309	c.922C>T	c.(922-924)Ctg>Ttg	p.L308L	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	308					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						GCTTGGCGCAGGCTGCTGTTC	0.587																																					p.L308L		Atlas-SNP	.											.	RCOR2	43	.	0			c.C922T						.						56.0	44.0	48.0					11																	63680389		2201	4297	6498	SO:0001819	synonymous_variant	283248	exon9			GGCGCAGGCTGCT	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.922C>T	chr11.hg19:g.63680389G>A		101.0	0.0		54.0	14.0	NM_173587	Q96FP3	Silent	SNP	ENST00000301459.4	hg19	CCDS8052.1																																																																																			.	.		0.587	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587	
RCOR2	283248	hgsc.bcm.edu	37	11	63680410	63680410	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:63680410T>C	ENST00000301459.4	-	9	1288	c.901A>G	c.(901-903)Atg>Gtg	p.M301V	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	301					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						GTCTGCTTCATGCTCTGTACC	0.577																																					p.M301V		Atlas-SNP	.											.	RCOR2	43	.	0			c.A901G						.						52.0	40.0	44.0					11																	63680410		2200	4297	6497	SO:0001583	missense	283248	exon9			GCTTCATGCTCTG	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.901A>G	chr11.hg19:g.63680410T>C	ENSP00000301459:p.Met301Val	89.0	0.0		52.0	4.0	NM_173587	Q96FP3	Missense_Mutation	SNP	ENST00000301459.4	hg19	CCDS8052.1	.	.	.	.	.	.	.	.	.	.	T	12.48	1.950469	0.34377	.	.	ENSG00000167771	ENST00000301459	T	0.40476	1.03	4.56	4.56	0.56223	.	0.097021	0.64402	D	0.000001	T	0.20659	0.0497	N	0.03608	-0.345	0.28674	N	0.905484	B	0.02656	0.0	B	0.04013	0.001	T	0.09015	-1.0694	10	0.23891	T	0.37	.	13.3293	0.60477	0.0:0.0:0.0:1.0	.	301	Q8IZ40	RCOR2_HUMAN	V	301	ENSP00000301459:M301V	ENSP00000301459:M301V	M	-	1	0	RCOR2	63436986	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.651000	0.54431	2.053000	0.61076	0.459000	0.35465	ATG	.	.		0.577	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587	
TEX40	25858	hgsc.bcm.edu	37	11	64071271	64071271	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:64071271G>T	ENST00000328404.6	+	4	479	c.459G>T	c.(457-459)atG>atT	p.M153I	TEX40_ENST00000539943.1_Missense_Mutation_p.M111I|RP11-783K16.10_ENST00000539086.1_RNA|ESRRA_ENST00000000442.6_5'Flank|ESRRA_ENST00000406310.1_5'Flank|ESRRA_ENST00000405666.1_5'Flank	NM_001039496.1	NP_001034585.1	Q9NTU4	TEX40_HUMAN	testis expressed 40	153					cell differentiation (GO:0030154)|male meiosis (GO:0007140)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)											TGGAACTCATGGAGAATGAAG	0.572																																					p.M153I		Atlas-SNP	.											.	.	.	.	0			c.G459T						.						32.0	35.0	34.0					11																	64071271		2001	4157	6158	SO:0001583	missense	25858	exon4			ACTCATGGAGAAT			11q13.1	2013-01-11	2013-01-11	2013-01-11	ENSG00000219435	ENSG00000219435			19231	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 20"""	C11orf20			Standard	NM_001039496		Approved	DKFZP566E164	uc009ypm.3	Q9NTU4	OTTHUMG00000167820	ENST00000328404.6:c.459G>T	chr11.hg19:g.64071271G>T	ENSP00000330877:p.Met153Ile	127.0	0.0		95.0	4.0	NM_001039496		Missense_Mutation	SNP	ENST00000328404.6	hg19		.	.	.	.	.	.	.	.	.	.	G	14.78	2.638230	0.47153	.	.	ENSG00000219435	ENST00000328404;ENST00000539943	T;T	0.52526	0.66;0.67	4.22	4.22	0.49857	.	.	.	.	.	T	0.56077	0.1961	L	0.29908	0.895	0.29521	N	0.853477	D	0.76494	0.999	D	0.83275	0.996	T	0.52533	-0.8563	9	0.66056	D	0.02	-18.6491	12.29	0.54812	0.0:0.0:1.0:0.0	.	153	Q9NTU4	CK020_HUMAN	I	153;111	ENSP00000330877:M153I;ENSP00000443917:M111I	ENSP00000330877:M153I	M	+	3	0	C11orf20	63827847	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	4.427000	0.59888	2.365000	0.80145	0.555000	0.69702	ATG	.	.		0.572	TEX40-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001039496	
SLC22A11	55867	hgsc.bcm.edu	37	11	64323631	64323631	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:64323631C>T	ENST00000301891.4	+	1	534	c.160C>T	c.(160-162)Ctg>Ttg	p.L54L	SLC22A11_ENST00000377585.3_Silent_p.L54L|SLC22A11_ENST00000490834.1_3'UTR|SLC22A11_ENST00000377581.3_Silent_p.L54L	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 11	54					organic anion transport (GO:0015711)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23					Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495)	GACACACATGCTGGACAATGG	0.622											OREG0004031	type=REGULATORY REGION|Gene=SLC22A11|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.L54L		Atlas-SNP	.											.	SLC22A11	54	.	0			c.C160T						.						170.0	148.0	155.0					11																	64323631		2201	4297	6498	SO:0001819	synonymous_variant	55867	exon1			CACATGCTGGACA	AB026116	CCDS8074.1	11q13.3	2013-05-22	2008-01-11		ENSG00000168065	ENSG00000168065		"""Solute carriers"""	18120	protein-coding gene	gene with protein product		607097				10660625, 15576633, 17229912	Standard	NM_018484		Approved	OAT4	uc001oai.3	Q9NSA0	OTTHUMG00000045142	ENST00000301891.4:c.160C>T	chr11.hg19:g.64323631C>T		177.0	0.0	1075	90.0	34.0	NM_018484	A8K426|Q53GR2|Q6ZP72|Q8NBU4	Silent	SNP	ENST00000301891.4	hg19	CCDS8074.1																																																																																			.	.		0.622	SLC22A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104886.4	NM_018484	
NRXN2	9379	hgsc.bcm.edu	37	11	64436058	64436058	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:64436058C>A	ENST00000377551.1	-	7	1427	c.1216G>T	c.(1216-1218)Ggg>Tgg	p.G406W	NRXN2_ENST00000377559.3_Missense_Mutation_p.G375W|NRXN2_ENST00000265459.6_Missense_Mutation_p.G406W|NRXN2_ENST00000409571.1_Missense_Mutation_p.G399W			Q9P2S2	NRX2A_HUMAN	neurexin 2	406	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						GTCAGGATCCCGTCCACCGAG	0.572																																					p.G406W		Atlas-SNP	.											.	NRXN2	247	.	0			c.G1216T						.						124.0	111.0	115.0					11																	64436058		2201	4297	6498	SO:0001583	missense	9379	exon8			GGATCCCGTCCAC		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"""neurexin II"""	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.1216G>T	chr11.hg19:g.64436058C>A	ENSP00000366774:p.Gly406Trp	123.0	0.0		81.0	4.0	NM_015080	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	hg19	CCDS8077.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.2|24.2	4.501927|4.501927	0.85176|0.85176	.|.	.|.	ENSG00000110076|ENSG00000110076	ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571;ENST00000442300|ENST00000437746	D;D;D;D;D|.	0.82167|.	-1.58;-1.5;-1.58;-1.58;-1.58|.	4.91|4.91	4.91|4.91	0.64330|0.64330	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);|.	0.000000|.	0.43416|.	U|.	0.000563|.	T|T	0.78780|0.78780	0.4337|0.4337	M|M	0.84773|0.84773	2.715|2.715	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;0.999|.	T|T	0.81152|0.81152	-0.1063|-0.1063	10|5	0.87932|.	D|.	0|.	.|.	15.6315|15.6315	0.76912|0.76912	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	375;406;152|.	Q9P2S2-2;Q9P2S2;E7EV67|.	.;NRX2A_HUMAN;.|.	W|L	406;375;406;375;399;162|180	ENSP00000366774:G406W;ENSP00000366782:G375W;ENSP00000265459:G406W;ENSP00000386416:G399W;ENSP00000388971:G162W|.	ENSP00000265459:G406W|.	G|R	-|-	1|2	0|0	NRXN2|NRXN2	64192634|64192634	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.600000|7.600000	0.82769|0.82769	2.531000|2.531000	0.85337|0.85337	0.650000|0.650000	0.86243|0.86243	GGG|CGG	.	.		0.572	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080	
ATG2A	23130	hgsc.bcm.edu	37	11	64681337	64681337	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:64681337C>T	ENST00000377264.3	-	4	658	c.546G>A	c.(544-546)ccG>ccA	p.P182P	ATG2A_ENST00000421419.2_Silent_p.P182P	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	182					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)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						CCCCATCACCCGGAGAGTGCT	0.617																																					p.P182P		Atlas-SNP	.											.	ATG2A	133	.	0			c.G546A						.						116.0	98.0	104.0					11																	64681337		2201	4297	6498	SO:0001819	synonymous_variant	23130	exon4			ATCACCCGGAGAG		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.546G>A	chr11.hg19:g.64681337C>T		143.0	0.0		79.0	4.0	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Silent	SNP	ENST00000377264.3	hg19	CCDS31602.1																																																																																			.	.		0.617	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
CAPN1	823	hgsc.bcm.edu	37	11	64977828	64977828	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:64977828T>C	ENST00000527323.1	+	19	2204	c.1964T>C	c.(1963-1965)cTg>cCg	p.L655P	CAPN1_ENST00000524773.1_Missense_Mutation_p.L655P|CAPN1_ENST00000533129.1_Missense_Mutation_p.L655P|CAPN1_ENST00000279247.6_Missense_Mutation_p.L655P|CAPN1_ENST00000533820.1_Missense_Mutation_p.L655P			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit	655	Domain IV.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		AACAAGAAGCTGTACGAGCTC	0.597																																					p.L655P		Atlas-SNP	.											.	CAPN1	44	.	0			c.T1964C						.						54.0	56.0	55.0					11																	64977828		2020	4191	6211	SO:0001583	missense	823	exon20			AGAAGCTGTACGA	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"""EF-hand domain containing"""	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614	ENST00000527323.1:c.1964T>C	chr11.hg19:g.64977828T>C	ENSP00000431984:p.Leu655Pro	116.0	0.0		108.0	5.0	NM_001198869	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	hg19	CCDS44644.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.759861	0.69763	.	.	ENSG00000014216	ENST00000533820;ENST00000533129;ENST00000524773;ENST00000279247;ENST00000259755;ENST00000527323	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	4.21	4.21	0.49690	EF-hand-like domain (1);	0.000000	0.64402	D	0.000003	T	0.55369	0.1916	M	0.85462	2.755	0.80722	D	1	D	0.71674	0.998	D	0.64776	0.929	T	0.63207	-0.6689	10	0.87932	D	0	.	11.5655	0.50802	0.0:0.0:0.0:1.0	.	655	P07384	CAN1_HUMAN	P	655;655;655;655;601;655	ENSP00000435272:L655P;ENSP00000431686:L655P;ENSP00000434176:L655P;ENSP00000279247:L655P;ENSP00000431984:L655P	ENSP00000259755:L601P	L	+	2	0	CAPN1	64734404	1.000000	0.71417	0.991000	0.47740	0.683000	0.39861	7.682000	0.84083	1.701000	0.51217	0.460000	0.39030	CTG	.	.		0.597	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
DPF2	5977	hgsc.bcm.edu	37	11	65113180	65113180	+	Missense_Mutation	SNP	C	C	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:65113180C>G	ENST00000528416.1	+	7	814	c.681C>G	c.(679-681)caC>caG	p.H227Q	DPF2_ENST00000415073.2_Intron|DPF2_ENST00000532264.1_3'UTR|DPF2_ENST00000252268.4_Missense_Mutation_p.H241Q	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	227					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)	23						TCAGTTACCACTATGCCCACT	0.522																																					p.H227Q		Atlas-SNP	.											.	DPF2	54	.	0			c.C681G						.						86.0	77.0	80.0					11																	65113180		2201	4297	6498	SO:0001583	missense	5977	exon7			TTACCACTATGCC	U94585	CCDS8100.1	11q13.1	2014-05-13	2003-10-06	2003-10-08	ENSG00000133884	ENSG00000133884		"""Zinc fingers, PHD-type"""	9964	protein-coding gene	gene with protein product		601671	"""requiem, apoptosis response zinc finger gene"""	REQ		11845289	Standard	NM_006268		Approved	ubi-d4, BAF45d	uc001odm.3	Q92785	OTTHUMG00000165985	ENST00000528416.1:c.681C>G	chr11.hg19:g.65113180C>G	ENSP00000436901:p.His227Gln	79.0	0.0		57.0	4.0	NM_006268	A8K7C9|B4DT58	Missense_Mutation	SNP	ENST00000528416.1	hg19	CCDS8100.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.447906	0.63178	.	.	ENSG00000133884	ENST00000528416;ENST00000252268	D;D	0.94793	-3.52;-3.06	5.24	4.34	0.51931	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39834	N	0.001260	D	0.92984	0.7767	M	0.83774	2.66	0.48975	D	0.999737	P	0.37864	0.61	B	0.35550	0.205	D	0.91947	0.5568	10	0.59425	D	0.04	-32.7354	7.682	0.28520	0.0:0.8178:0.0:0.1822	.	227	Q92785	REQU_HUMAN	Q	227;241	ENSP00000436901:H227Q;ENSP00000252268:H241Q	ENSP00000252268:H241Q	H	+	3	2	DPF2	64869756	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.871000	0.39539	1.446000	0.47643	0.561000	0.74099	CAC	.	.		0.522	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268	
FIBP	9158	hgsc.bcm.edu	37	11	65652450	65652450	+	Silent	SNP	G	G	T	rs368306000		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:65652450G>T	ENST00000338369.2	-	7	908	c.796C>A	c.(796-798)Cgg>Agg	p.R266R	FIBP_ENST00000533045.1_Silent_p.R256R|FIBP_ENST00000357519.4_Silent_p.R259R|FIBP_ENST00000426652.2_5'Flank	NM_198897.1	NP_942600.1	O43427	FIBP_HUMAN	fibroblast growth factor (acidic) intracellular binding protein	266					fibroblast growth factor receptor signaling pathway (GO:0008543)|platelet aggregation (GO:0070527)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	10				READ - Rectum adenocarcinoma(159;0.166)		AGCTTTCCCCGGAGAGCAGTG	0.622											OREG0021089	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R266R		Atlas-SNP	.											.	FIBP	28	.	0			c.C796A						.						69.0	66.0	67.0					11																	65652450		2201	4296	6497	SO:0001819	synonymous_variant	9158	exon7			TTCCCCGGAGAGC	AF010187	CCDS8118.1, CCDS8119.1	11q13.1	2006-06-15			ENSG00000172500	ENSG00000172500			3705	protein-coding gene	gene with protein product		608296				9806903	Standard	NM_004214		Approved	FGFIBP	uc001ogd.3	O43427	OTTHUMG00000166846	ENST00000338369.2:c.796C>A	chr11.hg19:g.65652450G>T		132.0	0.0	1085	89.0	4.0	NM_198897	A8K0J7|Q27Q85|Q6IBQ3|Q9HD65	Silent	SNP	ENST00000338369.2	hg19	CCDS8119.1																																																																																			.	.		0.622	FIBP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000391575.2	NM_198897	
POLD4	57804	hgsc.bcm.edu	37	11	67120247	67120247	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:67120247G>A	ENST00000312419.3	-	3	360	c.214C>T	c.(214-216)Cgg>Tgg	p.R72W	AP003419.11_ENST00000543494.1_RNA|POLD4_ENST00000539074.1_Intron|POLD4_ENST00000529704.1_5'UTR	NM_021173.4	NP_066996.3	Q9HCU8	DPOD4_HUMAN	polymerase (DNA-directed), delta 4, accessory subunit	72					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|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)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)	p.R72W(1)		breast(1)|endometrium(1)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(15;3.08e-06)			TGCTTGGCCCGACACCAGCGC	0.637																																					p.R72W		Atlas-SNP	.											POLD4_ENST00000312419,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	POLD4	9	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.C214T						.						23.0	25.0	24.0					11																	67120247		2194	4285	6479	SO:0001583	missense	57804	exon3			TGGCCCGACACCA	AF179890	CCDS8158.1, CCDS58149.1	11q13	2012-05-18	2012-05-18		ENSG00000175482	ENSG00000175482		"""DNA polymerases"""	14106	protein-coding gene	gene with protein product	"""DNA polymerase delta smallest subunit p12"""	611525	"""polymerase (DNA-directed), delta 4"""			10751307	Standard	NM_021173		Approved	p12, POLDS	uc001okm.4	Q9HCU8	OTTHUMG00000167135	ENST00000312419.3:c.214C>T	chr11.hg19:g.67120247G>A	ENSP00000311368:p.Arg72Trp	43.0	0.0		34.0	3.0	NM_021173	F5H506	Missense_Mutation	SNP	ENST00000312419.3	hg19	CCDS8158.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.008205	0.75046	.	.	ENSG00000175482	ENST00000312419	T	0.51817	0.69	4.3	3.36	0.38483	.	0.000000	0.41194	D	0.000935	T	0.69708	0.3141	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72931	-0.4142	10	0.87932	D	0	-14.981	9.1342	0.36863	0.0:0.0:0.7822:0.2178	.	72	Q9HCU8	DPOD4_HUMAN	W	72	ENSP00000311368:R72W	ENSP00000311368:R72W	R	-	1	2	POLD4	66876823	1.000000	0.71417	0.998000	0.56505	0.881000	0.50899	3.198000	0.51035	0.990000	0.38787	0.462000	0.41574	CGG	.	.		0.637	POLD4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393336.1	NM_021173	
PITPNM1	9600	hgsc.bcm.edu	37	11	67270152	67270152	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:67270152C>T	ENST00000534749.1	-	2	304	c.116G>A	c.(115-117)gGc>gAc	p.G39D	PITPNM1_ENST00000436757.2_Missense_Mutation_p.G39D|PITPNM1_ENST00000356404.3_Missense_Mutation_p.G39D			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	39					brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3)	18						GATCTCCACGCCGCTGCCCTC	0.652																																					p.G39D	GBM(28;144 709 4607 5525)	Atlas-SNP	.											.	PITPNM1	84	.	0			c.G116A						.						57.0	57.0	57.0					11																	67270152		2200	4295	6495	SO:0001583	missense	9600	exon3			TCCACGCCGCTGC	X98654	CCDS31620.1, CCDS44659.1	11q13	2008-07-21		2003-05-16	ENSG00000110697	ENSG00000110697			9003	protein-coding gene	gene with protein product	"""PYK2 N-terminal domain-interacting receptor 2"", ""retinal degeneration B alpha 1"""	608794		PITPNM		9680295	Standard	NM_004910		Approved	DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB	uc001oly.3	O00562	OTTHUMG00000167675	ENST00000534749.1:c.116G>A	chr11.hg19:g.67270152C>T	ENSP00000437286:p.Gly39Asp	118.0	0.0		91.0	4.0	NM_001130848	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Missense_Mutation	SNP	ENST00000534749.1	hg19	CCDS31620.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.830897	0.91036	.	.	ENSG00000110697	ENST00000534749;ENST00000436757;ENST00000356404;ENST00000533391;ENST00000532703;ENST00000528559;ENST00000524901	T;T;T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02;0.02;0.02	4.17	4.17	0.49024	START-like domain (1);	0.000000	0.46145	D	0.000320	D	0.85141	0.5629	H	0.96301	3.8	0.52501	D	0.999955	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90218	0.4269	10	0.87932	D	0	-26.5468	15.5871	0.76491	0.0:1.0:0.0:0.0	.	39;39	O00562-2;O00562	.;PITM1_HUMAN	D	39	ENSP00000437286:G39D;ENSP00000398787:G39D;ENSP00000348772:G39D;ENSP00000434046:G39D;ENSP00000432977:G39D;ENSP00000434904:G39D;ENSP00000432746:G39D	ENSP00000348772:G39D	G	-	2	0	PITPNM1	67026728	1.000000	0.71417	0.989000	0.46669	0.996000	0.88848	7.417000	0.80156	2.313000	0.78055	0.561000	0.74099	GGC	.	.		0.652	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910	
ALDH3B1	221	hgsc.bcm.edu	37	11	67787182	67787182	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:67787182A>G	ENST00000434449.1	+	6	521		c.e6-1		ALDH3B1_ENST00000316367.6_Splice_Site|ALDH3B1_ENST00000539229.1_Splice_Site|ALDH3B1_ENST00000342456.6_Splice_Site|ALDH3B1_ENST00000007633.8_Splice_Site			P43353	AL3B1_HUMAN	aldehyde dehydrogenase 3 family, member B1						alcohol metabolic process (GO:0006066)|aldehyde catabolic process (GO:0046185)|cellular response to oxidative stress (GO:0034599)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)										CCCGCCTTGCAGAGCTGCTTT	0.672																																					.		Atlas-SNP	.											.	.	.	.	0			c.480-2A>G						.						69.0	80.0	76.0					11																	67787182		2200	4294	6494	SO:0001630	splice_region_variant	221	exon6			CCTTGCAGAGCTG	U10868	CCDS73335.1, CCDS73336.1	11q13	2010-04-27			ENSG00000006534	ENSG00000006534	1.2.1.5	"""Aldehyde dehydrogenases"""	410	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase 7"", ""aldehyde dehydrogenase 3B1"""	600466		ALDH7		9161417, 7828891	Standard	NM_000694		Approved		uc001ona.3	P43353	OTTHUMG00000154910	ENST00000434449.1:c.522-1A>G	chr11.hg19:g.67787182A>G		211.0	0.0		98.0	4.0	NM_001161473	A3FMP9|Q53XL5|Q8N515|Q96CK8	Splice_Site	SNP	ENST00000434449.1	hg19																																																																																				.	.		0.672	ALDH3B1-001	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000337614.1	NM_000694	Intron
CPT1A	1374	hgsc.bcm.edu	37	11	68580046	68580046	+	Splice_Site	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:68580046T>A	ENST00000265641.5	-	3	296		c.e3-2		CPT1A_ENST00000539743.1_Splice_Site|CPT1A_ENST00000376618.2_Splice_Site|CPT1A_ENST00000540367.1_Splice_Site	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)						carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	GATGCCGTTCTAAAGACAGAC	0.622																																					.		Atlas-SNP	.											.	CPT1A	89	.	0			c.142-2A>T						.						91.0	71.0	78.0					11																	68580046		2200	4294	6494	SO:0001630	splice_region_variant	1374	exon4			CCGTTCTAAAGAC	L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.142-2A>T	chr11.hg19:g.68580046T>A		126.0	0.0		98.0	4.0	NM_001031847	Q8TCU0|Q9BWK0	Splice_Site	SNP	ENST00000265641.5	hg19	CCDS8185.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.128112	0.56721	.	.	ENSG00000110090	ENST00000540367;ENST00000376618;ENST00000265641;ENST00000538308;ENST00000539743	.	.	.	4.64	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2355	0.65925	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CPT1A	68336622	1.000000	0.71417	0.870000	0.34147	0.522000	0.34438	7.572000	0.82409	1.945000	0.56424	0.402000	0.26972	.	.	.		0.622	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876	Intron
KRTAP5-11	440051	hgsc.bcm.edu	37	11	71293531	71293531	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:71293531T>C	ENST00000398530.1	-	1	390	c.353A>G	c.(352-354)cAg>cGg	p.Q118R	KRTAP5-11_ENST00000526239.1_Intron|AP000867.1_ENST00000343767.3_Intron	NM_001005405.2	NP_001005405.1	Q6L8G4	KR511_HUMAN	keratin associated protein 5-11	118	6 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						gcagctggactggcagcagct	0.622																																					p.Q118R		Atlas-SNP	.											.	KRTAP5-11	36	.	0			c.A353G						.						55.0	69.0	64.0					11																	71293531		2200	4293	6493	SO:0001583	missense	440051	exon1			CTGGACTGGCAGC	AB126080	CCDS41685.1	11q13.4	2008-11-06			ENSG00000204571	ENSG00000204571		"""Keratin associated proteins"""	23606	protein-coding gene	gene with protein product						15144888	Standard	NM_001005405		Approved	KRTAP5.11, KRTAP5-6	uc001oqu.3	Q6L8G4	OTTHUMG00000057586	ENST00000398530.1:c.353A>G	chr11.hg19:g.71293531T>C	ENSP00000381541:p.Gln118Arg	165.0	0.0		102.0	7.0	NM_001005405		Missense_Mutation	SNP	ENST00000398530.1	hg19	CCDS41685.1	.	.	.	.	.	.	.	.	.	.	.	3.786	-0.044685	0.07452	.	.	ENSG00000204571	ENST00000376535;ENST00000398530	T	0.01464	4.86	1.87	0.597	0.17504	.	.	.	.	.	T	0.01661	0.0053	M	0.71581	2.175	0.21782	N	0.999545	P	0.48016	0.904	B	0.34385	0.181	T	0.38112	-0.9676	9	0.07813	T	0.8	.	3.9756	0.09473	0.3203:0.0:0.0:0.6797	.	118	Q6L8G4	KR511_HUMAN	R	118	ENSP00000381541:Q118R	ENSP00000365718:Q118R	Q	-	2	0	KRTAP5-11	70971179	0.997000	0.39634	0.983000	0.44433	0.701000	0.40568	0.913000	0.28611	0.153000	0.19213	0.361000	0.22055	CAG	.	.		0.622	KRTAP5-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127969.1	NM_001005405	
RNF169	254225	hgsc.bcm.edu	37	11	74546594	74546594	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:74546594A>G	ENST00000299563.4	+	6	959	c.946A>G	c.(946-948)Aca>Gca	p.T316A		NM_001098638.1	NP_001092108.1	Q8NCN4	RN169_HUMAN	ring finger protein 169	316					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of double-strand break repair (GO:2000780)|protein ubiquitination (GO:0016567)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|site of double-strand break (GO:0035861)	K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	15						CTTTCAGGTCACAACTATGAC	0.458																																					p.T316A		Atlas-SNP	.											.	RNF169	36	.	0			c.A946G						.						65.0	68.0	67.0					11																	74546594		2011	4164	6175	SO:0001583	missense	254225	exon6			CAGGTCACAACTA	AB082522	CCDS41691.1	11q13.4	2008-02-05			ENSG00000166439	ENSG00000166439		"""RING-type (C3HC4) zinc fingers"""	26961	protein-coding gene	gene with protein product						12056414	Standard	NM_001098638		Approved	KIAA1991	uc001ovl.4	Q8NCN4	OTTHUMG00000165516	ENST00000299563.4:c.946A>G	chr11.hg19:g.74546594A>G	ENSP00000299563:p.Thr316Ala	98.0	0.0		87.0	4.0	NM_001098638	Q6N015	Missense_Mutation	SNP	ENST00000299563.4	hg19	CCDS41691.1	.	.	.	.	.	.	.	.	.	.	A	9.720	1.159330	0.21454	.	.	ENSG00000166439	ENST00000299563	T	0.43688	0.94	5.82	3.52	0.40303	.	0.378221	0.31102	N	0.008254	T	0.39682	0.1087	M	0.70595	2.14	0.80722	D	1	P	0.52170	0.951	B	0.44224	0.444	T	0.19549	-1.0302	10	0.35671	T	0.21	-19.5797	4.9872	0.14196	0.6842:0.1555:0.1603:0.0	.	316	Q8NCN4	RN169_HUMAN	A	316	ENSP00000299563:T316A	ENSP00000299563:T316A	T	+	1	0	RNF169	74224242	0.025000	0.19082	0.998000	0.56505	0.262000	0.26303	1.020000	0.30027	0.483000	0.27608	-0.264000	0.10439	ACA	.	.		0.458	RNF169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384741.1	XM_495886	
UVRAG	7405	hgsc.bcm.edu	37	11	75851784	75851784	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:75851784C>A	ENST00000356136.3	+	15	1668	c.1427C>A	c.(1426-1428)cCt>cAt	p.P476H	UVRAG_ENST00000538870.1_Missense_Mutation_p.P32H|UVRAG_ENST00000532130.1_Missense_Mutation_p.P104H|UVRAG_ENST00000533454.1_Missense_Mutation_p.P104H|UVRAG_ENST00000528420.1_Missense_Mutation_p.P375H|UVRAG_ENST00000531818.1_Missense_Mutation_p.P104H|UVRAG_ENST00000539288.1_Missense_Mutation_p.P104H	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	476					DNA repair (GO:0006281)|positive regulation of autophagy (GO:0010508)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						AGTGCAATCCCTGTTCCTAAG	0.478																																					p.P476H		Atlas-SNP	.											.	UVRAG	69	.	0			c.C1427A						.						67.0	70.0	69.0					11																	75851784		2200	4293	6493	SO:0001583	missense	7405	exon15			CAATCCCTGTTCC	X99050, AB012958	CCDS8241.1	11q13	2012-11-15	2012-11-15		ENSG00000198382	ENSG00000198382			12640	protein-coding gene	gene with protein product	"""beclin 1 binding protein"""	602493	"""UV radiation resistance associated gene"""			9169138, 16799551, 18843052	Standard	NM_003369		Approved	VPS38	uc001oxc.3	Q9P2Y5	OTTHUMG00000165319	ENST00000356136.3:c.1427C>A	chr11.hg19:g.75851784C>A	ENSP00000348455:p.Pro476His	119.0	0.0		74.0	4.0	NM_003369	B3KTC1|O00392	Missense_Mutation	SNP	ENST00000356136.3	hg19	CCDS8241.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.440907	0.83993	.	.	ENSG00000198382	ENST00000356136;ENST00000528420;ENST00000533454;ENST00000531818;ENST00000532130;ENST00000539288;ENST00000538870	T	0.52526	0.66	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.60599	0.2281	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.95	T	0.61855	-0.6977	10	0.66056	D	0.02	-13.7312	18.8301	0.92135	0.0:1.0:0.0:0.0	.	32;476	B7Z6A0;Q9P2Y5	.;UVRAG_HUMAN	H	476;375;104;104;104;104;32	ENSP00000348455:P476H	ENSP00000348455:P476H	P	+	2	0	UVRAG	75529432	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.206000	0.77891	2.764000	0.94973	0.655000	0.94253	CCT	.	.		0.478	UVRAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383430.1	NM_003369	
INTS4	92105	hgsc.bcm.edu	37	11	77692604	77692604	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:77692604T>C	ENST00000534064.1	-	3	299	c.265A>G	c.(265-267)Aga>Gga	p.R89G	INTS4_ENST00000529807.1_Missense_Mutation_p.R89G	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	89					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			ATTTTCAGTCTCACAGATGGA	0.383																																					p.R89G		Atlas-SNP	.											.	INTS4	89	.	0			c.A265G						.						116.0	106.0	109.0					11																	77692604		2200	4292	6492	SO:0001583	missense	92105	exon3			TCAGTCTCACAGA	BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.265A>G	chr11.hg19:g.77692604T>C	ENSP00000434466:p.Arg89Gly	166.0	0.0		122.0	5.0	NM_033547	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	hg19	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.987070	0.74589	.	.	ENSG00000149262	ENST00000534064;ENST00000529807	T;T	0.75477	-0.94;0.67	4.75	3.59	0.41128	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.83857	0.5345	M	0.75777	2.31	0.80722	D	1	D	0.57899	0.981	D	0.69824	0.966	D	0.84611	0.0678	10	0.87932	D	0	-13.7668	11.4727	0.50280	0.0:0.0:0.1508:0.8492	.	89	Q96HW7	INT4_HUMAN	G	89	ENSP00000434466:R89G;ENSP00000433644:R89G	ENSP00000407787:R89G	R	-	1	2	INTS4	77370252	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.329000	0.43876	0.818000	0.34468	0.482000	0.46254	AGA	.	.		0.383	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547	
TMEM135	65084	hgsc.bcm.edu	37	11	87029247	87029247	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:87029247T>C	ENST00000305494.5	+	13	1185	c.1146T>C	c.(1144-1146)taT>taC	p.Y382Y	TMEM135_ENST00000340353.7_Silent_p.Y360Y|TMEM135_ENST00000532959.1_Silent_p.Y253Y|TMEM135_ENST00000535167.1_Silent_p.Y243Y	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	382					peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CTATCATCTATTCCATCTCTA	0.348																																					p.Y382Y		Atlas-SNP	.											.	TMEM135	40	.	0			c.T1146C						.						176.0	165.0	168.0					11																	87029247		2201	4299	6500	SO:0001819	synonymous_variant	65084	exon13			CATCTATTCCATC	BX648678	CCDS8280.1, CCDS53692.1	11q14.2	2006-03-09			ENSG00000166575	ENSG00000166575			26167	protein-coding gene	gene with protein product						12477932	Standard	NM_022918		Approved	FLJ22104	uc001pch.3	Q86UB9	OTTHUMG00000167248	ENST00000305494.5:c.1146T>C	chr11.hg19:g.87029247T>C		103.0	0.0		69.0	4.0	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Silent	SNP	ENST00000305494.5	hg19	CCDS8280.1																																																																																			.	.		0.348	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918	
KIAA1731	85459	hgsc.bcm.edu	37	11	93462654	93462654	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:93462654G>A	ENST00000325212.6	+	26	7519	c.7357G>A	c.(7357-7359)Gta>Ata	p.V2453I	SNORA8_ENST00000384574.1_RNA|SNORA32_ENST00000384072.1_RNA|SNORA25_ENST00000384384.1_RNA|KIAA1731_ENST00000411936.1_Missense_Mutation_p.V2453I|SNORA1_ENST00000384107.1_RNA|KIAA1731_ENST00000344196.4_Missense_Mutation_p.V633I|KIAA1731_ENST00000531700.1_Missense_Mutation_p.V633I|SNORD6_ENST00000365444.1_RNA|TAF1D_ENST00000546088.1_5'Flank			Q9C0D2	K1731_HUMAN	KIAA1731	2453						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)				TTATCCAGCTGTATCAGAACT	0.408																																					p.V2453I		Atlas-SNP	.											.	KIAA1731	173	.	0			c.G7357A						.						102.0	89.0	93.0					11																	93462654		692	1591	2283	SO:0001583	missense	85459	exon26			CCAGCTGTATCAG	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.7357G>A	chr11.hg19:g.93462654G>A	ENSP00000316681:p.Val2453Ile	86.0	0.0		80.0	28.0	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Missense_Mutation	SNP	ENST00000325212.6	hg19	CCDS44708.1	.	.	.	.	.	.	.	.	.	.	G	10.18	1.280331	0.23392	.	.	ENSG00000166004	ENST00000325212;ENST00000411936;ENST00000344196;ENST00000531700;ENST00000531404	T;T	0.10382	2.88;2.89	3.49	-2.17	0.07059	.	.	.	.	.	T	0.06962	0.0177	L	0.34521	1.04	0.09310	N	1	B;B;B	0.13145	0.007;0.003;0.007	B;B;B	0.13407	0.005;0.005;0.009	T	0.37314	-0.9711	9	0.42905	T	0.14	.	3.5331	0.07784	0.467:0.0:0.3516:0.1814	.	2453;2453;633	Q9C0D2;Q9C0D2-3;Q9C0D2-2	K1731_HUMAN;.;.	I	2453;2453;633;633;465	ENSP00000316681:V2453I;ENSP00000406505:V2453I	ENSP00000316681:V2453I	V	+	1	0	KIAA1731	93102302	0.000000	0.05858	0.000000	0.03702	0.353000	0.29299	-0.275000	0.08525	-0.461000	0.06993	0.655000	0.94253	GTA	.	.		0.408	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
AMOTL1	154810	hgsc.bcm.edu	37	11	94602390	94602390	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:94602390A>G	ENST00000433060.2	+	12	2657	c.2516A>G	c.(2515-2517)gAg>gGg	p.E839G	AMOTL1_ENST00000317829.8_Missense_Mutation_p.E789G|AMOTL1_ENST00000317837.9_Missense_Mutation_p.E426G	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	839					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				GAGCACCATGAGCATGCCTCT	0.522																																					p.E839G		Atlas-SNP	.											.	AMOTL1	95	.	0			c.A2516G						.						29.0	37.0	34.0					11																	94602390		2138	4240	6378	SO:0001583	missense	154810	exon12			ACCATGAGCATGC	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2516A>G	chr11.hg19:g.94602390A>G	ENSP00000387739:p.Glu839Gly	108.0	0.0		93.0	5.0	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	hg19	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	A	13.50	2.257003	0.39896	.	.	ENSG00000166025	ENST00000317829;ENST00000317837;ENST00000433060	T;T;T	0.46451	2.2;0.87;2.19	5.59	4.47	0.54385	.	0.389493	0.26286	N	0.025245	T	0.25754	0.0627	N	0.16478	0.41	0.22762	N	0.998762	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.14615	-1.0466	10	0.24483	T	0.36	-4.8031	10.6353	0.45560	0.9243:0.0:0.0757:0.0	.	789;839	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	G	789;426;839	ENSP00000320968:E789G;ENSP00000323474:E426G;ENSP00000387739:E839G	ENSP00000320968:E789G	E	+	2	0	AMOTL1	94242038	0.994000	0.37717	0.020000	0.16555	0.056000	0.15407	3.144000	0.50616	0.984000	0.38629	0.459000	0.35465	GAG	.	.		0.522	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100843960	100843960	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:100843960A>G	ENST00000298815.8	+	18	1608	c.1605A>G	c.(1603-1605)atA>atG	p.I535M	ARHGAP42_ENST00000524892.2_Missense_Mutation_p.I501M	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	535	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TTGGTGTCATATTTGGCCCAA	0.338																																					p.I535M		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.A1605G						.						45.0	39.0	41.0					11																	100843960		692	1591	2283	SO:0001583	missense	143872	exon18			TGTCATATTTGGC			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.1605A>G	chr11.hg19:g.100843960A>G	ENSP00000298815:p.Ile535Met	123.0	0.0		75.0	5.0	NM_152432	Q96M56	Missense_Mutation	SNP	ENST00000298815.8	hg19		.	.	.	.	.	.	.	.	.	.	A	20.7	4.040623	0.75732	.	.	ENSG00000165895	ENST00000524892;ENST00000298815	T;T	0.21191	2.02;2.02	6.17	-9.26	0.00662	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.32102	0.0818	M	0.62266	1.93	0.51012	D	0.999904	D	0.69078	0.997	D	0.70227	0.968	T	0.59742	-0.7397	10	0.87932	D	0	.	12.8772	0.57998	0.2171:0.5761:0.0:0.2068	.	535	A6NI28	RHG42_HUMAN	M	501;535	ENSP00000431776:I501M;ENSP00000298815:I535M	ENSP00000298815:I535M	I	+	3	3	ARHGAP42	100349170	1.000000	0.71417	0.906000	0.35671	0.964000	0.63967	0.896000	0.28377	-1.166000	0.02783	-1.236000	0.01555	ATA	.	.		0.338	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
MMP1	4312	hgsc.bcm.edu	37	11	102663360	102663360	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:102663360T>C	ENST00000315274.6	-	7	1076	c.1009A>G	c.(1009-1011)Aga>Gga	p.R337G	WTAPP1_ENST00000525739.2_RNA	NM_001145938.1|NM_002421.3	NP_001139410.1|NP_002412.1	P03956	MMP1_HUMAN	matrix metallopeptidase 1 (interstitial collagenase)	337					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|proteolysis (GO:0006508)|viral process (GO:0016032)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)	Marimastat(DB00786)	ACTTCATCTCTGTCGGCAAAT	0.398																																					p.R337G		Atlas-SNP	.											.	MMP1	74	.	0			c.A1009G						.						122.0	125.0	124.0					11																	102663360		2203	4299	6502	SO:0001583	missense	4312	exon7			CATCTCTGTCGGC	X54925	CCDS8322.1	11q21-q22	2014-01-30	2005-08-08		ENSG00000196611	ENSG00000196611	3.4.24.7	"""Endogenous ligands"""	7155	protein-coding gene	gene with protein product		120353	"""matrix metalloproteinase 1 (interstitial collagenase)"""	CLG			Standard	NM_002421		Approved		uc001phi.2	P03956	OTTHUMG00000048192	ENST00000315274.6:c.1009A>G	chr11.hg19:g.102663360T>C	ENSP00000322788:p.Arg337Gly	105.0	0.0		83.0	4.0	NM_002421	P08156	Missense_Mutation	SNP	ENST00000315274.6	hg19	CCDS8322.1	.	.	.	.	.	.	.	.	.	.	t	12.15	1.852757	0.32699	.	.	ENSG00000196611	ENST00000315274	T	0.13196	2.61	6.16	5.05	0.67936	Hemopexin/matrixin (2);	0.280687	0.33161	N	0.005207	T	0.16300	0.0392	L	0.58428	1.81	0.09310	N	1	B	0.24426	0.103	B	0.31614	0.133	T	0.23368	-1.0190	10	0.72032	D	0.01	.	7.2058	0.25907	0.0:0.0735:0.1465:0.7799	.	337	P03956	MMP1_HUMAN	G	337	ENSP00000322788:R337G	ENSP00000322788:R337G	R	-	1	2	MMP1	102168570	0.004000	0.15560	0.045000	0.18777	0.727000	0.41649	1.439000	0.35013	1.163000	0.42636	0.528000	0.53228	AGA	.	.		0.398	MMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109632.1	NM_002421	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103058312	103058312	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:103058312A>G	ENST00000375735.2	+	43	7281	c.7137A>G	c.(7135-7137)caA>caG	p.Q2379Q	DYNC2H1_ENST00000398093.3_Silent_p.Q2379Q|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2379	AAA 3. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CATTCCTACAACAGGTAAGTC	0.328																																					p.Q2379Q		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A7137G						.						66.0	60.0	62.0					11																	103058312		1835	4084	5919	SO:0001819	synonymous_variant	79659	exon43			CCTACAACAGGTA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.7137A>G	chr11.hg19:g.103058312A>G		106.0	0.0		88.0	4.0	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	hg19	CCDS53701.1																																																																																			.	.		0.328	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
PCSK7	9159	hgsc.bcm.edu	37	11	117100222	117100222	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:117100222G>T	ENST00000320934.3	-	3	969	c.339C>A	c.(337-339)atC>atA	p.I113I		NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	113					peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CCTGCTGCCGGATGGCCTCCA	0.652			T	IGH@	MLCLS																																p.I113I		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.C339A						.						52.0	57.0	55.0					11																	117100222		2201	4296	6497	SO:0001819	synonymous_variant	9159	exon3			CTGCCGGATGGCC	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.339C>A	chr11.hg19:g.117100222G>T		86.0	0.0		50.0	4.0	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	hg19	CCDS8382.1																																																																																			.	.		0.652	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
CEP164	22897	hgsc.bcm.edu	37	11	117214976	117214976	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:117214976T>C	ENST00000278935.3	+	4	324	c.177T>C	c.(175-177)ccT>ccC	p.P59P		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	59	Interaction with ATRIP.|WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		CCCCACTGCCTGGAGAGTGGA	0.552																																					p.P59P		Atlas-SNP	.											.	CEP164	121	.	0			c.T177C						.						36.0	33.0	34.0					11																	117214976		2201	4296	6497	SO:0001819	synonymous_variant	22897	exon3			ACTGCCTGGAGAG	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.177T>C	chr11.hg19:g.117214976T>C		134.0	0.0		106.0	5.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Silent	SNP	ENST00000278935.3	hg19	CCDS31683.1																																																																																			.	.		0.552	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
UBE4A	9354	hgsc.bcm.edu	37	11	118245776	118245776	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:118245776A>G	ENST00000431736.2	+	9	1375	c.1303A>G	c.(1303-1305)Atg>Gtg	p.M435V	UBE4A_ENST00000252108.3_Missense_Mutation_p.M428V					ubiquitination factor E4A											autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		CTTTTTCCAAATGTATGCCTC	0.468																																					p.M435V		Atlas-SNP	.											.	UBE4A	97	.	0			c.A1303G						.						103.0	92.0	96.0					11																	118245776		2200	4296	6496	SO:0001583	missense	9354	exon9			TTCCAAATGTATG	D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"""U-box domain containing"""	12499	protein-coding gene	gene with protein product		603753	"""ubiquitination factor E4A (homologous to yeast UFD2)"", ""ubiquitination factor E4A (UFD2 homolog, yeast)"""			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.1303A>G	chr11.hg19:g.118245776A>G	ENSP00000387362:p.Met435Val	158.0	0.0		95.0	4.0	NM_004788		Missense_Mutation	SNP	ENST00000431736.2	hg19	CCDS8396.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.761719	0.31228	.	.	ENSG00000110344	ENST00000252108;ENST00000431736	T;T	0.39997	1.05;1.05	5.85	5.85	0.93711	Ubiquitin conjugation factor E4, core (1);	0.072733	0.85682	D	0.000000	T	0.32071	0.0817	N	0.24115	0.695	0.80722	D	1	B;B	0.20780	0.048;0.012	B;B	0.22386	0.039;0.015	T	0.07712	-1.0758	10	0.25106	T	0.35	-18.7866	16.2268	0.82300	1.0:0.0:0.0:0.0	.	428;435	Q14139;Q14139-2	UBE4A_HUMAN;.	V	428;435	ENSP00000252108:M428V;ENSP00000387362:M435V	ENSP00000252108:M428V	M	+	1	0	UBE4A	117750986	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.967000	0.76079	2.242000	0.73789	0.402000	0.26972	ATG	.	.		0.468	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788	
KMT2A	4297	hgsc.bcm.edu	37	11	118392112	118392112	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:118392112G>A	ENST00000389506.5	+	35	11614	c.11614G>A	c.(11614-11616)Gaa>Aaa	p.E3872K	RP11-770J1.3_ENST00000528578.1_RNA|KMT2A_ENST00000354520.4_Missense_Mutation_p.E3834K|KMT2A_ENST00000534358.1_Missense_Mutation_p.E3875K|RP11-770J1.3_ENST00000554407.1_RNA|RP11-770J1.3_ENST00000532597.1_RNA|RP11-770J1.3_ENST00000525992.2_RNA|RP11-770J1.3_ENST00000556583.1_RNA			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3872	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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)										TGACAAGCGGGAAAAGTATTA	0.483																																					p.E3875K		Atlas-SNP	.											.	MLL	548	.	0			c.G11623A						.						94.0	85.0	88.0					11																	118392112		2200	4295	6495	SO:0001583	missense	4297	exon35			AAGCGGGAAAAGT	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.11614G>A	chr11.hg19:g.118392112G>A	ENSP00000374157:p.Glu3872Lys	113.0	0.0		82.0	4.0	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.293663	0.80914	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	T;T;T	0.81078	-1.45;-1.45;-1.45	5.82	5.82	0.92795	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.90263	0.6955	M	0.88979	2.995	0.80722	D	1	D;D	0.65815	0.995;0.995	P;P	0.56916	0.809;0.809	D	0.91460	0.5188	10	0.87932	D	0	.	20.1008	0.97874	0.0:0.0:1.0:0.0	.	3875;3872	E9PQG7;Q03164	.;MLL1_HUMAN	K	3875;3872;3834;2782	ENSP00000436786:E3875K;ENSP00000374157:E3872K;ENSP00000346516:E3834K	ENSP00000346516:E3834K	E	+	1	0	MLL	117897322	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.577000	0.82486	2.748000	0.94277	0.591000	0.81541	GAA	.	.		0.483	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
ABCG4	64137	hgsc.bcm.edu	37	11	119029042	119029042	+	Splice_Site	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:119029042G>T	ENST00000449422.2	+	10	1355	c.1167G>T	c.(1165-1167)acG>acT	p.T389T	ABCG4_ENST00000307417.3_Splice_Site_p.T389T|AP002956.1_ENST00000599663.1_5'Flank|ABCG4_ENST00000531739.1_Splice_Site_p.T389T	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	389	ABC transmembrane type-2.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.T389T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		TCAGGGACACGGTGAGGCGTC	0.587																																					p.T389T		Atlas-SNP	.											ABCG4,NS,carcinoma,0,1	ABCG4	77	.	1	Substitution - coding silent(1)	lung(1)	c.G1167T						.						176.0	158.0	164.0					11																	119029042		2200	4295	6495	SO:0001630	splice_region_variant	64137	exon10			GGACACGGTGAGG	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.1167+1G>T	chr11.hg19:g.119029042G>T		113.0	0.0		68.0	3.0	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Silent	SNP	ENST00000449422.2	hg19	CCDS8415.1																																																																																			.	.		0.587	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	Silent
SORL1	6653	hgsc.bcm.edu	37	11	121478830	121478830	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:121478830T>C	ENST00000260197.7	+	38	5313	c.5184T>C	c.(5182-5184)agT>agC	p.S1728S	SORL1_ENST00000527934.1_Silent_p.S343S|SORL1_ENST00000532694.1_Silent_p.S574S|SORL1_ENST00000534286.1_Silent_p.S638S|SORL1_ENST00000525532.1_Silent_p.S672S	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1728	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		CGGTGACTAGTCGTGGAATAG	0.363																																					p.S1728S		Atlas-SNP	.											.	SORL1	218	.	0			c.T5184C						.						107.0	102.0	104.0					11																	121478830		2202	4299	6501	SO:0001819	synonymous_variant	6653	exon38			GACTAGTCGTGGA	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.5184T>C	chr11.hg19:g.121478830T>C		75.0	0.0		76.0	4.0	NM_003105	B2RNX7|Q92856	Silent	SNP	ENST00000260197.7	hg19	CCDS8436.1																																																																																			.	.		0.363	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	
FOXRED1	55572	hgsc.bcm.edu	37	11	126146997	126146997	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:126146997T>C	ENST00000263578.5	+	10	1207	c.1133T>C	c.(1132-1134)gTg>gCg	p.V378A	FOXRED1_ENST00000532125.1_Missense_Mutation_p.V364A|FOXRED1_ENST00000442061.2_Missense_Mutation_p.V208A|FOXRED1_ENST00000534011.1_3'UTR	NM_017547.3	NP_060017.1	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing 1	378						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		AACCTGGAAGTGGACCATGAT	0.547																																					p.V378A		Atlas-SNP	.											.	FOXRED1	38	.	0			c.T1133C						.						82.0	75.0	78.0					11																	126146997		2201	4298	6499	SO:0001583	missense	55572	exon10			TGGAAGTGGACCA		CCDS8471.1	11q24.2	2006-02-03			ENSG00000110074	ENSG00000110074			26927	protein-coding gene	gene with protein product		613622				10497265	Standard	NM_017547		Approved	H17	uc001qdi.3	Q96CU9	OTTHUMG00000165827	ENST00000263578.5:c.1133T>C	chr11.hg19:g.126146997T>C	ENSP00000263578:p.Val378Ala	189.0	0.0		108.0	5.0	NM_017547	B3KN84|B4DHU2|Q71MG0|Q9BU39|Q9UKY9	Missense_Mutation	SNP	ENST00000263578.5	hg19	CCDS8471.1	.	.	.	.	.	.	.	.	.	.	T	34	5.374574	0.95923	.	.	ENSG00000110074	ENST00000263578;ENST00000442061;ENST00000532125	D;D;D	0.82619	-1.63;-1.63;-1.63	5.79	5.79	0.91817	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	D	0.91549	0.7331	M	0.82193	2.58	0.80722	D	1	D;D;D	0.89917	0.985;1.0;0.988	P;D;P	0.91635	0.828;0.999;0.893	D	0.92337	0.5878	10	0.59425	D	0.04	-22.3541	15.7901	0.78350	0.0:0.0:0.0:1.0	.	364;245;378	Q96CU9-3;B4DI59;Q96CU9	.;.;FXRD1_HUMAN	A	378;208;364	ENSP00000263578:V378A;ENSP00000404371:V208A;ENSP00000434178:V364A	ENSP00000263578:V378A	V	+	2	0	FOXRED1	125652207	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.718000	0.84743	2.213000	0.71641	0.477000	0.44152	GTG	.	.		0.547	FOXRED1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386434.1	NM_017547	
GLB1L2	89944	hgsc.bcm.edu	37	11	134238603	134238603	+	Nonsense_Mutation	SNP	G	G	T	rs138130138	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr11:134238603G>T	ENST00000535456.2	+	10	1143	c.955G>T	c.(955-957)Gga>Tga	p.G319*	GLB1L2_ENST00000389881.3_Nonsense_Mutation_p.G319*|GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Nonsense_Mutation_p.G319*	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	319					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		CATGTTCCACGGAGGCACCAA	0.527																																					p.G319X		Atlas-SNP	.											GLB1L2,NS,carcinoma,0,1	GLB1L2	79	.	0			c.G955T						.						112.0	88.0	96.0					11																	134238603		2201	4297	6498	SO:0001587	stop_gained	89944	exon10			TTCCACGGAGGCA		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.955G>T	chr11.hg19:g.134238603G>T	ENSP00000444628:p.Gly319*	76.0	0.0		52.0	4.0	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Nonsense_Mutation	SNP	ENST00000535456.2	hg19	CCDS31724.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.892637|5.892637	0.97074|0.97074	.|.	.|.	ENSG00000149328|ENSG00000149328	ENST00000339772;ENST00000535456;ENST00000389881|ENST00000525089;ENST00000533324	.|.	.|.	.|.	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	0.055211|.	0.64402|.	D|.	0.000001|.	.|T	.|0.73544	.|0.3600	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73742	.|-0.3887	.|3	0.87932|.	D|.	0|.	-16.874|-16.874	17.4812|17.4812	0.87673|0.87673	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	319|257;146	.|.	ENSP00000344659:G319X|.	G|R	+|+	1|2	0|0	GLB1L2|GLB1L2	133743813|133743813	1.000000|1.000000	0.71417|0.71417	0.558000|0.558000	0.28319|0.28319	0.965000|0.965000	0.64279|0.64279	9.048000|9.048000	0.93830|0.93830	2.408000|2.408000	0.81797|0.81797	0.655000|0.655000	0.94253|0.94253	GGA|CGG	.	G|0.997;A|0.003		0.527	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342	
WNK1	65125	hgsc.bcm.edu	37	12	922831	922831	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:922831G>T	ENST00000315939.6	+	2	1426	c.783G>T	c.(781-783)gaG>gaT	p.E261D	WNK1_ENST00000447667.2_Missense_Mutation_p.E261D|WNK1_ENST00000530271.2_Missense_Mutation_p.E261D|WNK1_ENST00000535572.1_Missense_Mutation_p.E261D|WNK1_ENST00000537687.1_Missense_Mutation_p.E261D	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CAAAGTCTGAGAGGCAGAGAT	0.318																																					p.E261D	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.G783T						.						74.0	72.0	72.0					12																	922831		2203	4300	6503	SO:0001583	missense	65125	exon2			GTCTGAGAGGCAG	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.783G>T	chr12.hg19:g.922831G>T	ENSP00000313059:p.Glu261Asp	113.0	0.0		74.0	5.0	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	hg19	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.050825	0.75960	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000447667;ENST00000530271	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	5.83	4.9	0.64082	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000003	T	0.58323	0.2114	N	0.16567	0.415	0.80722	D	1	P;P;B	0.38020	0.56;0.615;0.006	B;P;B	0.47118	0.403;0.538;0.014	T	0.62562	-0.6828	10	0.87932	D	0	-17.5842	8.8647	0.35278	0.1929:0.0:0.8071:0.0	.	261;261;261	F5GWT4;Q9H4A3;F6UYG0	.;WNK1_HUMAN;.	D	261	ENSP00000441972:E261D;ENSP00000313059:E261D;ENSP00000444465:E261D;ENSP00000392542:E261D;ENSP00000433548:E261D	ENSP00000313059:E261D	E	+	3	2	WNK1	793092	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.076000	0.57591	1.332000	0.45431	0.561000	0.74099	GAG	.	.		0.318	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
WNK1	65125	hgsc.bcm.edu	37	12	994233	994233	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:994233T>C	ENST00000315939.6	+	19	4906	c.4263T>C	c.(4261-4263)gtT>gtC	p.V1421V	WNK1_ENST00000530271.2_Silent_p.V1919V|WNK1_ENST00000535572.1_Silent_p.V1174V|WNK1_ENST00000340908.4_Silent_p.V1014V|WNK1_ENST00000537687.1_Silent_p.V1681V	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1421					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TACCTGCAGTTGTCTCAATAT	0.463																																					p.V1681V	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.T5043C						.						176.0	176.0	176.0					12																	994233		2203	4300	6503	SO:0001819	synonymous_variant	65125	exon19			TGCAGTTGTCTCA	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.4263T>C	chr12.hg19:g.994233T>C		103.0	0.0		99.0	4.0	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	hg19	CCDS8506.1																																																																																			.	.		0.463	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
FBXL14	144699	hgsc.bcm.edu	37	12	1702401	1702401	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:1702401T>C	ENST00000339235.3	-	1	930	c.832A>G	c.(832-834)Agc>Ggc	p.S278G	FBXL14_ENST00000543278.1_5'Flank|WNT5B_ENST00000537031.1_Intron	NM_152441.2	NP_689654.1	Q8N1E6	FXL14_HUMAN	F-box and leucine-rich repeat protein 14	278					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	8	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00115)			AGGCGCAGGCTGCCCATGGCC	0.612																																					p.S278G		Atlas-SNP	.											.	FBXL14	19	.	0			c.A832G						.						61.0	56.0	58.0					12																	1702401		2203	4300	6503	SO:0001583	missense	144699	exon1			GCAGGCTGCCCAT	BC028132	CCDS8509.1	12p13.33	2011-06-09			ENSG00000171823	ENSG00000171823		"""F-boxes / Leucine-rich repeats"""	28624	protein-coding gene	gene with protein product		609081				12477932	Standard	NM_152441		Approved	MGC40195, Fbl14	uc001qjh.3	Q8N1E6	OTTHUMG00000090369	ENST00000339235.3:c.832A>G	chr12.hg19:g.1702401T>C	ENSP00000344855:p.Ser278Gly	72.0	0.0		60.0	4.0	NM_152441		Missense_Mutation	SNP	ENST00000339235.3	hg19	CCDS8509.1	.	.	.	.	.	.	.	.	.	.	T	8.116	0.779902	0.16120	.	.	ENSG00000171823	ENST00000339235	T	0.02395	4.31	4.71	3.56	0.40772	.	0.244275	0.41712	D	0.000840	T	0.01124	0.0037	N	0.01874	-0.695	0.40520	D	0.980829	B	0.02656	0.0	B	0.01281	0.0	T	0.52734	-0.8536	10	0.15952	T	0.53	.	5.5706	0.17194	0.1512:0.0809:0.0:0.7678	.	278	Q8N1E6	FXL14_HUMAN	G	278	ENSP00000344855:S278G	ENSP00000344855:S278G	S	-	1	0	FBXL14	1572662	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.826000	0.55738	0.813000	0.34350	0.528000	0.53228	AGC	.	.		0.612	FBXL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206741.1	NM_152441	
DCP1B	196513	hgsc.bcm.edu	37	12	2062133	2062133	+	Nonsense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:2062133C>A	ENST00000280665.6	-	7	1052	c.973G>T	c.(973-975)Gga>Tga	p.G325*	DCP1B_ENST00000397173.4_Nonsense_Mutation_p.G223*|DCP1B_ENST00000541700.1_5'UTR|DCP1B_ENST00000540622.1_Nonsense_Mutation_p.G199*	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	325					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)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(10)|skin(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			AAAAATTCTCCCGCAGAATGG	0.502																																					p.G325X		Atlas-SNP	.											.	DCP1B	63	.	0			c.G973T						.						79.0	87.0	85.0					12																	2062133		2203	4300	6503	SO:0001587	stop_gained	196513	exon7			ATTCTCCCGCAGA	AY146652	CCDS31727.1	12p13.33	2013-05-02	2013-05-02		ENSG00000151065	ENSG00000151065			24451	protein-coding gene	gene with protein product		609843	"""DCP1 decapping enzyme homolog B (S. cerevisiae)"""			12417715, 15067023	Standard	NM_152640		Approved	FLJ31638	uc001qjx.1	Q8IZD4	OTTHUMG00000168113	ENST00000280665.6:c.973G>T	chr12.hg19:g.2062133C>A	ENSP00000280665:p.Gly325*	98.0	0.0		94.0	4.0	NM_152640	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Nonsense_Mutation	SNP	ENST00000280665.6	hg19	CCDS31727.1	.	.	.	.	.	.	.	.	.	.	C	13.02	2.113145	0.37339	.	.	ENSG00000151065	ENST00000280665;ENST00000397173;ENST00000540622	.	.	.	4.73	-1.34	0.09143	.	1.130390	0.06354	N	0.710400	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-0.6889	8.1265	0.31001	0.0:0.5862:0.1027:0.3111	.	.	.	.	X	325;223;199	.	ENSP00000280665:G325X	G	-	1	0	DCP1B	1932394	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.350000	0.07721	-0.863000	0.04084	-1.886000	0.00541	GGA	.	.		0.502	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640	
PARP11	57097	hgsc.bcm.edu	37	12	3923215	3923215	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:3923215C>T	ENST00000228820.4	-	7	832	c.688G>A	c.(688-690)Gtc>Atc	p.V230I	PARP11_ENST00000476985.1_5'UTR|PARP11_ENST00000397096.2_Missense_Mutation_p.V223I|PARP11_ENST00000427057.2_Missense_Mutation_p.V149I|PARP11_ENST00000447133.3_Missense_Mutation_p.V149I	NM_020367.4	NP_065100.2	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11	223	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.						NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	17			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)			TTTCCAAAGACAGCACCATGT	0.353																																					p.V230I		Atlas-SNP	.											.	PARP11	39	.	0			c.G688A						.						128.0	122.0	124.0					12																	3923215		2203	4300	6503	SO:0001583	missense	57097	exon7			CAAAGACAGCACC	AF263540	CCDS8523.2, CCDS66281.1	12p13.3	2014-01-28	2004-08-25	2004-08-26	ENSG00000111224	ENSG00000111224		"""Poly (ADP-ribose) polymerases"""	1186	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 6"""	C12orf6		15273990	Standard	NM_001286522		Approved		uc001qml.2	Q9NR21	OTTHUMG00000156442	ENST00000228820.4:c.688G>A	chr12.hg19:g.3923215C>T	ENSP00000228820:p.Val230Ile	134.0	0.0		97.0	4.0	NM_020367	B4DRQ0|Q68DS1|Q8N5Y9	Missense_Mutation	SNP	ENST00000228820.4	hg19	CCDS8523.2	.	.	.	.	.	.	.	.	.	.	C	9.723	1.160185	0.21454	.	.	ENSG00000111224	ENST00000397096;ENST00000427057;ENST00000228820;ENST00000447133	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.41	-0.0656	0.13768	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.342248	0.29964	N	0.010747	T	0.16257	0.0391	L	0.55990	1.75	0.36412	D	0.863777	B;B;B	0.23735	0.09;0.008;0.011	B;B;B	0.28011	0.085;0.028;0.047	T	0.20806	-1.0264	10	0.25751	T	0.34	.	19.145	0.93461	0.0:0.759:0.241:0.0	.	149;230;223	Q9NR21-2;Q9NR21-4;Q9NR21	.;.;PAR11_HUMAN	I	223;149;230;149	ENSP00000380284:V223I;ENSP00000397058:V149I;ENSP00000228820:V230I;ENSP00000405385:V149I	ENSP00000228820:V230I	V	-	1	0	PARP11	3793476	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	1.573000	0.36472	0.089000	0.17243	-0.274000	0.10170	GTC	.	.		0.353	PARP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344213.1		
C12orf4	57102	hgsc.bcm.edu	37	12	4600397	4600397	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:4600397T>C	ENST00000261250.3	-	12	1531	c.1444A>G	c.(1444-1446)Atg>Gtg	p.M482V	C12orf4_ENST00000545746.1_Missense_Mutation_p.M482V	NM_020374.2	NP_065107.1	Q9NQ89	CL004_HUMAN	chromosome 12 open reading frame 4	482										NS(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)		GGTATAGTCATTTCCTAAAAA	0.358																																					p.M482V		Atlas-SNP	.											.	C12orf4	58	.	0			c.A1444G						.						137.0	124.0	128.0					12																	4600397		2203	4300	6503	SO:0001583	missense	57102	exon12			TAGTCATTTCCTA	AJ272205	CCDS8528.1	12p13.3	2012-08-10			ENSG00000047621	ENSG00000047621			1184	protein-coding gene	gene with protein product							Standard	NM_020374		Approved		uc001qms.3	Q9NQ89	OTTHUMG00000168258	ENST00000261250.3:c.1444A>G	chr12.hg19:g.4600397T>C	ENSP00000261250:p.Met482Val	119.0	0.0		100.0	6.0	NM_020374	D3DUQ8|Q6MZH5	Missense_Mutation	SNP	ENST00000261250.3	hg19	CCDS8528.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.178888	0.78564	.	.	ENSG00000047621	ENST00000261250;ENST00000545746	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.76212	0.3956	M	0.84326	2.69	0.80722	D	1	P	0.51791	0.948	P	0.54499	0.754	T	0.81048	-0.1109	9	0.87932	D	0	.	15.5652	0.76287	0.0:0.0:0.0:1.0	.	482	Q9NQ89	CL004_HUMAN	V	482	.	ENSP00000261250:M482V	M	-	1	0	C12orf4	4470658	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.239000	0.78182	2.129000	0.65627	0.477000	0.44152	ATG	.	.		0.358	C12orf4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398992.1	NM_020374	
AKAP3	10566	hgsc.bcm.edu	37	12	4736342	4736342	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:4736342C>A	ENST00000545990.2	-	5	2250	c.1726G>T	c.(1726-1728)Gct>Tct	p.A576S	RP11-500M8.7_ENST00000536588.1_Intron|AKAP3_ENST00000228850.1_Missense_Mutation_p.A576S	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	576					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						ACAATGGGAGCAGACTTAAGG	0.468																																					p.A576S		Atlas-SNP	.											AKAP3_ENST00000545990,NS,carcinoma,0,4	AKAP3	212	.	0			c.G1726T						.						67.0	65.0	66.0					12																	4736342		2203	4300	6503	SO:0001583	missense	10566	exon4			TGGGAGCAGACTT	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.1726G>T	chr12.hg19:g.4736342C>A	ENSP00000440994:p.Ala576Ser	66.0	0.0		63.0	3.0	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	hg19	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.207578	0.00292	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.07327	3.2;3.2	5.82	-2.48	0.06423	A-kinase anchor 110kDa, C-terminal (1);	0.402656	0.24251	N	0.040167	T	0.02533	0.0077	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.38714	-0.9648	10	0.18710	T	0.47	-2.3172	1.1023	0.01687	0.2296:0.3516:0.1935:0.2253	.	576	O75969	AKAP3_HUMAN	S	576	ENSP00000228850:A576S;ENSP00000440994:A576S	ENSP00000228850:A576S	A	-	1	0	AKAP3	4606603	0.126000	0.22350	0.001000	0.08648	0.009000	0.06853	0.203000	0.17315	-0.107000	0.12088	-1.086000	0.02197	GCT	.	.		0.468	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
VWF	7450	hgsc.bcm.edu	37	12	6128323	6128323	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:6128323T>C	ENST00000261405.5	-	28	4515	c.4261A>G	c.(4261-4263)Aac>Gac	p.N1421D		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1421	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)	TGCTTGAGGTTGGCATGGGGC	0.592																																					p.N1421D		Atlas-SNP	.											.	VWF	338	.	0			c.A4261G						.						76.0	77.0	77.0					12																	6128323		2203	4300	6503	SO:0001583	missense	7450	exon28			TGAGGTTGGCATG		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.4261A>G	chr12.hg19:g.6128323T>C	ENSP00000261405:p.Asn1421Asp	142.0	0.0		96.0	4.0	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	hg19	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	.	12.82	2.053131	0.36181	.	.	ENSG00000110799	ENST00000261405	D	0.81821	-1.54	4.92	4.92	0.64577	von Willebrand factor, type A (3);	0.817450	0.10796	N	0.633182	D	0.84906	0.5576	M	0.69358	2.11	0.80722	D	1	B	0.29955	0.263	B	0.43251	0.413	T	0.80975	-0.1142	10	0.49607	T	0.09	.	13.8742	0.63643	0.0:0.0:0.0:1.0	.	1421	P04275	VWF_HUMAN	D	1421	ENSP00000261405:N1421D	ENSP00000261405:N1421D	N	-	1	0	VWF	5998584	0.994000	0.37717	0.613000	0.29037	0.423000	0.31445	4.583000	0.60964	2.077000	0.62373	0.454000	0.30748	AAC	.	.		0.592	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
CD4	920	hgsc.bcm.edu	37	12	6926435	6926435	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:6926435G>T	ENST00000011653.4	+	7	1353	c.1095G>T	c.(1093-1095)gcG>gcT	p.A365A		NM_000616.4|NM_001195015.2|NM_001195016.2|NM_001195017.2	NP_000607.1|NP_001181944.1|NP_001181945.1|NP_001181946.1	P01730	CD4_HUMAN	CD4 molecule	365	Ig-like C2-type 3.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cytokine production (GO:0001816)|defense response to Gram-negative bacterium (GO:0050829)|entry into host cell (GO:0030260)|enzyme linked receptor protein signaling pathway (GO:0007167)|immune response (GO:0006955)|induction by virus of host cell-cell fusion (GO:0006948)|innate immune response (GO:0045087)|maintenance of protein location in cell (GO:0032507)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase activity (GO:0045860)|protein palmitoleylation (GO:0045234)|regulation of defense response to virus by virus (GO:0050690)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|T cell selection (GO:0045058)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|enzyme binding (GO:0019899)|extracellular matrix structural constituent (GO:0005201)|glycoprotein binding (GO:0001948)|MHC class II protein binding (GO:0042289)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	23		Myeloproliferative disorder(1001;0.0122)			Antithymocyte globulin(DB00098)	ACCCTGAGGCGGGGATGTGGC	0.592																																					p.A365A		Atlas-SNP	.											CD4,NS,carcinoma,0,1	CD4	47	.	0			c.G1095T						.						73.0	59.0	63.0					12																	6926435		2203	4300	6503	SO:0001819	synonymous_variant	920	exon7			TGAGGCGGGGATG	M35160	CCDS8562.1	12p13.31	2013-01-11	2006-03-28		ENSG00000010610	ENSG00000010610		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	1678	protein-coding gene	gene with protein product		186940	"""CD4 antigen (p55)"", ""T-cell surface glycoprotein CD4"""				Standard	NM_000616		Approved		uc001qqv.2	P01730	OTTHUMG00000168514	ENST00000011653.4:c.1095G>T	chr12.hg19:g.6926435G>T		122.0	1.0		100.0	4.0	NM_000616	B2R737|D3DUS5|Q4ZGK2|Q5U066|Q9UDE5	Silent	SNP	ENST00000011653.4	hg19	CCDS8562.1																																																																																			.	.		0.592	CD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399978.1	NM_000616	
PEX5	5830	hgsc.bcm.edu	37	12	7344169	7344169	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:7344169T>C	ENST00000455147.2	+	6	901	c.321T>C	c.(319-321)ccT>ccC	p.P107P	RP11-273B20.3_ENST00000545794.1_RNA|PEX5_ENST00000266563.5_Silent_p.P107P|PEX5_ENST00000420616.2_Silent_p.P107P|PEX5_ENST00000266564.3_Silent_p.P107P|PEX5_ENST00000545220.1_3'UTR|RP11-273B20.3_ENST00000543061.1_RNA|PEX5_ENST00000434354.2_Silent_p.P122P|PEX5_ENST00000412720.2_Silent_p.P128P	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5	107					cell development (GO:0048468)|cerebral cortex cell migration (GO:0021795)|cerebral cortex neuron differentiation (GO:0021895)|endoplasmic reticulum organization (GO:0007029)|fatty acid beta-oxidation (GO:0006635)|mitochondrial membrane organization (GO:0007006)|negative regulation of protein homotetramerization (GO:1901094)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|positive regulation of multicellular organism growth (GO:0040018)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|protein import into peroxisome matrix, translocation (GO:0016561)|protein import into peroxisome membrane (GO:0045046)|protein targeting to peroxisome (GO:0006625)|protein tetramerization (GO:0051262)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|small GTPase binding (GO:0031267)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)	21						TTTAAGCCCCTGGTGTGGCAG	0.448																																					p.P122P		Atlas-SNP	.											.	PEX5	63	.	0			c.T366C						.						68.0	68.0	68.0					12																	7344169		2203	4300	6503	SO:0001819	synonymous_variant	5830	exon5			AGCCCCTGGTGTG	U19721	CCDS8576.1, CCDS44822.1, CCDS44823.1, CCDS44824.1, CCDS73433.1	12p	2013-01-10	2004-03-17	2004-03-19		ENSG00000139197		"""Tetratricopeptide (TTC) repeat domain containing"""	9719	protein-coding gene	gene with protein product		600414	"""peroxisome receptor 1"""	PXR1			Standard	NM_000319		Approved	PTS1R	uc010sgc.2	P50542		ENST00000455147.2:c.321T>C	chr12.hg19:g.7344169T>C		82.0	0.0		66.0	4.0	NM_001131023	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	Silent	SNP	ENST00000455147.2	hg19	CCDS44823.1																																																																																			.	.		0.448	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1	NM_000319	
PZP	5858	hgsc.bcm.edu	37	12	9318700	9318700	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:9318700T>C	ENST00000261336.2	-	18	2234	c.2206A>G	c.(2206-2208)Acg>Gcg	p.T736A	PZP_ENST00000539983.1_5'UTR|PZP_ENST00000381997.2_Missense_Mutation_p.T605A	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	736					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CTTCGCACCGTTTCAGGGACT	0.448																																					p.T736A	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A2206G						.						143.0	134.0	137.0					12																	9318700		2203	4300	6503	SO:0001583	missense	5858	exon18			GCACCGTTTCAGG	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2206A>G	chr12.hg19:g.9318700T>C	ENSP00000261336:p.Thr736Ala	143.0	0.0		74.0	4.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	hg19	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.258979	0.39896	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.37752	1.47;1.18	3.58	2.42	0.29668	.	0.243635	0.20220	U	0.096705	T	0.38081	0.1027	L	0.29908	0.895	0.20307	N	0.999916	P;D;P	0.54772	0.85;0.968;0.85	P;P;P	0.59115	0.507;0.852;0.507	T	0.10800	-1.0614	10	0.87932	D	0	.	6.6954	0.23195	0.0:0.1177:0.0:0.8823	.	736;605;736	B2R950;P20742-2;P20742	.;.;PZP_HUMAN	A	736;605	ENSP00000261336:T736A;ENSP00000371427:T605A	ENSP00000261336:T736A	T	-	1	0	PZP	9209967	0.963000	0.33076	0.004000	0.12327	0.352000	0.29268	2.567000	0.45956	0.533000	0.28675	0.383000	0.25322	ACG	.	.		0.448	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
TAS2R8	50836	hgsc.bcm.edu	37	12	10959161	10959161	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:10959161A>G	ENST00000240615.2	-	1	731	c.419T>C	c.(418-420)aTt>aCt	p.I140T		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	140					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CAACAAGGAAATGGCAAAGCA	0.398																																					p.I140T		Atlas-SNP	.											.	TAS2R8	42	.	0			c.T419C						.						110.0	99.0	103.0					12																	10959161		2203	4300	6503	SO:0001583	missense	50836	exon1			AAGGAAATGGCAA	AF227134	CCDS8632.1	12p13	2012-08-22			ENSG00000121314	ENSG00000121314		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14915	protein-coding gene	gene with protein product		604794				10761934, 10766242	Standard	NM_023918		Approved	T2R8, TRB5	uc010shh.2	Q9NYW2	OTTHUMG00000168506	ENST00000240615.2:c.419T>C	chr12.hg19:g.10959161A>G	ENSP00000240615:p.Ile140Thr	123.0	0.0		84.0	4.0	NM_023918	Q4KN29|Q645Y2	Missense_Mutation	SNP	ENST00000240615.2	hg19	CCDS8632.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.619150	0.46736	.	.	ENSG00000121314	ENST00000240615	T	0.00922	5.54	4.5	2.02	0.26589	GPCR, rhodopsin-like superfamily (1);	0.549996	0.14943	U	0.289365	T	0.01765	0.0056	M	0.69823	2.125	0.09310	N	1	B	0.30236	0.274	B	0.34301	0.179	T	0.34329	-0.9833	10	0.87932	D	0	.	8.0232	0.30421	0.675:0.0:0.0:0.325	.	140	Q9NYW2	TA2R8_HUMAN	T	140	ENSP00000240615:I140T	ENSP00000240615:I140T	I	-	2	0	TAS2R8	10850428	0.002000	0.14202	0.000000	0.03702	0.264000	0.26372	1.807000	0.38902	0.222000	0.20900	0.455000	0.32223	ATT	.	.		0.398	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1		
KIAA1551	55196	hgsc.bcm.edu	37	12	32135858	32135858	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:32135858A>G	ENST00000312561.4	+	4	2383	c.1969A>G	c.(1969-1971)Aca>Gca	p.T657A	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	657																	AGAATCCTCAACAAAAGGAAT	0.423																																					p.T657A		Atlas-SNP	.											.	.	.	.	0			c.A1969G						.						68.0	65.0	66.0					12																	32135858		2203	4299	6502	SO:0001583	missense	55196	exon4			TCCTCAACAAAAG	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.1969A>G	chr12.hg19:g.32135858A>G	ENSP00000310338:p.Thr657Ala	87.0	0.0		73.0	4.0	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	hg19	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	A	8.364	0.833877	0.16820	.	.	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.05258	4.15;3.47	4.99	-5.19	0.02832	.	1.410390	0.04860	N	0.443996	T	0.02929	0.0087	N	0.12182	0.205	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.44877	-0.9299	9	.	.	.	.	3.1103	0.06356	0.2884:0.1292:0.4554:0.1271	.	657	Q9HCM1	CL035_HUMAN	A	657	ENSP00000310338:T657A;ENSP00000370442:T657A	.	T	+	1	0	C12orf35	32027125	0.000000	0.05858	0.000000	0.03702	0.508000	0.34012	-1.927000	0.01561	-0.440000	0.07211	0.460000	0.39030	ACA	.	.		0.423	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
DNM1L	10059	hgsc.bcm.edu	37	12	32890048	32890048	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:32890048A>G	ENST00000549701.1	+	14	1623	c.1549A>G	c.(1549-1551)Aga>Gga	p.R517G	DNM1L_ENST00000547312.1_Missense_Mutation_p.R517G|DNM1L_ENST00000553257.1_Missense_Mutation_p.R530G|DNM1L_ENST00000358214.5_Missense_Mutation_p.R530G|DNM1L_ENST00000266481.6_Missense_Mutation_p.R517G|DNM1L_ENST00000452533.2_Missense_Mutation_p.R517G|DNM1L_ENST00000414834.2_Missense_Mutation_p.R314G|DNM1L_ENST00000381000.4_Missense_Mutation_p.R530G|YARS2_ENST00000551673.1_Intron			O00429	DNM1L_HUMAN	dynamin 1-like	517	B domain.|Interaction with GSK3B.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dynamin polymerization involved in mitochondrial fission (GO:0003374)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|membrane fission involved in mitochondrial fission (GO:0090149)|membrane fusion (GO:0061025)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion morphogenesis (GO:0070584)|necroptotic process (GO:0070266)|peroxisome fission (GO:0016559)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homotetramerization (GO:0051289)|protein localization to mitochondrion (GO:0070585)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|regulation of protein oligomerization (GO:0032459)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|protein complex (GO:0043234)|synapse (GO:0045202)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	23	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GGAACAAAGGAGAAACAGGCT	0.333																																					p.R517G		Atlas-SNP	.											.	DNM1L	52	.	0			c.A1549G						.						125.0	121.0	122.0					12																	32890048		2203	4300	6503	SO:0001583	missense	10059	exon14			CAAAGGAGAAACA	AF000430	CCDS8728.1, CCDS8729.1, CCDS8730.1, CCDS61095.1, CCDS61096.1, CCDS61098.1, CCDS61099.1	12p11.21	2012-10-02			ENSG00000087470	ENSG00000087470			2973	protein-coding gene	gene with protein product		603850				9348079, 9731200	Standard	NM_012062		Approved	DRP1, DVLP, HDYNIV, DYMPLE, VPS1	uc001rld.2	O00429	OTTHUMG00000169451	ENST00000549701.1:c.1549A>G	chr12.hg19:g.32890048A>G	ENSP00000450399:p.Arg517Gly	127.0	0.0		78.0	4.0	NM_012062	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Missense_Mutation	SNP	ENST00000549701.1	hg19	CCDS8729.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.240152	0.39598	.	.	ENSG00000087470	ENST00000452533;ENST00000411996;ENST00000266479;ENST00000553257;ENST00000549701;ENST00000358214;ENST00000266481;ENST00000547312;ENST00000414834;ENST00000381000	D;D;D;D;D;D;T;D	0.90563	-2.67;-2.69;-2.69;-2.68;-2.68;-2.69;-1.34;-2.69	5.47	3.0	0.34707	.	0.290262	0.34828	N	0.003657	D	0.83473	0.5262	N	0.02916	-0.46	0.80722	D	1	D;B;B;P;B;B	0.58268	0.982;0.001;0.006;0.778;0.001;0.006	P;B;B;P;B;B	0.60236	0.871;0.009;0.016;0.572;0.012;0.016	T	0.80598	-0.1311	10	0.35671	T	0.21	.	6.2486	0.20833	0.635:0.2753:0.0896:0.0	.	314;570;570;583;570;517	B4DGC9;D3DUW6;D3DUW5;F8W8D1;D3DUW7;O00429	.;.;.;.;.;DNM1L_HUMAN	G	517;583;517;530;517;530;517;517;314;530	ENSP00000415131:R517G;ENSP00000449089:R530G;ENSP00000450399:R517G;ENSP00000350948:R530G;ENSP00000266481:R517G;ENSP00000448610:R517G;ENSP00000404160:R314G;ENSP00000370388:R530G	ENSP00000266479:R517G	R	+	1	2	DNM1L	32781315	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.892000	0.39748	0.917000	0.36895	0.533000	0.62120	AGA	.	.		0.333	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062	
PKP2	5318	hgsc.bcm.edu	37	12	33031343	33031343	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:33031343C>T	ENST00000070846.6	-	3	495	c.471G>A	c.(469-471)gaG>gaA	p.E157E	PKP2_ENST00000340811.4_Silent_p.E157E	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	157					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					AGTGAGCCCTCTCCGGGCTGC	0.592																																					p.E157E		Atlas-SNP	.											.	PKP2	110	.	0			c.G471A						.						120.0	120.0	120.0					12																	33031343		2203	4297	6500	SO:0001819	synonymous_variant	5318	exon3			AGCCCTCTCCGGG	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.471G>A	chr12.hg19:g.33031343C>T		138.0	0.0		110.0	15.0	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Silent	SNP	ENST00000070846.6	hg19	CCDS8731.1																																																																																			.	.		0.592	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572	
LRRK2	120892	hgsc.bcm.edu	37	12	40677799	40677799	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:40677799C>T	ENST00000298910.7	+	19	2422	c.2364C>T	c.(2362-2364)agC>agT	p.S788S	LRRK2_ENST00000343742.2_Silent_p.S788S	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	788					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AGATCATCAGCTTGCTCTTAA	0.448																																					p.S788S		Atlas-SNP	.											.	LRRK2	763	.	0			c.C2364T						.						166.0	163.0	164.0					12																	40677799		2203	4300	6503	SO:0001819	synonymous_variant	120892	exon19			CATCAGCTTGCTC	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.2364C>T	chr12.hg19:g.40677799C>T		181.0	0.0		104.0	5.0	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	hg19	CCDS31774.1																																																																																			.	.		0.448	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43847742	43847742	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:43847742G>A	ENST00000389420.3	-	12	1727	c.1728C>T	c.(1726-1728)atC>atT	p.I576I	ADAMTS20_ENST00000553158.1_Silent_p.I576I	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	576	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TTGCACTTTCGATTCCGCCTC	0.413																																					p.I576I		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.C1728T						.						117.0	92.0	100.0					12																	43847742		2203	4300	6503	SO:0001819	synonymous_variant	80070	exon12			ACTTTCGATTCCG	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1728C>T	chr12.hg19:g.43847742G>A		105.0	0.0		76.0	46.0	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	hg19	CCDS31778.2																																																																																			.	.		0.413	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43847776	43847776	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:43847776T>C	ENST00000389420.3	-	12	1693	c.1694A>G	c.(1693-1695)tAc>tGc	p.Y565C	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.Y565C	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	565	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		ACAAGAACTGTAAGGTTCCCA	0.403																																					p.Y565C		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A1694G						.						115.0	93.0	100.0					12																	43847776		2203	4300	6503	SO:0001583	missense	80070	exon12			GAACTGTAAGGTT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.1694A>G	chr12.hg19:g.43847776T>C	ENSP00000374071:p.Tyr565Cys	114.0	0.0		86.0	47.0	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	17.96	3.517057	0.64634	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.53423	0.62;0.62	4.77	3.6	0.41247	.	0.153604	0.30151	N	0.010297	T	0.70413	0.3221	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.75161	-0.3415	10	0.87932	D	0	.	12.1553	0.54072	0.0:0.0:0.1435:0.8565	.	565	P59510	ATS20_HUMAN	C	565	ENSP00000374071:Y565C;ENSP00000448341:Y565C	ENSP00000374068:Y565C	Y	-	2	0	ADAMTS20	42134043	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.276000	0.43408	0.901000	0.36495	0.477000	0.44152	TAC	.	.		0.403	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
COL2A1	1280	hgsc.bcm.edu	37	12	48374364	48374364	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:48374364C>T	ENST00000380518.3	-	39	2762	c.2598G>A	c.(2596-2598)caG>caA	p.Q866Q	COL2A1_ENST00000337299.6_Silent_p.Q797Q|COL2A1_ENST00000493991.1_5'UTR	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	866	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CAGAGGGGCCCTGAGGACCAG	0.637																																					p.Q866Q		Atlas-SNP	.											.	COL2A1	368	.	0			c.G2598A						.						31.0	30.0	30.0					12																	48374364		2203	4300	6503	SO:0001819	synonymous_variant	1280	exon39			GGGGCCCTGAGGA	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"""Collagens"""	2200	protein-coding gene	gene with protein product		120140	"""collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)"", ""arthroophthalmopathy, progressive (Stickler syndrome)"""	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.2598G>A	chr12.hg19:g.48374364C>T		70.0	0.0		57.0	4.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	hg19	CCDS41778.1																																																																																			.	.		0.637	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
COL2A1	1280	hgsc.bcm.edu	37	12	48381091	48381091	+	Silent	SNP	G	G	A	rs570997824		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:48381091G>A	ENST00000380518.3	-	20	1391	c.1227C>T	c.(1225-1227)aaC>aaT	p.N409N	COL2A1_ENST00000337299.6_Silent_p.N340N|COL2A1_ENST00000493991.1_5'UTR	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	409	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CTGTTCCAGGGTTACCCTGAA	0.557																																					p.N409N		Atlas-SNP	.											.	COL2A1	368	.	0			c.C1227T						.						67.0	70.0	69.0					12																	48381091		2203	4300	6503	SO:0001819	synonymous_variant	1280	exon20			TCCAGGGTTACCC	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"""Collagens"""	2200	protein-coding gene	gene with protein product		120140	"""collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)"", ""arthroophthalmopathy, progressive (Stickler syndrome)"""	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.1227C>T	chr12.hg19:g.48381091G>A		172.0	0.0		100.0	4.0	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	hg19	CCDS41778.1																																																																																			.	.		0.557	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
KMT2D	8085	hgsc.bcm.edu	37	12	49421091	49421091	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:49421091T>C	ENST00000301067.7	-	48	14657	c.14658A>G	c.(14656-14658)ccA>ccG	p.P4886P		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4886					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)										TGGGTGGCTCTGGGGCGGGGC	0.602																																					p.P4886P		Atlas-SNP	.											.	MLL2	1173	.	0			c.A14658G						.						95.0	102.0	100.0					12																	49421091		1789	3830	5619	SO:0001819	synonymous_variant	8085	exon48			TGGCTCTGGGGCG	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.14658A>G	chr12.hg19:g.49421091T>C		172.0	0.0		114.0	5.0	NM_003482	O14687	Silent	SNP	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.		0.602	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
KMT2D	8085	hgsc.bcm.edu	37	12	49432443	49432443	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:49432443C>T	ENST00000301067.7	-	34	8695	c.8696G>A	c.(8695-8697)gGc>gAc	p.G2899D	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2899	Pro-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)										CTGAGGTGGGCCCTGACCAGG	0.622																																					p.G2899D		Atlas-SNP	.											.	MLL2	1173	.	0			c.G8696A						.						21.0	24.0	23.0					12																	49432443		1876	4101	5977	SO:0001583	missense	8085	exon34			GGTGGGCCCTGAC	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.8696G>A	chr12.hg19:g.49432443C>T	ENSP00000301067:p.Gly2899Asp	91.0	0.0		57.0	4.0	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	8.974	0.973577	0.18736	.	.	ENSG00000167548	ENST00000301067	T	0.80214	-1.35	5.32	5.32	0.75619	.	0.000000	0.39083	N	0.001464	T	0.78502	0.4293	L	0.29908	0.895	0.32354	N	0.558019	D	0.69078	0.997	P	0.57152	0.814	T	0.81538	-0.0887	10	0.87932	D	0	.	7.6716	0.28462	0.1658:0.7506:0.0:0.0835	.	2899	O14686	MLL2_HUMAN	D	2899	ENSP00000301067:G2899D	ENSP00000301067:G2899D	G	-	2	0	MLL2	47718710	0.175000	0.23083	0.979000	0.43373	0.851000	0.48451	1.915000	0.39976	2.878000	0.98634	0.650000	0.86243	GGC	.	.		0.622	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
DIP2B	57609	hgsc.bcm.edu	37	12	51069149	51069149	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:51069149G>T	ENST00000301180.5	+	7	868	c.834G>T	c.(832-834)caG>caT	p.Q278H		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	278						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						CAAAAATCCAGCAGCTTCTGA	0.368																																					p.Q278H		Atlas-SNP	.											.	DIP2B	167	.	0			c.G834T						.						92.0	94.0	94.0					12																	51069149		2203	4300	6503	SO:0001583	missense	57609	exon7			AATCCAGCAGCTT	AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.834G>T	chr12.hg19:g.51069149G>T	ENSP00000301180:p.Gln278His	164.0	0.0		102.0	5.0	NM_173602	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	hg19	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.039648	0.75732	.	.	ENSG00000066084	ENST00000455310;ENST00000301180	T	0.46819	0.86	5.03	2.24	0.28232	.	0.050417	0.85682	D	0.000000	T	0.66187	0.2764	M	0.80616	2.505	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.66164	-0.5992	10	0.66056	D	0.02	-11.9782	9.8151	0.40846	0.2874:0.0:0.7126:0.0	.	278;288	Q9P265;E9PHD6	DIP2B_HUMAN;.	H	288;278	ENSP00000301180:Q278H	ENSP00000301180:Q278H	Q	+	3	2	DIP2B	49355416	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	2.761000	0.47589	0.307000	0.22880	0.563000	0.77884	CAG	.	.		0.368	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602	
SLC4A8	9498	hgsc.bcm.edu	37	12	51844748	51844748	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:51844748A>G	ENST00000453097.2	+	3	436	c.219A>G	c.(217-219)agA>agG	p.R73R	SLC4A8_ENST00000394856.1_Silent_p.R20R|SLC4A8_ENST00000535225.2_Silent_p.R20R|SLC4A8_ENST00000514353.3_Silent_p.R20R|SLC4A8_ENST00000358657.3_Silent_p.R100R	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		AGCACCGGAGACGAGGGCGGG	0.657																																					p.R73R		Atlas-SNP	.											.	SLC4A8	292	.	0			c.A219G						.						18.0	19.0	19.0					12																	51844748		2203	4300	6503	SO:0001819	synonymous_variant	9498	exon3			CCGGAGACGAGGG	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"""Solute carriers"""	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.219A>G	chr12.hg19:g.51844748A>G		165.0	0.0		109.0	6.0	NM_001039960		Silent	SNP	ENST00000453097.2	hg19	CCDS44890.1																																																																																			.	.		0.657	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858	
KRT85	3891	hgsc.bcm.edu	37	12	52754781	52754781	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:52754781G>A	ENST00000257901.3	-	9	1455	c.1380C>T	c.(1378-1380)agC>agT	p.S460S	KRT85_ENST00000544265.1_Silent_p.S248S	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	460	Tail.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CTGGGGTGGTGCTGTAGGAGA	0.657																																					p.S460S		Atlas-SNP	.											.	KRT85	78	.	0			c.C1380T						.						26.0	28.0	27.0					12																	52754781		2203	4300	6503	SO:0001819	synonymous_variant	3891	exon9			GGTGGTGCTGTAG	X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6462	protein-coding gene	gene with protein product	"""hard keratin type II"""	602767	"""keratin, hair, basic, 5"""	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.1380C>T	chr12.hg19:g.52754781G>A		117.0	0.0		79.0	4.0	NM_002283	Q9NSB1	Silent	SNP	ENST00000257901.3	hg19	CCDS8824.1																																																																																			.	.		0.657	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283	
TENC1	23371	hgsc.bcm.edu	37	12	53456471	53456471	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:53456471T>C	ENST00000314250.6	+	25	4103	c.3813T>C	c.(3811-3813)cgT>cgC	p.R1271R	TENC1_ENST00000314276.3_Silent_p.R1281R|TENC1_ENST00000549700.1_Silent_p.R1206R|TENC1_ENST00000552570.1_Silent_p.R1271R|TENC1_ENST00000546602.1_Silent_p.R1174R|TENC1_ENST00000379902.3_Silent_p.R1147R|TENC1_ENST00000451358.1_Silent_p.R1261R	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	1271					cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						ACCTCCTGCGTCAGGGTGCTG	0.617																																					p.R1281R		Atlas-SNP	.											.	TENC1	148	.	0			c.T3843C						.						68.0	54.0	59.0					12																	53456471		2203	4300	6503	SO:0001819	synonymous_variant	23371	exon25			CCTGCGTCAGGGT	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	19737	protein-coding gene	gene with protein product	"""tensin 2"""	607717	"""tensin like C1 domain-containing phosphatase"""				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.3813T>C	chr12.hg19:g.53456471T>C		86.0	0.0		57.0	4.0	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Silent	SNP	ENST00000314250.6	hg19	CCDS8843.1																																																																																			.	.		0.617	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754	
SPRYD3	84926	hgsc.bcm.edu	37	12	53467190	53467190	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:53467190C>T	ENST00000301463.4	-	6	659	c.573G>A	c.(571-573)ctG>ctA	p.L191L	SPRYD3_ENST00000547837.1_Silent_p.L228L	NM_032840.2	NP_116229.1	Q8NCJ5	SPRY3_HUMAN	SPRY domain containing 3	191	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.									central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						CCTCCTCACCCAGGGAGTGCA	0.632																																					p.L191L		Atlas-SNP	.											.	SPRYD3	29	.	0			c.G573A						.						83.0	60.0	67.0					12																	53467190		2201	4298	6499	SO:0001819	synonymous_variant	84926	exon6			CTCACCCAGGGAG	AK074694	CCDS8845.1	12q13.13	2006-11-29		2006-02-02		ENSG00000167778			25920	protein-coding gene	gene with protein product						14702039	Standard	NM_032840		Approved	FLJ14800	uc001sbt.2	Q8NCJ5	OTTHUMG00000170101	ENST00000301463.4:c.573G>A	chr12.hg19:g.53467190C>T		97.0	0.0		80.0	4.0	NM_032840	B9EG99|Q96SK5	Silent	SNP	ENST00000301463.4	hg19	CCDS8845.1																																																																																			.	.		0.632	SPRYD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407264.1	NM_032840	
ITGB7	3695	hgsc.bcm.edu	37	12	53586193	53586193	+	Silent	SNP	G	G	A	rs549027525		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:53586193G>A	ENST00000267082.5	-	14	2307	c.2076C>T	c.(2074-2076)acC>acT	p.T692T	ITGB7_ENST00000338737.4_Silent_p.T544T|ITGB7_ENST00000550743.2_Silent_p.T544T|ITGB7_ENST00000422257.3_Silent_p.T692T	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	692					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GGTTGTCCAGGGTCCGCTCTT	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		22424	0.0		0.0	False		,,,				2504	0.001				p.T692T		Atlas-SNP	.											.	ITGB7	60	.	0			c.C2076T						.						140.0	126.0	131.0					12																	53586193		2203	4300	6503	SO:0001819	synonymous_variant	3695	exon14			GTCCAGGGTCCGC		CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"""Integrins"""	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.2076C>T	chr12.hg19:g.53586193G>A		55.0	0.0		35.0	5.0	NM_000889	Q9UCP7|Q9UCS7	Silent	SNP	ENST00000267082.5	hg19	CCDS8849.1																																																																																			.	.		0.582	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2		
NCKAP1L	3071	hgsc.bcm.edu	37	12	54932744	54932744	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:54932744T>C	ENST00000293373.6	+	30	3339	c.3260T>C	c.(3259-3261)cTg>cCg	p.L1087P	NCKAP1L_ENST00000545638.2_Missense_Mutation_p.L1037P	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	1087					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						TCCATTTCTCTGCTCATGCGC	0.468																																					p.L1087P		Atlas-SNP	.											.	NCKAP1L	180	.	0			c.T3260C						.						92.0	80.0	84.0					12																	54932744		2203	4300	6503	SO:0001583	missense	3071	exon30			TTTCTCTGCTCAT	AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"""hematopoietic protein 1"""	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.3260T>C	chr12.hg19:g.54932744T>C	ENSP00000293373:p.Leu1087Pro	99.0	0.0		66.0	4.0	NM_005337	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	hg19	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	T	19.43	3.826512	0.71143	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.41400	1.0;1.0	4.25	4.25	0.50352	.	0.095554	0.43110	D	0.000615	T	0.58850	0.2151	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.62760	-0.6786	10	0.87932	D	0	-7.923	11.6366	0.51207	0.0:0.0:0.0:1.0	.	1087	P55160	NCKPL_HUMAN	P	1087;1037	ENSP00000293373:L1087P;ENSP00000445596:L1037P	ENSP00000293373:L1087P	L	+	2	0	NCKAP1L	53219011	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.111000	0.77077	1.930000	0.55929	0.533000	0.62120	CTG	.	.		0.468	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337	
METTL7B	196410	hgsc.bcm.edu	37	12	56076035	56076035	+	Splice_Site	SNP	C	C	A	rs555960398		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:56076035C>A	ENST00000394252.3	+	1	706	c.497C>A	c.(496-498)cCg>cAg	p.P166Q		NM_152637.2	NP_689850.2	Q6UX53	MET7B_HUMAN	methyltransferase like 7B	166							methyltransferase activity (GO:0008168)			kidney(1)|large_intestine(1)|lung(4)	6						GTACTGAGACCGGTAAGCAGG	0.622																																					p.P166Q		Atlas-SNP	.											METTL7B_ENST00000394252,NS,carcinoma,-1,2	METTL7B	35	.	0			c.C497A						.						33.0	29.0	30.0					12																	56076035		2203	4300	6503	SO:0001630	splice_region_variant	196410	exon1			TGAGACCGGTAAG		CCDS8887.2	12q13.2	2012-06-12			ENSG00000170439	ENSG00000170439			28276	protein-coding gene	gene with protein product	"""associated with lipid droplets 1"""					17004324	Standard	NM_152637		Approved	MGC17301, ALDI	uc010spr.2	Q6UX53	OTTHUMG00000152665	ENST00000394252.3:c.498+1C>A	chr12.hg19:g.56076035C>A		141.0	0.0		73.0	3.0	NM_152637	A8K247|Q8WUI1	Missense_Mutation	SNP	ENST00000394252.3	hg19	CCDS8887.2	.	.	.	.	.	.	.	.	.	.	C	17.20	3.330263	0.60743	.	.	ENSG00000170439	ENST00000394252	T	0.37411	1.2	4.86	4.86	0.63082	Methyltransferase type 11 (1);	0.117466	0.64402	D	0.000015	T	0.69646	0.3134	H	0.94658	3.565	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.78889	-0.2026	10	0.66056	D	0.02	-3.9477	15.5599	0.76237	0.0:1.0:0.0:0.0	.	166	Q6UX53	MET7B_HUMAN	Q	166	ENSP00000377796:P166Q	ENSP00000377796:P166Q	P	+	2	0	METTL7B	54362302	0.961000	0.32948	1.000000	0.80357	0.186000	0.23388	1.997000	0.40786	2.508000	0.84585	0.655000	0.94253	CCG	.	.		0.622	METTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327271.1	NM_152637	Missense_Mutation
ERBB3	2065	hgsc.bcm.edu	37	12	56493513	56493513	+	Missense_Mutation	SNP	G	G	T	rs376939275		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:56493513G>T	ENST00000267101.3	+	24	3361	c.2921G>T	c.(2920-2922)cGg>cTg	p.R974L	RP11-603J24.9_ENST00000548861.1_5'Flank|ERBB3_ENST00000549832.1_Missense_Mutation_p.R94L|ERBB3_ENST00000415288.2_Missense_Mutation_p.R915L|ERBB3_ENST00000450146.2_Missense_Mutation_p.R331L|ERBB3_ENST00000553131.1_Missense_Mutation_p.R215L	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	974					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|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)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			GACCCACCACGGTATCTGGTC	0.468																																					p.R974L		Atlas-SNP	.											.	ERBB3	350	.	0			c.G2921T						.						82.0	73.0	76.0					12																	56493513		2203	4300	6503	SO:0001583	missense	2065	exon24			CACCACGGTATCT	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"""lethal congenital contracture syndrome 2"""	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.2921G>T	chr12.hg19:g.56493513G>T	ENSP00000267101:p.Arg974Leu	164.0	0.0		92.0	4.0	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	hg19	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	G	34	5.408020	0.96051	.	.	ENSG00000065361	ENST00000267101;ENST00000450146;ENST00000415288;ENST00000550070;ENST00000553131;ENST00000549832	T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14	6.17	6.17	0.99709	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000004	T	0.67998	0.2953	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.85130	0.982;0.997;0.994	T	0.69427	-0.5148	10	0.87932	D	0	.	19.6509	0.95805	0.0:0.0:1.0:0.0	.	915;94;974	P21860-4;B3KWG5;P21860	.;.;ERBB3_HUMAN	L	974;331;915;97;215;94	ENSP00000267101:R974L;ENSP00000399178:R331L;ENSP00000408340:R915L;ENSP00000449129:R215L;ENSP00000448729:R94L	ENSP00000267101:R974L	R	+	2	0	ERBB3	54779780	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	9.513000	0.98010	2.941000	0.99782	0.655000	0.94253	CGG	.	.		0.468	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3		
PAN2	9924	hgsc.bcm.edu	37	12	56726754	56726754	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:56726754T>C	ENST00000425394.2	-	2	501	c.125A>G	c.(124-126)gAg>gGg	p.E42G	PAN2_ENST00000257931.5_Missense_Mutation_p.E42G|PAN2_ENST00000440411.3_Missense_Mutation_p.E42G|PAN2_ENST00000548043.1_Missense_Mutation_p.E42G	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	GGCCACTCCCTCTGGGTCCAG	0.562																																					p.E42G		Atlas-SNP	.											.	PAN2	107	.	0			c.A125G						.						116.0	97.0	103.0					12																	56726754		2203	4300	6503	SO:0001583	missense	9924	exon2			ACTCCCTCTGGGT	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"""Ubiquitin-specific peptidases"""	20074	protein-coding gene	gene with protein product	"""PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"""		"""ubiquitin specific protease 52"", ""ubiquitin specific peptidase 52"", ""PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"""	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.125A>G	chr12.hg19:g.56726754T>C	ENSP00000401721:p.Glu42Gly	57.0	0.0		61.0	4.0	NM_014871		Missense_Mutation	SNP	ENST00000425394.2	hg19	CCDS44922.1	.	.	.	.	.	.	.	.	.	.	T	18.95	3.731979	0.69189	.	.	ENSG00000135473	ENST00000425394;ENST00000440411;ENST00000257931;ENST00000548043	T;T;T;T	0.06294	3.32;3.32;3.32;3.32	4.72	4.72	0.59763	.	0.111020	0.64402	D	0.000012	T	0.05273	0.0140	N	0.25647	0.755	0.47905	D	0.999544	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.08055	0.003;0.003;0.001	T	0.39187	-0.9626	10	0.14252	T	0.57	-11.5693	13.6203	0.62134	0.0:0.0:0.0:1.0	.	42;42;42	Q504Q3-3;Q504Q3-2;Q504Q3	.;.;PAN2_HUMAN	G	42	ENSP00000401721:E42G;ENSP00000388231:E42G;ENSP00000257931:E42G;ENSP00000449861:E42G	ENSP00000257931:E42G	E	-	2	0	PAN2	55013021	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.370000	0.79589	2.133000	0.65898	0.477000	0.44152	GAG	.	.		0.562	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871	
BAZ2A	11176	hgsc.bcm.edu	37	12	56993526	56993526	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:56993526A>G	ENST00000551812.1	-	26	5331	c.5138T>C	c.(5137-5139)gTc>gCc	p.V1713A	BAZ2A_ENST00000549884.1_Missense_Mutation_p.V1711A|BAZ2A_ENST00000179765.5_Missense_Mutation_p.V1681A|BAZ2A_ENST00000379441.3_Missense_Mutation_p.V1683A|BAZ2A_ENST00000553222.1_5'Flank	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1713					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						TCCTTCTGGGACAGCCTCCAT	0.483																																					p.V1713A		Atlas-SNP	.											.	BAZ2A	263	.	0			c.T5138C						.						100.0	104.0	103.0					12																	56993526		2028	4187	6215	SO:0001583	missense	11176	exon26			TCTGGGACAGCCT	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"""Zinc fingers, PHD-type"""	962	protein-coding gene	gene with protein product	"""TTF-I interacting peptide 5"""	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.5138T>C	chr12.hg19:g.56993526A>G	ENSP00000446880:p.Val1713Ala	105.0	0.0		55.0	4.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.497299	0.85069	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	D;D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31;-2.31	5.11	5.11	0.69529	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.071486	0.56097	D	0.000032	D	0.91971	0.7457	M	0.69248	2.105	0.58432	D	0.999997	D;D;D;D	0.71674	0.994;0.987;0.998;0.997	D;D;D;D	0.74023	0.954;0.958;0.982;0.941	D	0.91769	0.5426	10	0.45353	T	0.12	-15.8885	14.5836	0.68308	1.0:0.0:0.0:0.0	.	1711;1709;1713;1686	F8VU39;Q9UIF9-3;Q9UIF9;Q9UIF9-2	.;.;BAZ2A_HUMAN;.	A	1683;1681;1713;645;1711	ENSP00000368754:V1683A;ENSP00000179765:V1681A;ENSP00000446880:V1713A;ENSP00000448760:V645A;ENSP00000447941:V1711A	ENSP00000179765:V1681A	V	-	2	0	BAZ2A	55279793	0.986000	0.35501	1.000000	0.80357	0.997000	0.91878	8.500000	0.90498	2.223000	0.72356	0.533000	0.62120	GTC	.	.		0.483	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449	
BAZ2A	11176	hgsc.bcm.edu	37	12	56998905	56998905	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:56998905C>T	ENST00000551812.1	-	14	2899	c.2706G>A	c.(2704-2706)agG>agA	p.R902R	BAZ2A_ENST00000549884.1_Silent_p.R900R|BAZ2A_ENST00000179765.5_Silent_p.R870R|BAZ2A_ENST00000379441.3_Silent_p.R872R	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	902	DDT. {ECO:0000255|PROSITE- ProRule:PRU00063}.				chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						CCTTCAGCAGCCTGACCAGCA	0.552																																					p.R902R		Atlas-SNP	.											.	BAZ2A	263	.	0			c.G2706A						.						69.0	70.0	70.0					12																	56998905		2107	4231	6338	SO:0001819	synonymous_variant	11176	exon14			CAGCAGCCTGACC	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"""Zinc fingers, PHD-type"""	962	protein-coding gene	gene with protein product	"""TTF-I interacting peptide 5"""	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.2706G>A	chr12.hg19:g.56998905C>T		122.0	0.0		83.0	5.0	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Silent	SNP	ENST00000551812.1	hg19	CCDS44924.1																																																																																			.	.		0.552	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449	
SDR9C7	121214	hgsc.bcm.edu	37	12	57327864	57327864	+	Missense_Mutation	SNP	C	C	T	rs147708476		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:57327864C>T	ENST00000293502.1	-	1	325	c.182G>A	c.(181-183)gGa>gAa	p.G61E		NM_148897.2	NP_683695.1	Q8NEX9	DR9C7_HUMAN	short chain dehydrogenase/reductase family 9C, member 7	61					oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	retinol dehydrogenase activity (GO:0004745)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|pancreas(1)	7						TTTCTGGGATCCCTCCTCAGT	0.592																																					p.G61E		Atlas-SNP	.											.	SDR9C7	31	.	0			c.G182A						.	C	GLU/GLY	0,4406		0,0,2203	82.0	75.0	77.0		182	5.0	1.0	12	dbSNP_134	77	1,8599	1.2+/-3.3	0,1,4299	no	missense	SDR9C7	NM_148897.2	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	61/314	57327864	1,13005	2203	4300	6503	SO:0001583	missense	121214	exon1			TGGGATCCCTCCT	AY044434	CCDS8926.1	12q13.3	2014-09-04			ENSG00000170426	ENSG00000170426	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	29958	protein-coding gene	gene with protein product		609769				12234675, 19027726	Standard	NM_148897		Approved	SDR-O, RDHS	uc010sqw.2	Q8NEX9	OTTHUMG00000171004	ENST00000293502.1:c.182G>A	chr12.hg19:g.57327864C>T	ENSP00000293502:p.Gly61Glu	87.0	0.0		74.0	4.0	NM_148897	B3KVB4	Missense_Mutation	SNP	ENST00000293502.1	hg19	CCDS8926.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.569039	0.65765	0.0	1.16E-4	ENSG00000170426	ENST00000293502	T	0.50813	0.73	5.0	5.0	0.66597	NAD(P)-binding domain (1);	0.000000	0.64402	D	0.000014	T	0.66665	0.2812	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.68911	-0.5284	10	0.66056	D	0.02	.	17.2355	0.86997	0.0:1.0:0.0:0.0	.	61	Q8NEX9	DR9C7_HUMAN	E	61	ENSP00000293502:G61E	ENSP00000293502:G61E	G	-	2	0	SDR9C7	55614131	1.000000	0.71417	1.000000	0.80357	0.121000	0.20230	5.737000	0.68606	2.602000	0.87976	0.650000	0.86243	GGA	.	C|1.000;T|0.000		0.592	SDR9C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411211.1	NM_148897	
RDH16	8608	hgsc.bcm.edu	37	12	57351019	57351019	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:57351019C>T	ENST00000398138.3	-	1	1084	c.228G>A	c.(226-228)agG>agA	p.R76R	RDH16_ENST00000360752.4_5'UTR	NM_003708.3	NP_003699.3	O75452	RDH16_HUMAN	retinol dehydrogenase 16 (all-trans)	76					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	electron carrier activity (GO:0009055)|retinol dehydrogenase activity (GO:0004745)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)	16						CCGTCTCCAGCCTGTCTGAAG	0.602																																					p.R76R	GBM(179;741 2921 43105 45298)	Atlas-SNP	.											.	RDH16	33	.	0			c.G228A						.						68.0	73.0	71.0					12																	57351019		2203	4300	6503	SO:0001819	synonymous_variant	8608	exon1			CTCCAGCCTGTCT		CCDS41797.1	12q13.3	2011-09-14	2006-05-09			ENSG00000139547		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	29674	protein-coding gene	gene with protein product	"""microsomal NAD+ dependent retinol dehydrogenase 4"", ""short chain dehydrogenase/reductase family 9C, member 8"""		"""retinol dehydrogenase 16 (all-trans and 13-cis)"""			9677409, 10329026, 19027726	Standard	NM_003708		Approved	RODH-4, SDR9C8	uc001smi.4	O75452		ENST00000398138.3:c.228G>A	chr12.hg19:g.57351019C>T		188.0	0.0		114.0	5.0	NM_003708	Q9UNV2	Silent	SNP	ENST00000398138.3	hg19	CCDS41797.1																																																																																			.	.		0.602	RDH16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410898.1	NM_003708	
SHMT2	6472	hgsc.bcm.edu	37	12	57625269	57625269	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:57625269C>A	ENST00000328923.3	+	3	689	c.237C>A	c.(235-237)ttC>ttA	p.F79L	SHMT2_ENST00000393827.4_Intron|SHMT2_ENST00000553474.1_Missense_Mutation_p.F58L|SHMT2_ENST00000557487.1_Missense_Mutation_p.F79L|SHMT2_ENST00000449049.3_Missense_Mutation_p.F58L|SHMT2_ENST00000554600.1_3'UTR|SHMT2_ENST00000414700.3_Missense_Mutation_p.F58L	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	79					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	CCCAGAACTTCTGCAGCCGAG	0.622																																					p.F79L	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.C237A						.						42.0	43.0	42.0					12																	57625269		2203	4300	6503	SO:0001583	missense	6472	exon3			GAACTTCTGCAGC	AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.237C>A	chr12.hg19:g.57625269C>A	ENSP00000333667:p.Phe79Leu	179.0	0.0		148.0	80.0	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	hg19	CCDS8934.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.387402	0.82902	.	.	ENSG00000182199	ENST00000328923;ENST00000557487;ENST00000556689;ENST00000414700;ENST00000557703;ENST00000553529;ENST00000554310;ENST00000557427;ENST00000553474;ENST00000555773;ENST00000554975;ENST00000449049;ENST00000556737	T;T;T;T;T;T;T;T;T;T;T;T;T	0.44881	1.45;0.91;0.91;1.45;1.45;1.45;1.45;1.45;1.45;1.45;1.45;1.45;1.45	4.49	3.6	0.41247	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.62380	0.2423	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.992;1.0	T	0.65335	-0.6193	10	0.72032	D	0.01	.	9.0184	0.36184	0.0:0.8188:0.0:0.1812	.	79;79	Q8N1A5;P34897	.;GLYM_HUMAN	L	79;79;79;58;58;58;58;58;58;58;58;58;58	ENSP00000333667:F79L;ENSP00000452315:F79L;ENSP00000452035:F79L;ENSP00000406881:F58L;ENSP00000450452:F58L;ENSP00000452161:F58L;ENSP00000450893:F58L;ENSP00000452045:F58L;ENSP00000452419:F58L;ENSP00000451968:F58L;ENSP00000452404:F58L;ENSP00000413770:F58L;ENSP00000451495:F58L	ENSP00000333667:F79L	F	+	3	2	SHMT2	55911536	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	0.956000	0.29202	1.263000	0.44181	0.561000	0.74099	TTC	.	.		0.622	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412	
INHBC	3626	hgsc.bcm.edu	37	12	57828719	57828719	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:57828719T>C	ENST00000309668.2	+	1	177	c.50T>C	c.(49-51)gTg>gCg	p.V17A	RP11-756H6.1_ENST00000547552.1_lincRNA	NM_005538.2	NP_005529.1	P55103	INHBC_HUMAN	inhibin, beta C	17					growth (GO:0040007)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	transforming growth factor beta receptor binding (GO:0005160)			breast(2)|endometrium(1)|large_intestine(6)|liver(2)|lung(4)|prostate(1)	16						CCAACCACAGTGGCCACTCCC	0.597																																					p.V17A		Atlas-SNP	.											.	INHBC	28	.	0			c.T50C						.						37.0	38.0	38.0					12																	57828719		2203	4300	6503	SO:0001583	missense	3626	exon1			CCACAGTGGCCAC		CCDS8938.1	12q13	2008-02-05				ENSG00000175189			6068	protein-coding gene	gene with protein product		601233				7826378	Standard	NM_005538		Approved		uc001snv.1	P55103	OTTHUMG00000169994	ENST00000309668.2:c.50T>C	chr12.hg19:g.57828719T>C	ENSP00000308716:p.Val17Ala	114.0	0.0		68.0	4.0	NM_005538	A1L3Y2	Missense_Mutation	SNP	ENST00000309668.2	hg19	CCDS8938.1	.	.	.	.	.	.	.	.	.	.	T	1.176	-0.639654	0.03557	.	.	ENSG00000175189	ENST00000550133;ENST00000309668	T	0.80123	-1.34	4.62	1.04	0.20106	.	1.112010	0.06779	N	0.784892	T	0.74928	0.3781	L	0.58810	1.83	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.55717	-0.8097	10	0.23302	T	0.38	-1.9667	7.5577	0.27833	0.0:0.2773:0.0:0.7227	.	17	P55103	INHBC_HUMAN	A	17	ENSP00000308716:V17A	ENSP00000308716:V17A	V	+	2	0	INHBC	56114986	0.004000	0.15560	0.009000	0.14445	0.004000	0.04260	0.525000	0.22956	0.363000	0.24346	-0.411000	0.06167	GTG	.	.		0.597	INHBC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406770.1	NM_005538	
KIF5A	3798	hgsc.bcm.edu	37	12	57944131	57944131	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:57944131G>T	ENST00000455537.2	+	1	351	c.77G>T	c.(76-78)cGg>cTg	p.R26L	KIF5A_ENST00000286452.5_Missense_Mutation_p.R26L	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	26	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						GAGATTCTGCGGGGAGACAAG	0.607																																					p.R26L		Atlas-SNP	.											.	KIF5A	143	.	0			c.G77T						.						88.0	77.0	81.0					12																	57944131		2203	4300	6503	SO:0001583	missense	3798	exon1			TTCTGCGGGGAGA	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"""Kinesins"""	6323	protein-coding gene	gene with protein product		602821	"""spastic paraplegia 10 (autosomal dominant)"""	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.77G>T	chr12.hg19:g.57944131G>T	ENSP00000408979:p.Arg26Leu	154.0	0.0		97.0	4.0	NM_004984	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	hg19	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.100487	0.76983	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	T;T	0.72051	-0.62;-0.62	3.58	3.58	0.41010	Kinesin, motor domain (3);	0.060761	0.64402	D	0.000005	T	0.68165	0.2971	N	0.25245	0.725	0.33602	D	0.602487	D;P	0.57571	0.98;0.835	P;B	0.56823	0.807;0.224	T	0.72221	-0.4356	10	0.25106	T	0.35	.	15.2387	0.73452	0.0:0.0:1.0:0.0	.	26;26	B7Z2M7;Q12840	.;KIF5A_HUMAN	L	26	ENSP00000408979:R26L;ENSP00000286452:R26L	ENSP00000286452:R26L	R	+	2	0	KIF5A	56230398	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.941000	0.92964	2.317000	0.78254	0.645000	0.84053	CGG	.	.		0.607	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984	
USP15	9958	hgsc.bcm.edu	37	12	62783254	62783254	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:62783254G>T	ENST00000280377.5	+	12	1575	c.1517G>T	c.(1516-1518)tGt>tTt	p.C506F	USP15_ENST00000393654.3_Missense_Mutation_p.C481F|USP15_ENST00000353364.3_Missense_Mutation_p.C477F	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	506	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)		TTAGATCTTTGTACAGCATTG	0.299																																					p.C506F	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											USP15,NS,carcinoma,0,2	USP15	105	.	0			c.G1517T						.						106.0	110.0	109.0					12																	62783254		2203	4300	6503	SO:0001583	missense	9958	exon12			ATCTTTGTACAGC	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.1517G>T	chr12.hg19:g.62783254G>T	ENSP00000280377:p.Cys506Phe	149.0	0.0		89.0	5.0	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Missense_Mutation	SNP	ENST00000280377.5	hg19	CCDS58251.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.293338	0.80914	.	.	ENSG00000135655	ENST00000353364;ENST00000280377;ENST00000393654	T;T;T	0.19532	2.16;2.14;2.15	5.59	5.59	0.84812	RNA 3&apos (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta (1);	0.105195	0.64402	D	0.000003	T	0.44393	0.1291	L	0.55990	1.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.07947	-1.0746	9	.	.	.	-12.2114	19.5944	0.95530	0.0:0.0:1.0:0.0	.	506;477	Q9Y4E8;Q9Y4E8-2	UBP15_HUMAN;.	F	477;506;481	ENSP00000258123:C477F;ENSP00000280377:C506F;ENSP00000377264:C481F	.	C	+	2	0	USP15	61069521	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	6.524000	0.73791	2.642000	0.89623	0.561000	0.74099	TGT	.	.		0.299	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313	
CPM	1368	hgsc.bcm.edu	37	12	69279594	69279594	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:69279594A>G	ENST00000551568.1	-	3	296	c.236T>C	c.(235-237)gTg>gCg	p.V79A	CPM_ENST00000338356.3_Missense_Mutation_p.V79A|CPM_ENST00000546373.1_Missense_Mutation_p.V79A	NM_001005502.2|NM_198320.3	NP_001005502.1|NP_938079.1	P14384	CBPM_HUMAN	carboxypeptidase M	79					anatomical structure morphogenesis (GO:0009653)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)|prostate(2)	9	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			CATATTTGCCACGTATTTGAA	0.433																																					p.V79A		Atlas-SNP	.											.	CPM	30	.	0			c.T236C						.						177.0	171.0	173.0					12																	69279594		2203	4300	6503	SO:0001583	missense	1368	exon3			TTTGCCACGTATT	AF368463	CCDS8987.1	12q15	2012-02-10			ENSG00000135678	ENSG00000135678	3.4.17.12		2311	protein-coding gene	gene with protein product	"""renal carboxypeptidase"", ""urinary carboxypeptidase B"""	114860				8586455	Standard	NM_001874		Approved		uc001suq.3	P14384	OTTHUMG00000169300	ENST00000551568.1:c.236T>C	chr12.hg19:g.69279594A>G	ENSP00000448517:p.Val79Ala	134.0	0.0		98.0	4.0	NM_001005502	B2R800|Q9H2K9	Missense_Mutation	SNP	ENST00000551568.1	hg19	CCDS8987.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.472935	0.84640	.	.	ENSG00000135678	ENST00000551568;ENST00000338356;ENST00000546373;ENST00000548954;ENST00000548262	T;T;T;T;T	0.11277	2.79;2.79;2.79;2.79;2.79	5.08	5.08	0.68730	Peptidase M14, carboxypeptidase A (4);	0.062842	0.64402	D	0.000007	T	0.42040	0.1185	M	0.94063	3.49	0.58432	D	0.999999	D	0.60575	0.988	D	0.72338	0.977	T	0.54708	-0.8253	9	.	.	.	-19.74	12.6851	0.56944	1.0:0.0:0.0:0.0	.	79	P14384	CBPM_HUMAN	A	79	ENSP00000448517:V79A;ENSP00000339157:V79A;ENSP00000447255:V79A;ENSP00000446799:V79A;ENSP00000449911:V79A	.	V	-	2	0	CPM	67565861	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.302000	0.72788	2.048000	0.60808	0.455000	0.32223	GTG	.	.		0.433	CPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403355.1	NM_198320	
LGR5	8549	hgsc.bcm.edu	37	12	71955573	71955573	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:71955573C>T	ENST00000266674.5	+	8	1109	c.798C>T	c.(796-798)agC>agT	p.S266S	LGR5_ENST00000540815.2_Intron|LGR5_ENST00000536515.1_Silent_p.S194S			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	266					G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						GATTTCATAGCAACAATATCA	0.373																																					p.S266S		Atlas-SNP	.											.	LGR5	103	.	0			c.C798T						.						71.0	63.0	66.0					12																	71955573		2203	4300	6503	SO:0001819	synonymous_variant	8549	exon8			TCATAGCAACAAT	AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"""GPCR / Class A : Orphans"""	4504	protein-coding gene	gene with protein product		606667	"""G protein-coupled receptor 49"", ""leucine-rich repeat-containing G protein-coupled receptor 5"""	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	ENST00000266674.5:c.798C>T	chr12.hg19:g.71955573C>T		81.0	0.0		59.0	4.0	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Silent	SNP	ENST00000266674.5	hg19	CCDS9000.1																																																																																			.	.		0.373	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667	
DUSP6	1848	hgsc.bcm.edu	37	12	89744396	89744396	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:89744396G>T	ENST00000279488.7	-	2	2038	c.807C>A	c.(805-807)tcC>tcA	p.S269S	DUSP6_ENST00000547291.1_Silent_p.S144S|DUSP6_ENST00000308385.6_Intron|DUSP6_ENST00000547140.1_5'UTR	NM_001946.2	NP_001937.2	Q16828	DUS6_HUMAN	dual specificity phosphatase 6	269	Tyrosine-protein phosphatase.				cell differentiation (GO:0030154)|dorsal/ventral pattern formation (GO:0009953)|inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|regulation of endodermal cell fate specification (GO:0042663)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of heart growth (GO:0060420)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to organic cyclic compound (GO:0014070)|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)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)			large_intestine(5)|lung(8)|skin(2)|urinary_tract(1)	16						GGAAAAACTGGGACAGGTTTT	0.423																																					p.S269S	Colon(132;3456 5224)	Atlas-SNP	.											.	DUSP6	30	.	0			c.C807A						.						112.0	123.0	120.0					12																	89744396		2203	4300	6503	SO:0001819	synonymous_variant	1848	exon2			AAACTGGGACAGG	BC037236	CCDS9033.1, CCDS9034.1	12q22-q23	2011-06-09				ENSG00000139318		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3072	protein-coding gene	gene with protein product		602748				8626780, 9205128	Standard	NM_001946		Approved	MKP-3, PYST1	uc001tay.3	Q16828		ENST00000279488.7:c.807C>A	chr12.hg19:g.89744396G>T		105.0	0.0		68.0	4.0	NM_001946	O75109|Q53Y75|Q9BSH6	Silent	SNP	ENST00000279488.7	hg19	CCDS9033.1																																																																																			.	.		0.423	DUSP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406534.2	NM_001946, NM_022652	
ATP2B1	490	hgsc.bcm.edu	37	12	89997695	89997695	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:89997695G>T	ENST00000428670.3	-	17	3098	c.2642C>A	c.(2641-2643)cCg>cAg	p.P881Q	ATP2B1_ENST00000348959.3_Missense_Mutation_p.P881Q|ATP2B1_ENST00000393164.2_Missense_Mutation_p.P624Q|ATP2B1_ENST00000261173.2_Missense_Mutation_p.P881Q|ATP2B1_ENST00000359142.3_Missense_Mutation_p.P881Q			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	881					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						AGCCTTAAGCGGTGAGTCCTA	0.463																																					p.P881Q		Atlas-SNP	.											.	ATP2B1	191	.	0			c.C2642A						.						59.0	54.0	56.0					12																	89997695		2203	4300	6503	SO:0001583	missense	490	exon16			TTAAGCGGTGAGT	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"""ATPases / P-type"""	814	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 1"""	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.2642C>A	chr12.hg19:g.89997695G>T	ENSP00000392043:p.Pro881Gln	168.0	0.0		131.0	7.0	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	hg19	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.902002	0.92035	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	D;D;D;D;D	0.97665	-4.48;-4.48;-4.48;-4.48;-2.38	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.99165	0.9711	H	0.97390	3.995	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	D	0.98874	1.0767	10	0.87932	D	0	-16.217	20.3242	0.98691	0.0:0.0:1.0:0.0	.	881;881;881	P20020-3;P20020-2;P20020-6	.;.;.	Q	881;881;881;881;624	ENSP00000261173:P881Q;ENSP00000343599:P881Q;ENSP00000352054:P881Q;ENSP00000392043:P881Q;ENSP00000376869:P624Q	ENSP00000261173:P881Q	P	-	2	0	ATP2B1	88521826	1.000000	0.71417	0.978000	0.43139	0.994000	0.84299	9.813000	0.99286	2.882000	0.98803	0.655000	0.94253	CCG	.	.		0.463	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682	
BTG1	694	hgsc.bcm.edu	37	12	92538064	92538064	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:92538064G>A	ENST00000256015.3	-	2	669	c.308C>T	c.(307-309)aCa>aTa	p.T103I	RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000546975.1_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000551843.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	103					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				AACCCAGAGTGTGAGTTCACT	0.507			T	MYC	BCLL						OREG0022024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T103I		Atlas-SNP	.		Dom	yes		12	12q22	694	"""B-cell translocation gene 1, anti-proliferative"""		L	.	BTG1	30	.	0			c.C308T						.						120.0	119.0	119.0					12																	92538064		2203	4300	6503	SO:0001583	missense	694	exon2			CAGAGTGTGAGTT		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.308C>T	chr12.hg19:g.92538064G>A	ENSP00000256015:p.Thr103Ile	127.0	0.0	1291	83.0	4.0	NM_001731	P31607	Missense_Mutation	SNP	ENST00000256015.3	hg19	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	G	19.25	3.791487	0.70452	.	.	ENSG00000133639	ENST00000256015;ENST00000552315	T;T	0.36340	1.56;1.26	5.8	5.8	0.92144	Anti-proliferative protein (4);	0.000000	0.85682	D	0.000000	T	0.67097	0.2857	M	0.84773	2.715	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	T	0.71048	-0.4705	10	0.87932	D	0	-3.4656	20.0608	0.97674	0.0:0.0:1.0:0.0	.	103	P62324	BTG1_HUMAN	I	103;28	ENSP00000256015:T103I;ENSP00000447551:T28I	ENSP00000256015:T103I	T	-	2	0	BTG1	91062195	1.000000	0.71417	0.991000	0.47740	0.996000	0.88848	9.413000	0.97351	2.733000	0.93635	0.650000	0.86243	ACA	.	.		0.507	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1		
NTN4	59277	hgsc.bcm.edu	37	12	96180818	96180818	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:96180818T>C	ENST00000343702.4	-	2	932	c.484A>G	c.(484-486)Act>Gct	p.T162A	NTN4_ENST00000344911.4_Missense_Mutation_p.T125A|NTN4_ENST00000538383.1_Missense_Mutation_p.T125A|NTN4_ENST00000553059.1_Missense_Mutation_p.T162A	NM_021229.3	NP_067052.2	Q9HB63	NET4_HUMAN	netrin 4	162	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|extracellular matrix organization (GO:0030198)|neuron remodeling (GO:0016322)|regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling (GO:0060668)	basement membrane (GO:0005604)|plasma membrane (GO:0005886)				NS(2)|breast(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						GAGCAGTTAGTCGCAAAGTAC	0.493																																					p.T162A		Atlas-SNP	.											.	NTN4	67	.	0			c.A484G						.						102.0	96.0	98.0					12																	96180818		2203	4300	6503	SO:0001583	missense	59277	exon2			AGTTAGTCGCAAA	AF119916	CCDS9054.1	12q22	2013-03-01			ENSG00000074527	ENSG00000074527		"""Netrins"""	13658	protein-coding gene	gene with protein product	"""beta-netrin"", ""Netrin-4"""	610401				11038171	Standard	NM_021229		Approved		uc001tei.3	Q9HB63	OTTHUMG00000170290	ENST00000343702.4:c.484A>G	chr12.hg19:g.96180818T>C	ENSP00000340998:p.Thr162Ala	169.0	0.0		96.0	4.0	NM_021229	B2RNC2|Q658K9|Q7L3F1|Q7L9D6|Q7Z5B6|Q9BZP1|Q9NT44|Q9P133	Missense_Mutation	SNP	ENST00000343702.4	hg19	CCDS9054.1	.	.	.	.	.	.	.	.	.	.	T	4.683	0.127052	0.08931	.	.	ENSG00000074527	ENST00000343702;ENST00000344911;ENST00000538383;ENST00000553059;ENST00000547980	T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83	5.62	3.26	0.37387	Laminin, N-terminal (3);	0.447252	0.27043	N	0.021205	T	0.48607	0.1509	N	0.11560	0.145	0.18873	N	0.999986	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.28299	-1.0048	10	0.05620	T	0.96	.	9.8162	0.40853	0.0:0.2014:0.0:0.7986	.	162;162	Q9HB63-2;Q9HB63	.;NET4_HUMAN	A	162;125;125;162;125	ENSP00000340998:T162A;ENSP00000339436:T125A;ENSP00000444432:T125A;ENSP00000447292:T162A;ENSP00000447594:T125A	ENSP00000340998:T162A	T	-	1	0	NTN4	94704949	0.000000	0.05858	0.930000	0.37139	0.807000	0.45602	-0.077000	0.11394	0.976000	0.38417	0.454000	0.30748	ACT	.	.		0.493	NTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408372.1	NM_021229	
C12orf42	374470	hgsc.bcm.edu	37	12	103699815	103699815	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:103699815T>C	ENST00000378113.2	-	5	793	c.568A>G	c.(568-570)Ata>Gta	p.I190V	C12orf42_ENST00000548789.1_5'UTR|C12orf42_ENST00000548883.1_Missense_Mutation_p.I190V|C12orf42_ENST00000548048.1_Missense_Mutation_p.I123V|C12orf42_ENST00000315192.8_Intron	NM_001099336.1	NP_001092806.1	Q96LP6	CL042_HUMAN	chromosome 12 open reading frame 42	190										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)	22						CTGATGTGTATGCCCTGAGCC	0.458																																					p.I190V		Atlas-SNP	.											.	C12orf42	50	.	0			c.A568G						.						143.0	141.0	142.0					12																	103699815		1935	4128	6063	SO:0001583	missense	374470	exon5			TGTGTATGCCCTG	AK058052	CCDS44963.1	12q23.2	2012-05-30			ENSG00000179088	ENSG00000179088			24729	protein-coding gene	gene with protein product							Standard	NM_001099336		Approved	FLJ25323	uc001tjt.2	Q96LP6	OTTHUMG00000169988	ENST00000378113.2:c.568A>G	chr12.hg19:g.103699815T>C	ENSP00000367353:p.Ile190Val	132.0	0.0		93.0	4.0	NM_001099336	Q49A64|Q4G0S2	Missense_Mutation	SNP	ENST00000378113.2	hg19	CCDS44963.1	.	.	.	.	.	.	.	.	.	.	T	0.745	-0.775082	0.02951	.	.	ENSG00000179088	ENST00000548883;ENST00000548048;ENST00000378113;ENST00000552578	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	2.98	0.605	0.17553	.	3.852820	0.01124	N	0.005841	T	0.26919	0.0659	N	0.19112	0.55	0.09310	N	1	B	0.18013	0.025	B	0.10450	0.005	T	0.09164	-1.0687	10	0.16420	T	0.52	5.8231	4.6812	0.12736	0.0:0.2848:0.0:0.7152	.	190	Q96LP6	CL042_HUMAN	V	190;123;190;190	ENSP00000447908:I190V;ENSP00000449362:I123V;ENSP00000367353:I190V;ENSP00000447795:I190V	ENSP00000367353:I190V	I	-	1	0	C12orf42	102223945	0.001000	0.12720	0.000000	0.03702	0.016000	0.09150	0.400000	0.20932	0.128000	0.18479	0.449000	0.29647	ATA	.	.		0.458	C12orf42-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406754.1	NM_198521	
ALDH1L2	160428	hgsc.bcm.edu	37	12	105428158	105428158	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:105428158A>G	ENST00000258494.9	-	19	2304	c.2164T>C	c.(2164-2166)Ttc>Ctc	p.F722L	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	722	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						CCTTTGTTGAAAAATACTGCT	0.428																																					p.F722L		Atlas-SNP	.											.	ALDH1L2	71	.	0			c.T2164C						.						91.0	78.0	83.0					12																	105428158		2203	4300	6503	SO:0001583	missense	160428	exon19			TGTTGAAAAATAC	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"""Aldehyde dehydrogenases"""	26777	protein-coding gene	gene with protein product	"""mitochondrial 10-formyltetrahydrofolate dehydrogenase"""	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2164T>C	chr12.hg19:g.105428158A>G	ENSP00000258494:p.Phe722Leu	162.0	0.0		122.0	5.0	NM_001034173	Q3SY68|Q68D62|Q6AI55|Q8N922	Missense_Mutation	SNP	ENST00000258494.9	hg19	CCDS31891.1	.	.	.	.	.	.	.	.	.	.	A	33	5.205711	0.95033	.	.	ENSG00000136010	ENST00000258494	T	0.15372	2.43	5.36	5.36	0.76844	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);Aldehyde dehydrogenase, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.31420	0.0796	L	0.33293	1	0.80722	D	1	D	0.76494	0.999	D	0.70227	0.968	T	0.04373	-1.0956	10	0.87932	D	0	.	15.662	0.77193	1.0:0.0:0.0:0.0	.	722	Q3SY69	AL1L2_HUMAN	L	722	ENSP00000258494:F722L	ENSP00000258494:F722L	F	-	1	0	ALDH1L2	103952288	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.071000	0.93980	2.159000	0.67721	0.454000	0.30748	TTC	.	.		0.428	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294	
RFX4	5992	hgsc.bcm.edu	37	12	107109249	107109249	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:107109249G>A	ENST00000392842.1	+	11	1479	c.1065G>A	c.(1063-1065)ctG>ctA	p.L355L	RP11-482D24.3_ENST00000552415.1_RNA|RFX4_ENST00000229387.5_Silent_p.L261L|RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000357881.4_Silent_p.L364L	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	355	Necessary for dimerization.				cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						ACGTGGACCTGAACAGCATCA	0.493																																					p.L364L		Atlas-SNP	.											.	RFX4	218	.	0			c.G1092A						.						227.0	170.0	190.0					12																	107109249		2203	4300	6503	SO:0001819	synonymous_variant	5992	exon11			GGACCTGAACAGC	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.1065G>A	chr12.hg19:g.107109249G>A		186.0	0.0		96.0	4.0	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	hg19	CCDS9106.1																																																																																			.	.		0.493	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491	
BRAP	8315	hgsc.bcm.edu	37	12	112098444	112098444	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:112098444G>A	ENST00000327551.6	-	7	982	c.842C>T	c.(841-843)cCa>cTa	p.P281L	BRAP_ENST00000419234.4_Missense_Mutation_p.P311L|BRAP_ENST00000539060.1_Missense_Mutation_p.P132L			Q6UWU4	CF089_HUMAN	BRCA1 associated protein	205					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)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						TTCTTCTACTGGCTCGGGCGT	0.403																																					p.P311L	Pancreas(146;846 1904 7830 25130 26065)	Atlas-SNP	.											.	BRAP	42	.	0			c.C932T						.						168.0	161.0	163.0					12																	112098444		2203	4300	6503	SO:0001583	missense	8315	exon7			TCTACTGGCTCGG	AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234		"""RING-type (C3HC4) zinc fingers"""	1099	protein-coding gene	gene with protein product	"""impedes mitogenic signal propagation"", ""galectin-2-binding protein"""	604986				9497340, 19198608	Standard	XM_005253944		Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000327551.6:c.842C>T	chr12.hg19:g.112098444G>A	ENSP00000330813:p.Pro281Leu	172.0	0.0		121.0	5.0	NM_006768	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000327551.6	hg19		.	.	.	.	.	.	.	.	.	.	G	9.696	1.153209	0.21371	.	.	ENSG00000089234	ENST00000419234;ENST00000539060;ENST00000327551;ENST00000547043	T;T;T	0.28895	1.59;1.59;1.59	5.14	5.14	0.70334	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.39009	0.1062	N	0.17564	0.495	0.80722	D	1	D;D	0.71674	0.998;0.994	D;P	0.73708	0.981;0.795	T	0.15037	-1.0451	10	0.18276	T	0.48	-11.8702	18.9406	0.92604	0.0:0.0:1.0:0.0	.	132;311	B4DRM1;Q7Z569	.;BRAP_HUMAN	L	311;132;281;93	ENSP00000403524:P311L;ENSP00000441659:P132L;ENSP00000330813:P281L	ENSP00000330813:P281L	P	-	2	0	BRAP	110582827	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.251000	0.78297	2.551000	0.86045	0.563000	0.77884	CCA	.	.		0.403	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2		
OAS1	4938	hgsc.bcm.edu	37	12	113354434	113354434	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:113354434T>C	ENST00000202917.5	+	4	1038	c.775T>C	c.(775-777)Ttg>Ctg	p.L259L	OAS1_ENST00000551241.1_Silent_p.L259L|RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Silent_p.L259L|OAS1_ENST00000452357.2_Silent_p.L259L	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	259					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						TCGGACGGTCTTGGAATTAGT	0.473																																					p.L259L		Atlas-SNP	.											.	OAS1	128	.	0			c.T775C						.						119.0	108.0	112.0					12																	113354434		2203	4300	6503	SO:0001819	synonymous_variant	4938	exon4			ACGGTCTTGGAAT	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"""2',5'-oligoadenylate synthetase 1 (40-46 kD)"""	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.775T>C	chr12.hg19:g.113354434T>C		162.0	0.0		94.0	4.0	NM_001032409	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Silent	SNP	ENST00000202917.5	hg19	CCDS41838.1																																																																																			.	.		0.473	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2		
OAS1	4938	hgsc.bcm.edu	37	12	113357220	113357220	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:113357220G>T	ENST00000202917.5	+	6	1328	c.1065G>T	c.(1063-1065)gaG>gaT	p.E355D	OAS1_ENST00000551241.1_Intron|RP1-71H24.1_ENST00000552784.1_RNA|OAS1_ENST00000445409.2_Intron	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	355					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|protein oligomerization (GO:0051259)|purine nucleotide biosynthetic process (GO:0006164)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)|skin(1)	16						CAGACGATGAGACCGACGATC	0.498																																					p.E355D		Atlas-SNP	.											.	OAS1	128	.	0			c.G1065T						.						95.0	92.0	93.0					12																	113357220		2203	4300	6503	SO:0001583	missense	4938	exon6			CGATGAGACCGAC	X04371	CCDS31905.1, CCDS41838.1, CCDS44980.1	12q24.2	2014-05-21	2011-07-21				2.7.7.-		8086	protein-coding gene	gene with protein product		164350	"""2',5'-oligoadenylate synthetase 1 (40-46 kD)"""	OIAS		9344649, 9325053	Standard	XM_006719434		Approved	OIASI, IFI-4	uc001tud.3	P00973		ENST00000202917.5:c.1065G>T	chr12.hg19:g.113357220G>T	ENSP00000202917:p.Glu355Asp	93.0	0.0		77.0	5.0	NM_016816	A8K4N8|P04820|P29080|P29081|P78485|P78486|Q16700|Q16701|Q1PG42|Q3ZM01|Q53GC5|Q53YA4|Q6A1Z3|Q6IPC6|Q6P7N9|Q96J61	Missense_Mutation	SNP	ENST00000202917.5	hg19	CCDS41838.1	.	.	.	.	.	.	.	.	.	.	G	2.728	-0.265134	0.05754	.	.	ENSG00000089127	ENST00000202917	T	0.04706	3.57	2.29	-2.98	0.05513	.	.	.	.	.	T	0.01976	0.0062	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48186	-0.9057	9	0.13853	T	0.58	.	3.9457	0.09347	0.1466:0.0:0.2602:0.5932	.	355	P00973	OAS1_HUMAN	D	355	ENSP00000202917:E355D	ENSP00000202917:E355D	E	+	3	2	OAS1	111841603	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.568000	0.02144	-0.774000	0.04590	0.557000	0.71058	GAG	.	.		0.498	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2		
OAS2	4939	hgsc.bcm.edu	37	12	113443013	113443013	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:113443013C>T	ENST00000342315.4	+	7	1668	c.1454C>T	c.(1453-1455)gCc>gTc	p.A485V	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Missense_Mutation_p.A485V	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	485	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GTGCTTCCTGCCTTTAATGCA	0.522																																					p.A485V	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											.	OAS2	86	.	0			c.C1454T						.						84.0	67.0	72.0					12																	113443013		2203	4300	6503	SO:0001583	missense	4939	exon7			TTCCTGCCTTTAA	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"""2'-5'-oligoadenylate synthetase 2 (69-71 kD)"""			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.1454C>T	chr12.hg19:g.113443013C>T	ENSP00000342278:p.Ala485Val	80.0	0.0		65.0	4.0	NM_002535	A8K9T1|Q6PJ33|Q86XX8	Missense_Mutation	SNP	ENST00000342315.4	hg19	CCDS31906.1	.	.	.	.	.	.	.	.	.	.	.	18.14	3.556919	0.65425	.	.	ENSG00000111335	ENST00000342315;ENST00000392583	T;T	0.16324	2.35;2.35	4.43	3.53	0.40419	.	0.000000	0.47455	D	0.000225	T	0.40886	0.1135	M	0.83223	2.63	0.52099	D	0.999944	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	T	0.33033	-0.9884	10	0.87932	D	0	-25.5517	8.3525	0.32310	0.0:0.8911:0.0:0.1089	.	485;485	P29728;P29728-2	OAS2_HUMAN;.	V	485	ENSP00000342278:A485V;ENSP00000376362:A485V	ENSP00000342278:A485V	A	+	2	0	OAS2	111927396	0.991000	0.36638	0.453000	0.27007	0.100000	0.18952	2.553000	0.45837	1.216000	0.43427	0.655000	0.94253	GCC	.	.		0.522	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1		
DDX54	79039	hgsc.bcm.edu	37	12	113607596	113607596	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:113607596G>T	ENST00000306014.5	-	12	1420	c.1393C>A	c.(1393-1395)Cga>Aga	p.R465R	DDX54_ENST00000314045.7_Silent_p.R465R	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	465	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TTGAGGGGTCGGGCGAGGGTG	0.652																																					p.R465R		Atlas-SNP	.											.	DDX54	73	.	0			c.C1393A						.						35.0	35.0	35.0					12																	113607596		2203	4300	6503	SO:0001819	synonymous_variant	79039	exon12			GGGGTCGGGCGAG	AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"""DEAD-boxes"""	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.1393C>A	chr12.hg19:g.113607596G>T		124.0	0.0		82.0	4.0	NM_024072	Q86YT8|Q9BRZ1	Silent	SNP	ENST00000306014.5	hg19	CCDS31907.1																																																																																			.	.		0.652	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072	
KSR2	283455	hgsc.bcm.edu	37	12	117969500	117969500	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:117969500T>C	ENST00000339824.5	-	11	2427	c.1700A>G	c.(1699-1701)tAc>tGc	p.Y567C	KSR2_ENST00000425217.1_Missense_Mutation_p.Y538C|KSR2_ENST00000302438.5_Missense_Mutation_p.Y264C|KSR2_ENST00000545002.1_5'UTR			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	567					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTTGTATTTGTAGTAGTGGGA	0.502																																					p.Y538C		Atlas-SNP	.											.	KSR2	208	.	0			c.A1613G						.						95.0	100.0	99.0					12																	117969500		1993	4160	6153	SO:0001583	missense	283455	exon11			TATTTGTAGTAGT	AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.1700A>G	chr12.hg19:g.117969500T>C	ENSP00000339952:p.Tyr567Cys	68.0	0.0		40.0	4.0	NM_173598	A0PJT2|Q3B828|Q8N775	Missense_Mutation	SNP	ENST00000339824.5	hg19		.	.	.	.	.	.	.	.	.	.	T	16.14	3.039148	0.55003	.	.	ENSG00000171435	ENST00000425217;ENST00000339824;ENST00000302438;ENST00000542378	T;T;D	0.85955	-1.17;-1.17;-2.05	4.66	4.66	0.58398	.	0.059761	0.64402	D	0.000001	D	0.82577	0.5067	L	0.44542	1.39	0.49798	D	0.999824	P	0.50710	0.938	P	0.46049	0.502	T	0.83154	-0.0102	10	0.42905	T	0.14	.	14.2572	0.66060	0.0:0.0:0.0:1.0	.	567	Q6VAB6	KSR2_HUMAN	C	538;567;264;239	ENSP00000389715:Y538C;ENSP00000339952:Y567C;ENSP00000305466:Y264C	ENSP00000305466:Y264C	Y	-	2	0	KSR2	116453883	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.691000	0.47010	1.934000	0.56057	0.402000	0.26972	TAC	.	.		0.502	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598	
WSB2	55884	hgsc.bcm.edu	37	12	118472835	118472835	+	Silent	SNP	C	C	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:118472835C>G	ENST00000315436.3	-	8	1149	c.1008G>C	c.(1006-1008)ggG>ggC	p.G336G	WSB2_ENST00000536738.1_5'Flank|WSB2_ENST00000542304.1_Silent_p.G111G|WSB2_ENST00000544233.1_Silent_p.G126G|WSB2_ENST00000441406.2_Silent_p.G353G|WSB2_ENST00000535496.1_Silent_p.G338G	NM_001278557.1|NM_018639.3	NP_001265486.1|NP_061109.1	Q9NYS7	WSB2_HUMAN	WD repeat and SOCS box containing 2	336					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGCAGCAAAGCCCATTGGTCA	0.478											OREG0022175	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G336G		Atlas-SNP	.											.	WSB2	32	.	0			c.G1008C						.						81.0	78.0	79.0					12																	118472835		2203	4300	6503	SO:0001819	synonymous_variant	55884	exon8			GCAAAGCCCATTG	AF038187	CCDS9186.1, CCDS61251.1, CCDS61252.1	12q24.23	2013-01-09	2011-01-25		ENSG00000176871	ENSG00000176871		"""WD repeat domain containing"""	19222	protein-coding gene	gene with protein product			"""WD repeat and SOCS box-containing 2"""			12076535	Standard	NM_018639		Approved	SBA2, MGC10210	uc001twr.2	Q9NYS7	OTTHUMG00000168885	ENST00000315436.3:c.1008G>C	chr12.hg19:g.118472835C>G		113.0	0.0	1488	117.0	9.0	NM_018639	B4DIE6|B4DPV6|Q9NRX9	Silent	SNP	ENST00000315436.3	hg19	CCDS9186.1																																																																																			.	.		0.478	WSB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401515.1	NM_018639	
RAB35	11021	hgsc.bcm.edu	37	12	120536685	120536685	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:120536685T>C	ENST00000229340.5	-	5	595	c.407A>G	c.(406-408)tAc>tGc	p.Y136C	RAB35_ENST00000534951.1_Intron|RAB35_ENST00000432953.2_Intron|RAB35_ENST00000543364.1_5'UTR	NM_001167606.1|NM_006861.6	NP_001161078.1|NP_006852.1	Q15286	RAB35_HUMAN	RAB35, member RAS oncogene family	136					antigen processing and presentation (GO:0019882)|cellular response to nerve growth factor stimulus (GO:1990090)|cytokinesis (GO:0000910)|endosomal transport (GO:0016197)|GTP catabolic process (GO:0006184)|neuron projection development (GO:0031175)|plasma membrane to endosome transport (GO:0048227)|protein localization (GO:0008104)|protein localization to endosome (GO:0036010)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cell projection membrane (GO:0031253)|clathrin-coated endocytic vesicle (GO:0045334)|coated pit (GO:0005905)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intercellular bridge (GO:0045171)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|ovary(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.248)		GGCGAATTTGTAGGCATCTTC	0.597																																					p.Y136C		Atlas-SNP	.											.	RAB35	18	.	0			c.A407G						.						118.0	125.0	123.0					12																	120536685		2101	4214	6315	SO:0001583	missense	11021	exon5			AATTTGTAGGCAT	X79781	CCDS41846.1, CCDS53836.1	12q24	2008-07-28			ENSG00000111737	ENSG00000111737		"""RAB, member RAS oncogene"""	9774	protein-coding gene	gene with protein product		604199					Standard	NM_001167606		Approved	H-ray	uc009zww.2	Q15286	OTTHUMG00000169159	ENST00000229340.5:c.407A>G	chr12.hg19:g.120536685T>C	ENSP00000229340:p.Tyr136Cys	144.0	0.0		94.0	4.0	NM_006861	B2R6E0|B4E390	Missense_Mutation	SNP	ENST00000229340.5	hg19	CCDS41846.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.958352	0.53400	.	.	ENSG00000111737	ENST00000229340;ENST00000538903	T;T	0.76709	-1.04;-1.04	4.77	4.77	0.60923	Small GTP-binding protein domain (1);	0.120787	0.64402	D	0.000017	T	0.64527	0.2606	N	0.14661	0.345	0.80722	D	1	B	0.25667	0.131	B	0.25614	0.062	T	0.66184	-0.5987	10	0.87932	D	0	.	14.4506	0.67382	0.0:0.0:0.0:1.0	.	136	Q15286	RAB35_HUMAN	C	136;120	ENSP00000229340:Y136C;ENSP00000443994:Y120C	ENSP00000229340:Y136C	Y	-	2	0	RAB35	119021068	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.858000	0.69532	1.980000	0.57719	0.533000	0.62120	TAC	.	.		0.597	RAB35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402599.2		
PXN	5829	hgsc.bcm.edu	37	12	120651722	120651722	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:120651722C>A	ENST00000228307.7	-	11	1573	c.1432G>T	c.(1432-1434)Ggc>Tgc	p.G478C	PXN_ENST00000267257.7_Missense_Mutation_p.G492C|PXN-AS1_ENST00000542265.1_RNA|PXN-AS1_ENST00000539446.1_RNA|PXN-AS1_ENST00000535200.1_RNA|PXN_ENST00000538144.1_5'UTR|PXN_ENST00000397506.3_Missense_Mutation_p.G290C|PXN_ENST00000424649.2_Missense_Mutation_p.G444C|PXN_ENST00000536957.1_Missense_Mutation_p.G476C|PXN_ENST00000458477.2_Missense_Mutation_p.G311C	NM_001080855.2	NP_001074324.1	P49023	PAXI_HUMAN	paxillin	478	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				activation of MAPK activity (GO:0000187)|branching morphogenesis of an epithelial tube (GO:0048754)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|growth hormone receptor signaling pathway (GO:0060396)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|muscle contraction (GO:0006936)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of cell shape (GO:0008360)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	beta-catenin binding (GO:0008013)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGGGCGCAGCCGCCACACTTG	0.602																																					p.G492C		Atlas-SNP	.											.	PXN	69	.	0			c.G1474T						.						29.0	39.0	35.0					12																	120651722		2033	4178	6211	SO:0001583	missense	5829	exon10			CGCAGCCGCCACA	U14588	CCDS44996.1, CCDS44997.1, CCDS44998.1, CCDS58281.1	12q24	2006-01-23			ENSG00000089159	ENSG00000089159			9718	protein-coding gene	gene with protein product		602505				7534286	Standard	NM_001080855		Approved		uc001txv.3	P49023	OTTHUMG00000169169	ENST00000228307.7:c.1432G>T	chr12.hg19:g.120651722C>A	ENSP00000228307:p.Gly478Cys	103.0	0.0		71.0	4.0	NM_001243756	B2RAI3|B7ZMB4|O14970|O14971|O60360|Q5HYA4	Missense_Mutation	SNP	ENST00000228307.7	hg19	CCDS44997.1	.	.	.	.	.	.	.	.	.	.	C	33	5.255159	0.95336	.	.	ENSG00000089159	ENST00000458477;ENST00000228307;ENST00000424649;ENST00000536957;ENST00000267257;ENST00000397506;ENST00000331257;ENST00000541856	D;D;D;D;D;D	0.89050	-2.46;-2.46;-2.46;-2.46;-2.46;-2.46	5.51	5.51	0.81932	Zinc finger, LIM-type (5);	.	.	.	.	D	0.96352	0.8810	H	0.94264	3.515	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;0.998;0.998;0.999	D	0.97152	0.9832	9	0.87932	D	0	.	19.4166	0.94703	0.0:1.0:0.0:0.0	.	444;492;290;478	P49023-2;P49023-3;E7EMK8;P49023	.;.;.;PAXI_HUMAN	C	311;478;444;476;492;290;106;203	ENSP00000395536:G311C;ENSP00000228307:G478C;ENSP00000391283:G444C;ENSP00000443887:G476C;ENSP00000267257:G492C;ENSP00000380643:G290C	ENSP00000228307:G478C	G	-	1	0	PXN	119136105	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	7.675000	0.84002	2.598000	0.87819	0.561000	0.74099	GGC	.	.		0.602	PXN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402679.4	NM_002859	
NCOR2	9612	hgsc.bcm.edu	37	12	124914172	124914172	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:124914172A>G	ENST00000405201.1	-	10	1136	c.1136T>C	c.(1135-1137)cTc>cCc	p.L379P	NCOR2_ENST00000397355.1_Missense_Mutation_p.L379P|NCOR2_ENST00000404621.1_Missense_Mutation_p.L378P|NCOR2_ENST00000429285.2_Missense_Mutation_p.L378P|NCOR2_ENST00000356219.3_Missense_Mutation_p.L379P|NCOR2_ENST00000404121.2_5'UTR			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	379					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		CTGCTCTGAGAGGCCATCGAT	0.662																																					p.L379P		Atlas-SNP	.											.	NCOR2	475	.	0			c.T1136C						.						28.0	33.0	32.0					12																	124914172		2096	4222	6318	SO:0001583	missense	9612	exon12			TCTGAGAGGCCAT	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.1136T>C	chr12.hg19:g.124914172A>G	ENSP00000384018:p.Leu379Pro	159.0	0.0		103.0	5.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	A	11.30	1.598702	0.28445	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000429285;ENST00000458234;ENST00000420698	T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88	3.57	3.57	0.40892	.	0.256680	0.30510	N	0.009470	T	0.60996	0.2312	M	0.71206	2.165	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74023	0.96;0.96;0.982	T	0.66344	-0.5947	10	0.87932	D	0	-32.9859	12.6178	0.56586	1.0:0.0:0.0:0.0	.	378;379;379	C9J0Q5;C9J239;C9JFD3	.;.;.	P	379;378;379;379;379;378;379;379	ENSP00000384018:L379P;ENSP00000384202:L378P;ENSP00000348551:L379P;ENSP00000380513:L379P;ENSP00000400281:L378P;ENSP00000402808:L379P;ENSP00000405367:L379P	ENSP00000348551:L379P	L	-	2	0	NCOR2	123480125	1.000000	0.71417	0.995000	0.50966	0.642000	0.38348	9.127000	0.94417	1.609000	0.50190	0.260000	0.18958	CTC	.	.		0.662	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
NCOR2	9612	hgsc.bcm.edu	37	12	124957667	124957667	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:124957667A>G	ENST00000405201.1	-	4	422	c.422T>C	c.(421-423)cTg>cCg	p.L141P	NCOR2_ENST00000397355.1_Missense_Mutation_p.L141P|NCOR2_ENST00000404621.1_Missense_Mutation_p.L141P|NCOR2_ENST00000429285.2_Missense_Mutation_p.L141P|NCOR2_ENST00000356219.3_Missense_Mutation_p.L141P|NCOR2_ENST00000404121.2_5'UTR			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	141					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		CTTGCCCGTCAGGCTACGGTC	0.612																																					p.L141P		Atlas-SNP	.											.	NCOR2	475	.	0			c.T422C						.						35.0	40.0	38.0					12																	124957667		1971	4140	6111	SO:0001583	missense	9612	exon6			CCCGTCAGGCTAC	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.422T>C	chr12.hg19:g.124957667A>G	ENSP00000384018:p.Leu141Pro	64.0	0.0		59.0	4.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.183|6.183	0.401919|0.401919	0.11696|0.11696	.|.	.|.	ENSG00000196498|ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000429285;ENST00000458234;ENST00000420698;ENST00000448008|ENST00000542927	T;T;T;T;T;T|.	0.35048|.	2.06;2.32;2.06;2.32;2.32;1.33|.	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	0.169966|.	0.41605|.	D|.	0.000857|.	T|.	0.67951|.	0.2948|.	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	D;D;D|.	0.65815|.	0.976;0.991;0.995|.	P;P;P|.	0.55161|.	0.454;0.593;0.77|.	T|.	0.65923|.	-0.6050|.	10|.	0.72032|.	D|.	0.01|.	-24.9984|-24.9984	15.6599|15.6599	0.77178|0.77178	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	141;141;141|.	C9J0Q5;C9J239;C9JFD3|.	.;.;.|.	P|R	141;141;141;141;141;141;141;141;62|64	ENSP00000384018:L141P;ENSP00000384202:L141P;ENSP00000348551:L141P;ENSP00000380513:L141P;ENSP00000400281:L141P;ENSP00000402808:L141P|.	ENSP00000348551:L141P|.	L|X	-|-	2|1	0|0	NCOR2|NCOR2	123523620|123523620	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.196000|0.196000	0.23810|0.23810	5.716000|5.716000	0.68437|0.68437	2.099000|2.099000	0.63709|0.63709	0.459000|0.459000	0.35465|0.35465	CTG|TGA	.	.		0.612	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
TMEM132B	114795	hgsc.bcm.edu	37	12	126139253	126139253	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:126139253G>A	ENST00000299308.3	+	9	3242	c.3234G>A	c.(3232-3234)atG>atA	p.M1078I	TMEM132B_ENST00000535886.1_Missense_Mutation_p.M590I	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	1078						integral component of membrane (GO:0016021)		p.M1078I(1)		NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		AAGACCAGATGTAAACTCCTT	0.408																																					p.M1078I		Atlas-SNP	.											TMEM132B,rectum,carcinoma,0,1	TMEM132B	207	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3234A						.						63.0	58.0	59.0					12																	126139253		1865	4084	5949	SO:0001583	missense	114795	exon9			CCAGATGTAAACT	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.3234G>A	chr12.hg19:g.126139253G>A	ENSP00000299308:p.Met1078Ile	128.0	0.0		70.0	3.0	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	hg19	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	G	13.31	2.198471	0.38806	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.08807	3.83;3.05	5.81	5.81	0.92471	.	0.131674	0.53938	D	0.000055	T	0.09949	0.0244	L	0.34521	1.04	0.43766	D	0.99628	B	0.28933	0.228	B	0.28011	0.085	T	0.17289	-1.0374	10	0.38643	T	0.18	.	20.0838	0.97793	0.0:0.0:1.0:0.0	.	1078	Q14DG7	T132B_HUMAN	I	1078;590	ENSP00000299308:M1078I;ENSP00000440436:M590I	ENSP00000299308:M1078I	M	+	3	0	TMEM132B	124705206	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.845000	0.92153	2.741000	0.93983	0.655000	0.94253	ATG	.	.		0.408	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
STX2	2054	hgsc.bcm.edu	37	12	131311746	131311746	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:131311746A>G	ENST00000392373.2	-	2	191	c.97T>C	c.(97-99)Ttc>Ctc	p.F33L	STX2_ENST00000261653.6_Missense_Mutation_p.F33L	NM_194356.2	NP_919337.1	P32856	STX2_HUMAN	syntaxin 2	33					acrosome reaction (GO:0007340)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|intracellular protein transport (GO:0006886)|organ morphogenesis (GO:0009887)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|signal transduction (GO:0007165)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)	calcium-dependent protein binding (GO:0048306)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)	16	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)		ACCTGATGGAAGAAATCATCC	0.443																																					p.F33L		Atlas-SNP	.											.	STX2	66	.	0			c.T97C						.						136.0	126.0	129.0					12																	131311746		2203	4300	6503	SO:0001583	missense	2054	exon2			GATGGAAGAAATC	D14582	CCDS9269.1, CCDS9270.1	12q24	2008-02-05	2006-04-25	2006-04-25	ENSG00000111450	ENSG00000111450			3403	protein-coding gene	gene with protein product		132350	"""epimorphin"""	STX2B, STX2C, STX2A, EPIM		8938452, 15943887	Standard	NM_001980		Approved	EPM	uc001uio.4	P32856	OTTHUMG00000168365	ENST00000392373.2:c.97T>C	chr12.hg19:g.131311746A>G	ENSP00000376178:p.Phe33Leu	125.0	0.0		83.0	4.0	NM_194356	Q86VW8	Missense_Mutation	SNP	ENST00000392373.2	hg19	CCDS9270.1	.	.	.	.	.	.	.	.	.	.	A	14.90	2.672813	0.47781	.	.	ENSG00000111450	ENST00000261653;ENST00000392373	T;T	0.19806	2.12;2.12	4.65	4.65	0.58169	t-SNARE (1);Syntaxin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.29061	0.0722	L	0.55990	1.75	0.58432	D	0.999999	B;B;P	0.41102	0.379;0.219;0.738	B;B;P	0.48368	0.097;0.07;0.575	T	0.02087	-1.1216	10	0.36615	T	0.2	-16.5748	12.0741	0.53634	1.0:0.0:0.0:0.0	.	33;33;33	P32856-3;P32856-2;P32856	.;.;STX2_HUMAN	L	33	ENSP00000261653:F33L;ENSP00000376178:F33L	ENSP00000261653:F33L	F	-	1	0	STX2	129877699	1.000000	0.71417	1.000000	0.80357	0.031000	0.12232	5.647000	0.67923	1.743000	0.51761	0.481000	0.45027	TTC	.	.		0.443	STX2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399455.2	NM_194356	
POLE	5426	hgsc.bcm.edu	37	12	133256186	133256186	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:133256186T>C	ENST00000320574.5	-	6	518	c.475A>G	c.(475-477)Act>Gct	p.T159A	POLE_ENST00000535270.1_Missense_Mutation_p.T132A	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	159					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|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)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	TCCTCCACAGTGTGGAAGGAC	0.493								DNA polymerases (catalytic subunits)																													p.T159A		Atlas-SNP	.											.	POLE	416	.	0			c.A475G						.						130.0	105.0	114.0					12																	133256186		2203	4300	6503	SO:0001583	missense	5426	exon6			CCACAGTGTGGAA		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.475A>G	chr12.hg19:g.133256186T>C	ENSP00000322570:p.Thr159Ala	110.0	0.0		78.0	4.0	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	hg19	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	T	12.82	2.051712	0.36181	.	.	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000376577	T;T;T	0.09817	2.94;2.94;2.94	5.95	5.95	0.96441	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.25158	0.0611	M	0.82193	2.58	0.46798	D	0.999204	P;P	0.41366	0.747;0.639	P;P	0.48921	0.46;0.595	T	0.01393	-1.1366	10	0.62326	D	0.03	.	10.2046	0.43105	0.2556:0.0:0.0:0.7444	.	132;159	F5H1D6;Q07864	.;DPOE1_HUMAN	A	159;170;132;94	ENSP00000322570:T159A;ENSP00000406383:T170A;ENSP00000445753:T132A	ENSP00000322570:T159A	T	-	1	0	POLE	131766259	1.000000	0.71417	0.997000	0.53966	0.171000	0.22731	4.835000	0.62781	2.279000	0.76181	0.402000	0.26972	ACT	.	.		0.493	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
ZNF140	7699	hgsc.bcm.edu	37	12	133682950	133682950	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr12:133682950G>T	ENST00000355557.2	+	5	2370	c.1087G>T	c.(1087-1089)Ggt>Tgt	p.G363C	ZNF140_ENST00000544426.1_Missense_Mutation_p.G260C|ZNF140_ENST00000440550.2_3'UTR	NM_003440.2	NP_003431.2	P52738	ZN140_HUMAN	zinc finger protein 140	363					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)|large_intestine(4)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.114)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		TGATGAATGTGGTAAAGTTTT	0.403																																					p.G363C		Atlas-SNP	.											.	ZNF140	18	.	0			c.G1087T						.						113.0	107.0	109.0					12																	133682950		2203	4300	6503	SO:0001583	missense	7699	exon5			GAATGTGGTAAAG	U09368	CCDS9282.1, CCDS73550.1	12q24.33	2013-01-08	2006-06-13		ENSG00000196387	ENSG00000196387		"""Zinc fingers, C2H2-type"", ""-"""	12925	protein-coding gene	gene with protein product		604082	"""zinc finger protein 140 (clone pHZ-39)"""			7557990	Standard	XR_245353		Approved	pHZ-39	uc001ulo.3	P52738	OTTHUMG00000167942	ENST00000355557.2:c.1087G>T	chr12.hg19:g.133682950G>T	ENSP00000347755:p.Gly363Cys	113.0	0.0		88.0	7.0	NM_003440	D3DXJ3|Q05CP6|Q8IV75	Missense_Mutation	SNP	ENST00000355557.2	hg19	CCDS9282.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.087520	0.76642	.	.	ENSG00000196387	ENST00000355557;ENST00000544426;ENST00000433577	T;T	0.01516	4.81;4.81	3.85	3.85	0.44370	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35708	N	0.003036	T	0.13200	0.0320	M	0.90309	3.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.01834	-1.1264	10	0.87932	D	0	.	15.0534	0.71894	0.0:0.0:1.0:0.0	.	363	P52738	ZN140_HUMAN	C	363;260;154	ENSP00000347755:G363C;ENSP00000445411:G260C	ENSP00000347755:G363C	G	+	1	0	ZNF140	132193023	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.688000	0.61715	2.139000	0.66308	0.563000	0.77884	GGT	.	.		0.403	ZNF140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397169.1	NM_003440	
MPHOSPH8	54737	hgsc.bcm.edu	37	13	20237233	20237233	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:20237233C>T	ENST00000361479.5	+	9	2054	c.1986C>T	c.(1984-1986)gtC>gtT	p.V662V	MPHOSPH8_ENST00000414242.2_Silent_p.V662V	NM_017520.3	NP_059990.2	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	662					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of DNA methylation (GO:0044030)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nuclear nucleosome (GO:0000788)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	methylated histone binding (GO:0035064)			breast(2)|endometrium(1)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)		TTGTAAATGTCCAGCAAAGCA	0.398																																					p.V662V		Atlas-SNP	.											.	MPHOSPH8	58	.	0			c.C1986T						.						140.0	144.0	142.0					13																	20237233		2203	4300	6503	SO:0001819	synonymous_variant	54737	exon9			AAATGTCCAGCAA	AK056785, AJ293409	CCDS9287.1	13q12.11	2013-01-10			ENSG00000196199	ENSG00000196199		"""Ankyrin repeat domain containing"""	29810	protein-coding gene	gene with protein product		611626				8885239	Standard	NM_017520		Approved	mpp8, HSMPP8	uc001umh.3	Q99549	OTTHUMG00000016498	ENST00000361479.5:c.1986C>T	chr13.hg19:g.20237233C>T		99.0	0.0		73.0	4.0	NM_017520	B7Z6F9|Q5JPE5|Q5JTQ0|Q86TK3|Q96MK4|Q9BTP1	Silent	SNP	ENST00000361479.5	hg19	CCDS9287.1																																																																																			.	.		0.398	MPHOSPH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044028.2	NM_017520	
SGCG	6445	hgsc.bcm.edu	37	13	23898576	23898576	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:23898576T>C	ENST00000218867.3	+	8	896	c.772T>C	c.(772-774)Tca>Cca	p.S258P	SGCG_ENST00000545013.1_Missense_Mutation_p.S258P|SGCG_ENST00000537476.1_Missense_Mutation_p.S258P	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	258					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		CTCTGGCAGCTCACAGAGCCT	0.562																																					p.S258P		Atlas-SNP	.											.	SGCG	64	.	0			c.T772C						.						113.0	92.0	99.0					13																	23898576		2203	4300	6503	SO:0001583	missense	6445	exon8			GGCAGCTCACAGA	U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"""Maghrebian myopathy (autosomal recessive)"", ""35kD dystrophin-associated glycoprotein"", ""limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)"", ""gamma sarcoglycan"""	608896	"""sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"""	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.772T>C	chr13.hg19:g.23898576T>C	ENSP00000218867:p.Ser258Pro	144.0	0.0		79.0	4.0	NM_000231	Q32M32|Q5T9J6	Missense_Mutation	SNP	ENST00000218867.3	hg19	CCDS9299.1	.	.	.	.	.	.	.	.	.	.	T	9.539	1.112812	0.20795	.	.	ENSG00000102683	ENST00000218867;ENST00000537476;ENST00000545013	D;D;D	0.94862	-3.54;-3.54;-3.54	5.28	-1.61	0.08399	.	0.452001	0.25164	N	0.032654	D	0.88190	0.6370	L	0.52364	1.645	0.09310	N	0.999993	B	0.06786	0.001	B	0.12156	0.007	T	0.75844	-0.3174	10	0.40728	T	0.16	-2.8715	1.4353	0.02342	0.1175:0.201:0.2427:0.4388	.	258	Q13326	SGCG_HUMAN	P	258	ENSP00000218867:S258P;ENSP00000444100:S258P;ENSP00000442232:S258P	ENSP00000218867:S258P	S	+	1	0	SGCG	22796576	0.014000	0.17966	0.032000	0.17829	0.300000	0.27592	0.752000	0.26362	-0.241000	0.09681	0.454000	0.30748	TCA	.	.		0.562	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231	
SACS	26278	hgsc.bcm.edu	37	13	23910918	23910918	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:23910918T>C	ENST00000382292.3	-	9	7370	c.7097A>G	c.(7096-7098)gAg>gGg	p.E2366G	SACS_ENST00000402364.1_Missense_Mutation_p.E1616G|SACS_ENST00000382298.3_Missense_Mutation_p.E2366G			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2366					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TGGTGCCGCCTCAAAATTTAA	0.348																																					p.E2366G		Atlas-SNP	.											.	SACS	871	.	0			c.A7097G						.						51.0	52.0	52.0					13																	23910918		2203	4298	6501	SO:0001583	missense	26278	exon10			GCCGCCTCAAAAT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.7097A>G	chr13.hg19:g.23910918T>C	ENSP00000371729:p.Glu2366Gly	131.0	0.0		98.0	4.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	11.46	1.645094	0.29246	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.95342	-3.68;-3.68;-3.68	5.68	5.68	0.88126	.	0.111701	0.64402	D	0.000009	D	0.90342	0.6978	L	0.29908	0.895	0.44539	D	0.997491	B	0.27559	0.181	B	0.24541	0.054	D	0.87717	0.2570	10	0.35671	T	0.21	.	15.9354	0.79698	0.0:0.0:0.0:1.0	.	2366	Q9NZJ4	SACS_HUMAN	G	2366;1616;2366	ENSP00000371729:E2366G;ENSP00000385844:E1616G;ENSP00000371735:E2366G	ENSP00000371729:E2366G	E	-	2	0	SACS	22808918	1.000000	0.71417	0.997000	0.53966	0.170000	0.22686	7.698000	0.84413	2.182000	0.69389	0.533000	0.62120	GAG	.	.		0.348	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
NBEA	26960	hgsc.bcm.edu	37	13	36046654	36046654	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:36046654T>C	ENST00000400445.3	+	41	7100	c.6566T>C	c.(6565-6567)tTc>tCc	p.F2189S	NBEA_ENST00000540320.1_Missense_Mutation_p.F2189S|NBEA_ENST00000310336.4_Missense_Mutation_p.F2189S|NBEA_ENST00000379939.2_Missense_Mutation_p.F2186S	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2189					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)		GATTCTGCCTTCAAGAAGATC	0.488																																					p.F2189S		Atlas-SNP	.											.	NBEA	340	.	0			c.T6566C						.						91.0	90.0	90.0					13																	36046654		1991	4172	6163	SO:0001583	missense	26960	exon41			CTGCCTTCAAGAA	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.6566T>C	chr13.hg19:g.36046654T>C	ENSP00000383295:p.Phe2189Ser	100.0	0.0		63.0	4.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.160120	0.78226	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.52295	0.67;0.67;0.67;0.67	5.51	5.51	0.81932	PH-BEACH domain (1);	0.000000	0.85682	D	0.000000	T	0.59238	0.2179	M	0.64997	1.995	0.80722	D	1	B;D	0.58268	0.218;0.982	B;P	0.54312	0.128;0.748	T	0.60535	-0.7244	10	0.45353	T	0.12	.	15.6376	0.76966	0.0:0.0:0.0:1.0	.	2189;2186	Q8NFP9;Q5T321	NBEA_HUMAN;.	S	2189;2189;2186;2189;816	ENSP00000440951:F2189S;ENSP00000383295:F2189S;ENSP00000369271:F2186S;ENSP00000308534:F2189S	ENSP00000308534:F2189S	F	+	2	0	NBEA	34944654	1.000000	0.71417	1.000000	0.80357	0.656000	0.38851	8.040000	0.89188	2.090000	0.63153	0.460000	0.39030	TTC	.	.		0.488	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
SUPT20H	55578	hgsc.bcm.edu	37	13	37591496	37591496	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:37591496T>C	ENST00000350612.6	-	23	2098	c.1878A>G	c.(1876-1878)ccA>ccG	p.P626P	SUPT20H_ENST00000475892.1_Silent_p.P705P|SUPT20H_ENST00000356185.3_Silent_p.P627P|SUPT20H_ENST00000464744.1_Silent_p.P627P|SUPT20H_ENST00000360252.4_Silent_p.P627P	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	626					autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										GTGAACCACCTGGAAGCTATT	0.343																																					p.P627P		Atlas-SNP	.											.	.	.	.	0			c.A1881G						.						80.0	76.0	77.0					13																	37591496		2203	4300	6503	SO:0001819	synonymous_variant	55578	exon23			ACCACCTGGAAGC	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"""p38 interacting protein"", ""transcription factor (p38 interacting protein)"""	613417	"""chromosome 13 open reading frame 19"", ""family with sequence similarity 48, member A"""	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.1878A>G	chr13.hg19:g.37591496T>C		207.0	0.0		137.0	6.0	NM_017569	E7ER46|Q71RF3|Q9Y6A6	Silent	SNP	ENST00000350612.6	hg19	CCDS31959.1																																																																																			.	.		0.343	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569	
FOXO1	2308	hgsc.bcm.edu	37	13	41239792	41239792	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:41239792G>A	ENST00000379561.5	-	1	942	c.558C>T	c.(556-558)atC>atT	p.I186I		NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	186					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blood vessel development (GO:0001568)|cellular glucose homeostasis (GO:0001678)|cellular response to cold (GO:0070417)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hyperoxia (GO:0071455)|cellular response to insulin stimulus (GO:0032869)|cellular response to nitric oxide (GO:0071732)|cellular response to oxidative stress (GO:0034599)|cellular response to starvation (GO:0009267)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|regulation of cell proliferation (GO:0042127)|regulation of energy homeostasis (GO:2000505)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|protein phosphatase 2A binding (GO:0051721)|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 (GO:0043565)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		TCCACTCGTAGATCTGCGACA	0.652																																					p.I186I		Atlas-SNP	.											.	FOXO1	110	.	0			c.C558T						.						33.0	27.0	29.0					13																	41239792		2203	4300	6503	SO:0001819	synonymous_variant	2308	exon1			CTCGTAGATCTGC		CCDS9371.1	13q14.1	2011-08-01	2007-05-02	2007-05-02	ENSG00000150907	ENSG00000150907		"""Forkhead boxes"""	3819	protein-coding gene	gene with protein product		136533	"""forkhead homolog in rhabdomyosarcoma"""	FKHR, FOXO1A		8275086, 15057823	Standard	NM_002015		Approved	FKH1	uc001uxl.4	Q12778	OTTHUMG00000016775	ENST00000379561.5:c.558C>T	chr13.hg19:g.41239792G>A		333.0	1.0		182.0	65.0	NM_002015	O43523|Q5VYC7|Q6NSK6	Silent	SNP	ENST00000379561.5	hg19	CCDS9371.1																																																																																			.	.		0.652	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015	
NAA16	79612	hgsc.bcm.edu	37	13	41946891	41946891	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:41946891T>C	ENST00000379406.3	+	17	2404	c.2080T>C	c.(2080-2082)Tct>Cct	p.S694P	NAA16_ENST00000497143.1_3'UTR	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	694					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						AATGCTGCAGTCTGTCAAACG	0.303																																					p.S694P		Atlas-SNP	.											.	NAA16	74	.	0			c.T2080C						.						84.0	86.0	85.0					13																	41946891		2202	4298	6500	SO:0001583	missense	79612	exon17			CTGCAGTCTGTCA	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"""N(alpha)-acetyltransferase subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	26164	protein-coding gene	gene with protein product			"""NMDA receptor regulated 1-like"""	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.2080T>C	chr13.hg19:g.41946891T>C	ENSP00000368716:p.Ser694Pro	121.0	0.0		89.0	4.0	NM_024561	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	hg19	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.454492	0.84209	.	.	ENSG00000172766	ENST00000379406	T	0.46819	0.86	5.3	5.3	0.74995	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000002	T	0.70753	0.3260	M	0.82323	2.585	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.75207	-0.3399	10	0.56958	D	0.05	-12.276	15.23	0.73381	0.0:0.0:0.0:1.0	.	694	Q6N069	NAA16_HUMAN	P	694	ENSP00000368716:S694P	ENSP00000368716:S694P	S	+	1	0	NAA16	40844891	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.127000	0.77210	2.006000	0.58801	0.533000	0.62120	TCT	.	.		0.303	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527	
KCTD4	386618	hgsc.bcm.edu	37	13	45768400	45768400	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:45768400G>T	ENST00000379108.1	-	1	452	c.303C>A	c.(301-303)ccC>ccA	p.P101P	KCTD4_ENST00000405872.1_Silent_p.P101P|GTF2F2_ENST00000340473.6_Intron			Q8WVF5	KCTD4_HUMAN	potassium channel tetramerization domain containing 4	101	BTB.				protein homooligomerization (GO:0051260)					breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8		Lung NSC(96;6.55e-05)|Breast(139;0.00378)|Prostate(109;0.00438)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000249)|BRCA - Breast invasive adenocarcinoma(63;0.207)		GAAACCCTTCGGGCAATAGAA	0.458																																					p.P101P		Atlas-SNP	.											.	KCTD4	18	.	0			c.C303A						.						105.0	103.0	104.0					13																	45768400		2203	4300	6503	SO:0001819	synonymous_variant	386618	exon2			CCCTTCGGGCAAT	BC018063	CCDS9396.1	13q14.12-q14.13	2013-06-20	2013-06-20		ENSG00000180332	ENSG00000180332			23227	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 4"""				Standard	NM_198404		Approved	bA321C24.3	uc001uzx.4	Q8WVF5	OTTHUMG00000016844	ENST00000379108.1:c.303C>A	chr13.hg19:g.45768400G>T		133.0	0.0		99.0	4.0	NM_198404	Q5W0P9	Silent	SNP	ENST00000379108.1	hg19	CCDS9396.1																																																																																			.	.		0.458	KCTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044757.1		
FAM124A	220108	hgsc.bcm.edu	37	13	51855022	51855022	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:51855022A>G	ENST00000322475.8	+	4	1406	c.1271A>G	c.(1270-1272)gAc>gGc	p.D424G	FAM124A_ENST00000280057.6_Missense_Mutation_p.D460G	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	424										breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		TCCTCATCGGACCTGTCTGTG	0.612																																					p.D460G		Atlas-SNP	.											.	FAM124A	61	.	0			c.A1379G						.						53.0	54.0	54.0					13																	51855022		2203	4300	6503	SO:0001583	missense	220108	exon5			CATCGGACCTGTC	AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.1271A>G	chr13.hg19:g.51855022A>G	ENSP00000324625:p.Asp424Gly	77.0	0.0		68.0	4.0	NM_145019	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	hg19	CCDS55900.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.337995	0.81911	.	.	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.60424	0.19;0.21	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000002	T	0.73690	0.3619	M	0.65498	2.005	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.87578	0.982;0.998	T	0.76852	-0.2806	10	0.72032	D	0.01	-10.6226	14.1985	0.65686	1.0:0.0:0.0:0.0	.	424;460	Q86V42;Q86V42-2	F124A_HUMAN;.	G	424;460	ENSP00000324625:D424G;ENSP00000280057:D460G	ENSP00000280057:D460G	D	+	2	0	FAM124A	50753023	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	6.735000	0.74806	1.949000	0.56562	0.533000	0.62120	GAC	.	.		0.612	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019	
THSD1	55901	hgsc.bcm.edu	37	13	52971400	52971400	+	Nonsense_Mutation	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:52971400T>A	ENST00000258613.4	-	3	1166	c.988A>T	c.(988-990)Aag>Tag	p.K330*	RNY4P24_ENST00000362735.1_RNA|THSD1_ENST00000544466.1_Intron|THSD1_ENST00000349258.4_Nonsense_Mutation_p.K330*	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	330					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		CACTCCTCCTTTGCAGAAAAA	0.328																																					p.K330X		Atlas-SNP	.											.	THSD1	89	.	0			c.A988T						.						53.0	55.0	55.0					13																	52971400		2203	4300	6503	SO:0001587	stop_gained	55901	exon3			CCTCCTTTGCAGA	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain 1"""				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.988A>T	chr13.hg19:g.52971400T>A	ENSP00000258613:p.Lys330*	139.0	0.0		99.0	4.0	NM_199263	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Nonsense_Mutation	SNP	ENST00000258613.4	hg19	CCDS9432.1	.	.	.	.	.	.	.	.	.	.	T	41	8.929775	0.99006	.	.	ENSG00000136114	ENST00000349258;ENST00000258613;ENST00000378095	.	.	.	5.32	4.12	0.48240	.	0.194119	0.44285	D	0.000466	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-39.6606	8.09	0.30795	0.0:0.1584:0.0:0.8416	.	.	.	.	X	330	.	ENSP00000258613:K330X	K	-	1	0	THSD1	51869401	1.000000	0.71417	0.948000	0.38648	0.996000	0.88848	2.627000	0.46469	2.007000	0.58848	0.459000	0.35465	AAG	.	.		0.328	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3		
VPS36	51028	hgsc.bcm.edu	37	13	53008984	53008984	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:53008984T>C	ENST00000378060.4	-	5	412	c.385A>G	c.(385-387)Aga>Gga	p.R129G	VPS36_ENST00000480923.1_5'UTR	NM_001282168.1|NM_001282169.1|NM_016075.2	NP_001269097.1|NP_001269098.1|NP_057159.2	Q86VN1	VPS36_HUMAN	vacuolar protein sorting 36 homolog (S. cerevisiae)	129	GLUE C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00828}.				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 (GO:0005768)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	17		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)		TCCCATCTTCTTTGTGTCATT	0.338																																					p.R129G		Atlas-SNP	.											.	VPS36	38	.	0			c.A385G						.						175.0	186.0	182.0					13																	53008984		2203	4300	6503	SO:0001583	missense	51028	exon5			ATCTTCTTTGTGT	AF151903	CCDS9434.1, CCDS73577.1	13q14.13	2008-02-05	2007-01-12	2005-08-02	ENSG00000136100	ENSG00000136100			20312	protein-coding gene	gene with protein product		610903	"""chromosome 13 open reading frame 9"", ""vacuolar protein sorting 36 homolog (yeast)"""	C13orf9		11278625, 15755741	Standard	NM_016075		Approved	CGI-145, Eap45	uc001vgs.3	Q86VN1	OTTHUMG00000016964	ENST00000378060.4:c.385A>G	chr13.hg19:g.53008984T>C	ENSP00000367299:p.Arg129Gly	134.0	0.0		98.0	4.0	NM_016075	A8K125|Q3ZCV7|Q5H9S1|Q5VXB6|Q9H8Z5|Q9Y3E3	Missense_Mutation	SNP	ENST00000378060.4	hg19	CCDS9434.1	.	.	.	.	.	.	.	.	.	.	.	16.66	3.186142	0.57909	.	.	ENSG00000136100	ENST00000378060	.	.	.	5.76	4.57	0.56435	.	0.134024	0.64402	D	0.000002	T	0.60431	0.2268	M	0.77616	2.38	0.54753	D	0.99998	B	0.31655	0.334	B	0.20577	0.03	T	0.62215	-0.6901	9	0.66056	D	0.02	-21.5871	12.2152	0.54402	0.0:0.0:0.2677:0.7323	.	129	Q86VN1	VPS36_HUMAN	G	129	.	ENSP00000367299:R129G	R	-	1	2	VPS36	51906985	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.214000	0.51161	0.988000	0.38734	0.460000	0.39030	AGA	.	.		0.338	VPS36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045059.3		
PIBF1	10464	hgsc.bcm.edu	37	13	73428292	73428292	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:73428292A>G	ENST00000326291.6	+	10	1659	c.1321A>G	c.(1321-1323)Agg>Ggg	p.R441G	AL391384.1_ENST00000408054.1_RNA	NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	441						centrosome (GO:0005813)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		GCTCTTAGACAGGTAAGCATC	0.333																																					p.R441G		Atlas-SNP	.											.	PIBF1	65	.	0			c.A1321G						.						88.0	90.0	89.0					13																	73428292		2203	4300	6503	SO:0001630	splice_region_variant	10464	exon10			TTAGACAGGTAAG	AF330046	CCDS31991.1	13q21.33	2014-02-20	2007-10-17	2007-10-17	ENSG00000083535	ENSG00000083535			23352	protein-coding gene	gene with protein product	"""progesterone-induced blocking factor 1"""	607532	"""chromosome 13 open reading frame 24"""	C13orf24		11935316	Standard	NM_006346		Approved	CEP90	uc001vjc.3	Q8WXW3	OTTHUMG00000017071	ENST00000326291.6:c.1322+1A>G	chr13.hg19:g.73428292A>G		100.0	0.0		80.0	4.0	NM_006346	O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	Missense_Mutation	SNP	ENST00000326291.6	hg19	CCDS31991.1	.	.	.	.	.	.	.	.	.	.	A	13.82	2.350367	0.41599	.	.	ENSG00000083535	ENST00000326291	T	0.22743	1.94	4.88	3.78	0.43462	.	0.059270	0.64402	D	0.000001	T	0.16811	0.0404	L	0.38175	1.15	0.33061	D	0.534035	B;B	0.24721	0.11;0.11	B;B	0.24848	0.056;0.056	T	0.15037	-1.0451	10	0.72032	D	0.01	-4.0035	9.2173	0.37355	0.5912:0.4088:0.0:0.0	.	441;441	Q8WXW3;Q4G0R1	PIBF1_HUMAN;.	G	441	ENSP00000317144:R441G	ENSP00000317144:R441G	R	+	1	2	PIBF1	72326293	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	4.148000	0.58085	1.840000	0.53500	0.455000	0.32223	AGG	.	.		0.333	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045255.1	NM_006346	Missense_Mutation
UCHL3	7347	hgsc.bcm.edu	37	13	76135000	76135000	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:76135000T>C	ENST00000377595.3	+	3	196	c.166T>C	c.(166-168)Ttt>Ctt	p.F56L	RP11-29G8.3_ENST00000563635.1_RNA	NM_001270952.1|NM_006002.4	NP_001257881.1|NP_005993.1	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)	56					protein catabolic process (GO:0030163)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(2)|lung(3)|skin(1)	7				GBM - Glioblastoma multiforme(99;0.0125)		CTTACTTCTCTTTCCTATTAC	0.348																																					p.F56L		Atlas-SNP	.											.	UCHL3	9	.	0			c.T166C						.						102.0	92.0	95.0					13																	76135000		2203	4300	6503	SO:0001583	missense	7347	exon3			CTTCTCTTTCCTA	M30496	CCDS9453.1, CCDS73586.1	13q21.33	2008-02-05			ENSG00000118939	ENSG00000118939	3.2.1.15		12515	protein-coding gene	gene with protein product		603090				2530630	Standard	NM_001270952		Approved		uc001vjq.4	P15374	OTTHUMG00000017090	ENST00000377595.3:c.166T>C	chr13.hg19:g.76135000T>C	ENSP00000366819:p.Phe56Leu	135.0	0.0		105.0	5.0	NM_006002	B2R970|Q5TBK8|Q6IBE9	Missense_Mutation	SNP	ENST00000377595.3	hg19	CCDS9453.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.909940	0.92107	.	.	ENSG00000118939	ENST00000377595;ENST00000377589	T	0.69175	-0.38	5.81	5.81	0.92471	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (4);	0.000000	0.85682	D	0.000000	D	0.85630	0.5741	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88762	0.3258	10	0.72032	D	0.01	-11.1154	16.1773	0.81862	0.0:0.0:0.0:1.0	.	56	P15374	UCHL3_HUMAN	L	56;13	ENSP00000366819:F56L	ENSP00000366813:F13L	F	+	1	0	UCHL3	75033001	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.698000	0.84413	2.217000	0.71921	0.482000	0.46254	TTT	.	.		0.348	UCHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045292.2	NM_006002	
DCT	1638	hgsc.bcm.edu	37	13	95131305	95131305	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:95131305T>C	ENST00000377028.5	-	1	618	c.205A>G	c.(205-207)Agg>Ggg	p.R69G	DCT_ENST00000446125.1_Missense_Mutation_p.R69G	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	69					cell development (GO:0048468)|developmental pigmentation (GO:0048066)|epidermis development (GO:0008544)|melanin biosynthetic process from tyrosine (GO:0006583)|positive regulation of neuroblast proliferation (GO:0002052)|ventricular zone neuroblast division (GO:0021847)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)	copper ion binding (GO:0005507)|dopachrome isomerase activity (GO:0004167)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		CTCCAGGGCCTTGTGTCGGCT	0.607																																					p.R69G		Atlas-SNP	.											.	DCT	186	.	0			c.A205G						.						89.0	77.0	81.0					13																	95131305		2203	4300	6503	SO:0001583	missense	1638	exon1			AGGGCCTTGTGTC	D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	5.3.3.12		2709	protein-coding gene	gene with protein product	"""dopachrome delta-isomerase"""	191275	"""tyrosine-related protein 2"""	TYRP2		8306979	Standard	NM_001922		Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.205A>G	chr13.hg19:g.95131305T>C	ENSP00000366227:p.Arg69Gly	147.0	0.0		97.0	4.0	NM_001129889	Q09GT4	Missense_Mutation	SNP	ENST00000377028.5	hg19	CCDS9470.1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.470693	0.43942	.	.	ENSG00000080166	ENST00000377028;ENST00000446125	D;D	0.84146	-1.81;-1.81	5.22	2.68	0.31781	.	0.103582	0.64402	D	0.000004	D	0.83580	0.5285	M	0.76574	2.34	0.38912	D	0.957554	P;P	0.47302	0.893;0.835	B;B	0.41813	0.367;0.363	T	0.80730	-0.1252	10	0.24483	T	0.36	-19.6539	13.7089	0.62656	0.0:0.0:0.5326:0.4674	.	69;69	Q09GT4;P40126	.;TYRP2_HUMAN	G	69	ENSP00000366227:R69G;ENSP00000392762:R69G	ENSP00000366227:R69G	R	-	1	2	DCT	93929306	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	2.493000	0.45320	0.275000	0.22094	-0.299000	0.09455	AGG	.	.		0.607	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3		
HS6ST3	266722	hgsc.bcm.edu	37	13	97484904	97484904	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:97484904T>C	ENST00000376705.2	+	2	892	c.868T>C	c.(868-870)Tgg>Cgg	p.W290R		NM_153456.3	NP_703157.2	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	290					heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)	integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)			NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					TGGGGATGACTGGTCTGGGGT	0.567																																					p.W290R		Atlas-SNP	.											.	HS6ST3	54	.	0			c.T868C						.						64.0	58.0	60.0					13																	97484904		2203	4300	6503	SO:0001583	missense	266722	exon2			GATGACTGGTCTG	AF539426	CCDS9481.1	13q32.2	2007-12-04			ENSG00000185352	ENSG00000185352		"""Sulfotransferases, membrane-bound"""	19134	protein-coding gene	gene with protein product		609401					Standard	NM_153456		Approved		uc001vmw.4	Q8IZP7	OTTHUMG00000017232	ENST00000376705.2:c.868T>C	chr13.hg19:g.97484904T>C	ENSP00000365895:p.Trp290Arg	105.0	0.0		93.0	4.0	NM_153456	Q5W0L0|Q68CW6	Missense_Mutation	SNP	ENST00000376705.2	hg19	CCDS9481.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.118453	0.77323	.	.	ENSG00000185352	ENST00000376705	T	0.74421	-0.84	5.6	5.6	0.85130	.	0.281587	0.38663	N	0.001619	D	0.88317	0.6404	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90578	0.4527	10	0.87932	D	0	-16.9535	15.7645	0.78114	0.0:0.0:0.0:1.0	.	290	Q8IZP7	H6ST3_HUMAN	R	290	ENSP00000365895:W290R	ENSP00000365895:W290R	W	+	1	0	HS6ST3	96282905	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.036000	0.88901	2.108000	0.64289	0.528000	0.53228	TGG	.	.		0.567	HS6ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045517.2	NM_153456	
DOCK9	23348	hgsc.bcm.edu	37	13	99519792	99519792	+	Splice_Site	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:99519792T>C	ENST00000376460.1	-	30	3255		c.e30-2		DOCK9_ENST00000339416.2_Splice_Site|DOCK9_ENST00000442173.1_Splice_Site|DOCK9_ENST00000448493.2_Splice_Site	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9						blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AAAGAGGGTCTGCAGGAAGAA	0.358																																					.		Atlas-SNP	.											.	DOCK9	311	.	0			c.3178-2A>G						.						140.0	131.0	134.0					13																	99519792		1830	4081	5911	SO:0001630	splice_region_variant	23348	exon31			AGGGTCTGCAGGA	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"""Pleckstrin homology (PH) domain containing"""	14132	protein-coding gene	gene with protein product	"""zizimin1"""	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.3175-2A>G	chr13.hg19:g.99519792T>C		45.0	0.0		38.0	4.0	NM_015296	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Splice_Site	SNP	ENST00000376460.1	hg19	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.605059	0.87157	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6438	0.85155	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DOCK9	98317793	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.625000	0.83145	2.333000	0.79357	0.533000	0.62120	.	.	.		0.358	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296	Intron
COL4A1	1282	hgsc.bcm.edu	37	13	110822983	110822983	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:110822983T>C	ENST00000375820.4	-	42	3774	c.3653A>G	c.(3652-3654)cAg>cGg	p.Q1218R		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1218	Triple-helical region.				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)			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)			CGGCTGTCCCTGGGGCCCCGG	0.647																																					p.Q1218R		Atlas-SNP	.											.	COL4A1	372	.	0			c.A3653G						.						24.0	28.0	27.0					13																	110822983		2203	4300	6503	SO:0001583	missense	1282	exon42			TGTCCCTGGGGCC	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.3653A>G	chr13.hg19:g.110822983T>C	ENSP00000364979:p.Gln1218Arg	86.0	0.0		50.0	4.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	T	11.51	1.660271	0.29515	.	.	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198	D	0.96073	-3.9	5.21	3.98	0.46160	.	0.191118	0.45867	D	0.000323	D	0.89584	0.6757	N	0.04245	-0.25	0.80722	D	1	P	0.37370	0.592	P	0.44447	0.45	D	0.87795	0.2621	10	0.19590	T	0.45	.	13.314	0.60397	0.0:0.0:0.2064:0.7936	.	1218	P02462	CO4A1_HUMAN	R	861;1218;867	ENSP00000364979:Q1218R	ENSP00000364973:Q861R	Q	-	2	0	COL4A1	109620984	1.000000	0.71417	0.973000	0.42090	0.367000	0.29736	2.304000	0.43655	1.970000	0.57323	0.529000	0.55759	CAG	.	.		0.647	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
COL4A1	1282	hgsc.bcm.edu	37	13	110833649	110833649	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:110833649T>C	ENST00000375820.4	-	29	2304	c.2183A>G	c.(2182-2184)cAg>cGg	p.Q728R		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	728	Triple-helical region.				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)			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)			CTTCTGGCCCTGCACACCTGG	0.547																																					p.Q728R		Atlas-SNP	.											.	COL4A1	372	.	0			c.A2183G						.						69.0	66.0	67.0					13																	110833649		2203	4300	6503	SO:0001583	missense	1282	exon29			TGGCCCTGCACAC	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.2183A>G	chr13.hg19:g.110833649T>C	ENSP00000364979:p.Gln728Arg	173.0	0.0		85.0	5.0	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	T	10.64	1.407870	0.25378	.	.	ENSG00000187498	ENST00000375820	D	0.92911	-3.13	4.96	3.1	0.35709	.	0.484707	0.21821	N	0.068614	D	0.87783	0.6264	N	0.16368	0.405	0.80722	D	1	D	0.53462	0.96	P	0.53593	0.73	T	0.82088	-0.0630	10	0.15499	T	0.54	.	10.8468	0.46746	0.0:0.0:0.4054:0.5946	.	728	P02462	CO4A1_HUMAN	R	728	ENSP00000364979:Q728R	ENSP00000364979:Q728R	Q	-	2	0	COL4A1	109631650	0.983000	0.35010	0.056000	0.19401	0.497000	0.33675	1.881000	0.39638	0.587000	0.29643	0.533000	0.62120	CAG	.	.		0.547	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
TUBGCP3	10426	hgsc.bcm.edu	37	13	113242240	113242240	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr13:113242240T>C	ENST00000261965.3	-	1	241	c.55A>G	c.(55-57)Agg>Ggg	p.R19G	TUBGCP3_ENST00000375669.3_Missense_Mutation_p.R19G	NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	19					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|single fertilization (GO:0007338)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|polar microtubule (GO:0005827)|spindle (GO:0005819)	gamma-tubulin binding (GO:0043015)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|urinary_tract(1)	25	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)					CCCAGGATCCTGCAGCACAGG	0.701																																					p.R19G		Atlas-SNP	.											.	TUBGCP3	74	.	0			c.A55G						.						31.0	29.0	30.0					13																	113242240		2203	4299	6502	SO:0001583	missense	10426	exon1			GGATCCTGCAGCA	AF042378	CCDS9525.1, CCDS66584.1, CCDS73599.1	13q34	2008-07-18			ENSG00000126216	ENSG00000126216			18598	protein-coding gene	gene with protein product	"""spindle pole body protein"""					9566967, 9566969	Standard	XM_005268293		Approved	GCP3, Spc98p, SPBC98	uc001vse.1	Q96CW5	OTTHUMG00000017367	ENST00000261965.3:c.55A>G	chr13.hg19:g.113242240T>C	ENSP00000261965:p.Arg19Gly	108.0	0.0		94.0	4.0	NM_006322	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Missense_Mutation	SNP	ENST00000261965.3	hg19	CCDS9525.1	.	.	.	.	.	.	.	.	.	.	t	16.76	3.213535	0.58452	.	.	ENSG00000126216	ENST00000261965;ENST00000375669	T;T	0.24723	1.84;1.84	4.4	3.54	0.40534	.	0.274242	0.35349	N	0.003274	T	0.29423	0.0733	M	0.66939	2.045	0.38890	D	0.957099	B;P;B;B	0.42296	0.02;0.775;0.078;0.02	B;B;B;B	0.39660	0.01;0.306;0.033;0.014	T	0.24297	-1.0164	10	0.59425	D	0.04	-24.9492	13.3616	0.60659	0.0:0.0:0.8348:0.1652	.	19;19;19;19	B4DYP7;Q96CW5-3;Q96CW5-2;Q96CW5	.;.;.;GCP3_HUMAN	G	19	ENSP00000261965:R19G;ENSP00000364821:R19G	ENSP00000261965:R19G	R	-	1	2	TUBGCP3	112290241	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	2.977000	0.49297	0.814000	0.34374	-0.650000	0.03912	AGG	.	.		0.701	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322	
TEP1	7011	hgsc.bcm.edu	37	14	20874483	20874483	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:20874483T>C	ENST00000262715.5	-	3	684	c.644A>G	c.(643-645)gAg>gGg	p.E215G	TEP1_ENST00000556935.1_Missense_Mutation_p.E215G	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	215					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		CACCTCCTCCTCCTCTCCCAA	0.493																																					p.E215G		Atlas-SNP	.											.	TEP1	224	.	0			c.A644G						.						118.0	104.0	109.0					14																	20874483		2203	4300	6503	SO:0001583	missense	7011	exon3			TCCTCCTCCTCTC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.644A>G	chr14.hg19:g.20874483T>C	ENSP00000262715:p.Glu215Gly	107.0	0.0		92.0	4.0	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.641459	0.29157	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.64260	0.47;-0.09	4.94	3.78	0.43462	.	0.239904	0.29293	N	0.012566	T	0.56171	0.1967	L	0.58101	1.795	0.47374	D	0.999405	B;B	0.33612	0.419;0.295	B;B	0.33690	0.168;0.081	T	0.58418	-0.7640	10	0.72032	D	0.01	-6.0532	8.9738	0.35924	0.0:0.0:0.187:0.813	.	215;215	G3V5X7;Q99973	.;TEP1_HUMAN	G	215	ENSP00000262715:E215G;ENSP00000452574:E215G	ENSP00000262715:E215G	E	-	2	0	TEP1	19944323	0.284000	0.24287	0.763000	0.31416	0.397000	0.30659	2.045000	0.41250	0.994000	0.38892	0.533000	0.62120	GAG	.	.		0.493	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
OSGEP	55644	hgsc.bcm.edu	37	14	20920172	20920172	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:20920172G>T	ENST00000206542.4	-	3	793	c.372C>A	c.(370-372)acC>acA	p.T124T	OSGEP_ENST00000556252.1_5'UTR|RP11-203M5.7_ENST00000555435.1_RNA|OSGEP_ENST00000555656.1_5'Flank|OSGEP_ENST00000554249.1_5'Flank	NM_017807.3	NP_060277.1			O-sialoglycoprotein endopeptidase											endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(4)|stomach(1)	11	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0231)|READ - Rectum adenocarcinoma(17;0.196)		CGGTTGGGCTGGTGGCTCCAG	0.512																																					p.T124T		Atlas-SNP	.											.	OSGEP	31	.	0			c.C372A						.						75.0	67.0	70.0					14																	20920172		2203	4300	6503	SO:0001819	synonymous_variant	55644	exon3			TGGGCTGGTGGCT	AB050442	CCDS9549.1	14q12	2010-03-19			ENSG00000092094	ENSG00000092094	3.4.24.57		18028	protein-coding gene	gene with protein product		610107				12039036	Standard	NM_017807		Approved	PRSMG1, GCPL1, OSGEP1, KAE1	uc001vxf.3	Q9NPF4	OTTHUMG00000029543	ENST00000206542.4:c.372C>A	chr14.hg19:g.20920172G>T		159.0	0.0		132.0	6.0	NM_017807		Silent	SNP	ENST00000206542.4	hg19	CCDS9549.1																																																																																			.	.		0.512	OSGEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073635.3	NM_017807	
RNASE10	338879	hgsc.bcm.edu	37	14	20978863	20978863	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:20978863C>A	ENST00000328444.5	+	1	252	c.233C>A	c.(232-234)cCt>cAt	p.P78H	RNASE10_ENST00000430083.1_Missense_Mutation_p.P106H	NM_001012975.1	NP_001012993.1	Q5GAN6	RNS10_HUMAN	ribonuclease, RNase A family, 10 (non-active)	78					epithelial cell morphogenesis (GO:0003382)|heterotypic cell-cell adhesion (GO:0034113)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of sperm motility (GO:1902093)|regulation of fertilization (GO:0080154)|seminiferous tubule development (GO:0072520)|single fertilization (GO:0007338)	extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	12	all_cancers(95;0.00123)		Epithelial(56;1.81e-07)|all cancers(55;1.86e-06)	GBM - Glioblastoma multiforme(265;0.022)|READ - Rectum adenocarcinoma(17;0.191)		GTGGTGCAACCTGGCTGGCCA	0.532																																					p.P78H		Atlas-SNP	.											.	RNASE10	28	.	0			c.C233A						.						69.0	69.0	69.0					14																	20978863		2203	4300	6503	SO:0001583	missense	338879	exon1			TGCAACCTGGCTG		CCDS32035.1	14q11.1	2004-11-16				ENSG00000182545		"""Ribonucleases, RNase A"""	19275	protein-coding gene	gene with protein product						12920233	Standard	XM_005267584		Approved	RNASE9	uc010tlj.2	Q5GAN6		ENST00000328444.5:c.233C>A	chr14.hg19:g.20978863C>A	ENSP00000333358:p.Pro78His	72.0	0.0		82.0	4.0	NM_001012975	A2RUQ3|B4DKY4	Missense_Mutation	SNP	ENST00000328444.5	hg19	CCDS32035.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.655953	0.29425	.	.	ENSG00000182545	ENST00000430083;ENST00000328444	T;T	0.19806	2.12;2.14	4.04	3.15	0.36227	.	0.539632	0.18794	N	0.130971	T	0.28001	0.0690	L	0.34521	1.04	0.09310	N	1	D;D	0.71674	0.996;0.998	P;P	0.61397	0.819;0.888	T	0.02789	-1.1110	10	0.87932	D	0	-11.9476	7.9922	0.30248	0.0:0.8892:0.0:0.1108	.	78;106	Q5GAN6;B4DKY4	RNS10_HUMAN;.	H	106;78	ENSP00000392996:P106H;ENSP00000333358:P78H	ENSP00000333358:P78H	P	+	2	0	RNASE10	20048703	0.002000	0.14202	0.021000	0.16686	0.174000	0.22865	1.496000	0.35638	1.289000	0.44618	0.655000	0.94253	CCT	.	.		0.532	RNASE10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411088.1	XM_292225	
EDDM3B	64184	hgsc.bcm.edu	37	14	21238598	21238598	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:21238598C>A	ENST00000326783.3	+	2	387	c.289C>A	c.(289-291)Cag>Aag	p.Q97K		NM_022360.4	NP_071755.1	P56851	EP3B_HUMAN	epididymal protein 3B	97						extracellular region (GO:0005576)				central_nervous_system(1)|kidney(1)|lung(3)|ovary(1)|skin(1)	7						TGTATGGGTCCAGAATCCTCT	0.413																																					p.Q97K		Atlas-SNP	.											.	EDDM3B	23	.	0			c.C289A						.						93.0	87.0	89.0					14																	21238598		2203	4300	6503	SO:0001583	missense	64184	exon2			TGGGTCCAGAATC	X76386	CCDS9557.1	14q11.1	2010-03-19	2010-01-27	2010-01-27	ENSG00000181552	ENSG00000181552			19223	protein-coding gene	gene with protein product		611582	"""family with sequence similarity 12, member B (epididymal)"""	FAM12B		7514008	Standard	NM_022360		Approved	HE3-BETA	uc001vyd.3	P56851	OTTHUMG00000029583	ENST00000326783.3:c.289C>A	chr14.hg19:g.21238598C>A	ENSP00000314810:p.Gln97Lys	109.0	0.0		95.0	4.0	NM_022360	A0PK89	Missense_Mutation	SNP	ENST00000326783.3	hg19	CCDS9557.1	.	.	.	.	.	.	.	.	.	.	C	0.793	-0.758120	0.03019	.	.	ENSG00000181552	ENST00000326783	T	0.71698	-0.59	3.98	-3.23	0.05109	Ribonuclease A, domain (3);	1.083060	0.07192	N	0.855893	T	0.46151	0.1378	N	0.19112	0.55	0.09310	N	1	B	0.18166	0.026	B	0.14023	0.01	T	0.40403	-0.9565	10	0.02654	T	1	.	7.3199	0.26521	0.5156:0.2234:0.261:0.0	.	97	P56851	EP3B_HUMAN	K	97	ENSP00000314810:Q97K	ENSP00000314810:Q97K	Q	+	1	0	EDDM3B	20308438	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.195000	0.09546	-0.285000	0.09089	-0.438000	0.05819	CAG	.	.		0.413	EDDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073745.2		
OR5AU1	390445	hgsc.bcm.edu	37	14	21623682	21623682	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:21623682G>T	ENST00000304418.3	-	1	540	c.503C>A	c.(502-504)gCc>gAc	p.A168D		NM_001004731.1	NP_001004731.1	Q8NGC0	O5AU1_HUMAN	olfactory receptor, family 5, subfamily AU, member 1	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(12)|pancreas(1)	21	all_cancers(95;0.00238)		Epithelial(56;6.88e-07)|all cancers(55;6.02e-06)	GBM - Glioblastoma multiforme(265;0.0192)		ATAGGCCATGGCAGCGATGAG	0.502																																					p.A168D		Atlas-SNP	.											.	OR5AU1	46	.	0			c.C503A						.						68.0	64.0	66.0					14																	21623682		2203	4300	6503	SO:0001583	missense	390445	exon1			GCCATGGCAGCGA	AL157687	CCDS32042.1	14q11.2	2013-09-23			ENSG00000169327	ENSG00000169327		"""GPCR / Class A : Olfactory receptors"""	15362	protein-coding gene	gene with protein product							Standard	NM_001004731		Approved		uc010tlp.2	Q8NGC0	OTTHUMG00000170753	ENST00000304418.3:c.503C>A	chr14.hg19:g.21623682G>T	ENSP00000302057:p.Ala168Asp	80.0	0.0		81.0	4.0	NM_001004731	B2RP78|Q6IEU2|Q96R10	Missense_Mutation	SNP	ENST00000304418.3	hg19	CCDS32042.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.492851	0.44352	.	.	ENSG00000169327	ENST00000304418	T	0.03152	4.03	4.22	4.22	0.49857	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.12902	0.0313	M	0.67953	2.075	0.39810	D	0.972689	D	0.71674	0.998	D	0.70487	0.969	T	0.00360	-1.1790	9	0.87932	D	0	.	7.8564	0.29485	0.1107:0.0:0.8893:0.0	.	168	Q8NGC0	O5AU1_HUMAN	D	168	ENSP00000302057:A168D	ENSP00000302057:A168D	A	-	2	0	OR5AU1	20693522	0.000000	0.05858	0.991000	0.47740	0.563000	0.35712	-0.022000	0.12480	2.189000	0.69895	0.313000	0.20887	GCC	.	.		0.502	OR5AU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410213.1		
PRMT5	10419	hgsc.bcm.edu	37	14	23393528	23393528	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:23393528G>T	ENST00000324366.8	-	11	1373	c.1150C>A	c.(1150-1152)Cgg>Agg	p.R384R	PRMT5_ENST00000553897.1_Silent_p.R340R|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5-AS1_ENST00000424245.2_RNA|PRMT5_ENST00000553641.1_5'Flank|PRMT5_ENST00000397440.4_Silent_p.R213R|PRMT5_ENST00000397441.2_Silent_p.R367R|PRMT5-AS1_ENST00000587245.2_RNA|PRMT5_ENST00000216350.8_Silent_p.R323R|PRMT5_ENST00000538452.1_Silent_p.R278R|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5-AS1_ENST00000609885.1_RNA|PRMT5-AS1_ENST00000457443.2_RNA	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	384	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		TTTATCCGCCGGTCGGCCTGC	0.552																																					p.R384R		Atlas-SNP	.											PRMT5_ENST00000397441,colon,carcinoma,0,2	PRMT5	101	.	0			c.C1150A						.						84.0	84.0	84.0					14																	23393528		2203	4300	6503	SO:0001819	synonymous_variant	10419	exon11			TCCGCCGGTCGGC	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"""Protein arginine methyltransferases"""	10894	protein-coding gene	gene with protein product		604045	"""skb1 (S. pombe) homolog"", ""SKB1 homolog (S. pombe)"""	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.1150C>A	chr14.hg19:g.23393528G>T		63.0	1.0		49.0	2.0	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Silent	SNP	ENST00000324366.8	hg19	CCDS9579.1																																																																																			.	.		0.552	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3		
PSMB11	122706	hgsc.bcm.edu	37	14	23511752	23511752	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:23511752G>T	ENST00000408907.2	+	1	377	c.318G>T	c.(316-318)cgG>cgT	p.R106R		NM_001099780.1	NP_001093250.1	A5LHX3	PSB11_HUMAN	proteasome (prosome, macropain) subunit, beta type, 11	106					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)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|kidney(2)|lung(4)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00643)		CCTGGTATCGGGTATTACAGC	0.602																																					p.R106R		Atlas-SNP	.											.	PSMB11	40	.	0			c.G318T						.						64.0	70.0	68.0					14																	23511752		2110	4233	6343	SO:0001819	synonymous_variant	122706	exon1			GTATCGGGTATTA		CCDS41923.1	14q11.2	2008-01-31				ENSG00000222028			31963	protein-coding gene	gene with protein product		611137				17540904	Standard	NM_001099780		Approved	beta5t	uc010ake.1	A5LHX3		ENST00000408907.2:c.318G>T	chr14.hg19:g.23511752G>T		102.0	0.0		78.0	4.0	NM_001099780		Silent	SNP	ENST00000408907.2	hg19	CCDS41923.1																																																																																			.	.		0.602	PSMB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408294.1	NM_001099780	
HOMEZ	57594	hgsc.bcm.edu	37	14	23745570	23745570	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:23745570A>G	ENST00000357460.5	-	2	1031	c.867T>C	c.(865-867)tcT>tcC	p.S289S	HOMEZ_ENST00000431326.2_Silent_p.S291S|HOMEZ_ENST00000561013.1_Silent_p.S291S	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	289	Poly-Ser.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		GGAAAGAAGAAGAGGTAGAGG	0.512																																					p.S289S		Atlas-SNP	.											.	HOMEZ	80	.	0			c.T867C						.						61.0	64.0	63.0					14																	23745570		2124	4222	6346	SO:0001819	synonymous_variant	57594	exon2			AGAAGAAGAGGTA	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.867T>C	chr14.hg19:g.23745570A>G		138.0	0.0		132.0	18.0	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	hg19	CCDS45085.1																																																																																			.	.		0.512	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
SLC22A17	51310	hgsc.bcm.edu	37	14	23816000	23816000	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:23816000G>T	ENST00000206544.8	-	9	1810	c.1474C>A	c.(1474-1476)Ctg>Atg	p.L492M	SLC22A17_ENST00000354772.3_Missense_Mutation_p.L474M|SLC22A17_ENST00000474057.1_5'UTR|SLC22A17_ENST00000397267.1_Missense_Mutation_p.L492M|SLC22A17_ENST00000397260.3_Missense_Mutation_p.L363M	NM_020372.2	NP_065105.2	Q8WUG5	S22AH_HUMAN	solute carrier family 22, member 17	492					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|vacuole (GO:0005773)	transmembrane signaling receptor activity (GO:0004888)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00643)		TCCGGCAGCAGCATAATGCTG	0.701																																					p.L492M		Atlas-SNP	.											.	SLC22A17	32	.	0			c.C1474A						.						7.0	9.0	9.0					14																	23816000		2131	4217	6348	SO:0001583	missense	51310	exon9			GCAGCAGCATAAT	AJ243653	CCDS9593.1, CCDS9594.2	14q11.2	2013-05-22	2008-01-11		ENSG00000092096	ENSG00000092096		"""Solute carriers"""	23095	protein-coding gene	gene with protein product	"""neutrophil gelatinase-associated lipocalin receptor"""	611461				16377569	Standard	NM_016609		Approved	BOCT, BOIT, NGALR	uc001wjl.3	Q8WUG5	OTTHUMG00000028740	ENST00000206544.8:c.1474C>A	chr14.hg19:g.23816000G>T	ENSP00000206544:p.Leu492Met	38.0	0.0		39.0	13.0	NM_020372	A4UA13|A8MUT0|Q2TAB0|Q5BKY8|Q86U04|Q9H1D3|Q9NQD5	Missense_Mutation	SNP	ENST00000206544.8	hg19	CCDS9593.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.239469	0.79800	.	.	ENSG00000092096	ENST00000354772;ENST00000397260;ENST00000206544;ENST00000397267	T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87	5.91	5.91	0.95273	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000004	D	0.87124	0.6099	M	0.77406	2.37	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87358	0.2342	10	0.66056	D	0.02	-11.6045	19.0661	0.93110	0.0:0.0:1.0:0.0	.	474;492	Q8WUG5-2;Q8WUG5	.;S22AH_HUMAN	M	474;363;492;492	ENSP00000346824:L474M;ENSP00000380430:L363M;ENSP00000206544:L492M;ENSP00000380437:L492M	ENSP00000206544:L492M	L	-	1	2	SLC22A17	22885840	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.332000	0.79203	2.804000	0.96469	0.462000	0.41574	CTG	.	.		0.701	SLC22A17-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157223.3	NM_020372	
MYH6	4624	hgsc.bcm.edu	37	14	23865912	23865912	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:23865912G>T	ENST00000356287.3	-	18	2312	c.2283C>A	c.(2281-2283)ggC>ggA	p.G761G	MYH6_ENST00000405093.3_Silent_p.G761G			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	761	Actin-binding.|Myosin motor.				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)		CCTTGGTGTGGCCAAACTTGT	0.547																																					p.G761G		Atlas-SNP	.											.	MYH6	274	.	0			c.C2283A						.						116.0	102.0	107.0					14																	23865912		2203	4300	6503	SO:0001819	synonymous_variant	4624	exon19			GGTGTGGCCAAAC	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.2283C>A	chr14.hg19:g.23865912G>T		156.0	0.0		124.0	5.0	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	hg19	CCDS9600.1																																																																																			.	.		0.547	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
DHRS4L1	728635	hgsc.bcm.edu	37	14	24507078	24507078	+	RNA	SNP	C	C	T	rs373705961		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:24507078C>T	ENST00000558293.1	+	0	176					NR_102693.1																						GCATGACGGGCACTGTGTGCC	0.652													C|||	1	0.000199681	0.0	0.0	5008	,	,		17195	0.0		0.001	False		,,,				2504	0.0				p.G85G		Atlas-SNP	.											.	.	.	.	0			c.C255T						.	C		0,4406		0,0,2203	32.0	34.0	33.0		255	2.4	1.0	14		33	1,8599		0,1,4299	no	coding-synonymous	DHRS4L1	NM_001082488.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		85/282	24507078	1,13005	2203	4300	6503			728635	exon2			GACGGGCACTGTG																													chr14.hg19:g.24507078C>T		415.0	0.0		306.0	130.0	NM_001082488		Silent	SNP	ENST00000558293.1	hg19																																																																																				.	.		0.652	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1		
LRRC16B	90668	hgsc.bcm.edu	37	14	24523931	24523931	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:24523931G>T	ENST00000342740.5	+	6	528	c.374G>T	c.(373-375)cGg>cTg	p.R125L	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	125						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		TGTTTGATCCGGCGTGGAAAC	0.552																																					p.R125L		Atlas-SNP	.											LRRC16B,NS,carcinoma,0,1	LRRC16B	120	.	0			c.G374T						.						42.0	47.0	45.0					14																	24523931		2203	4300	6503	SO:0001583	missense	90668	exon6			TGATCCGGCGTGG	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.374G>T	chr14.hg19:g.24523931G>T	ENSP00000340467:p.Arg125Leu	36.0	0.0		58.0	3.0	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	hg19	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.964994	0.53507	.	.	ENSG00000186648	ENST00000342740	T	0.16743	2.32	4.17	4.17	0.49024	.	0.261098	0.31963	N	0.006800	T	0.19565	0.0470	L	0.58810	1.83	0.80722	D	1	B	0.33135	0.399	B	0.34722	0.188	T	0.03268	-1.1054	10	0.52906	T	0.07	-22.025	12.1519	0.54053	0.0:0.0:1.0:0.0	.	125	Q8ND23	LR16B_HUMAN	L	125	ENSP00000340467:R125L	ENSP00000340467:R125L	R	+	2	0	LRRC16B	23593771	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.072000	0.57563	2.305000	0.77605	0.462000	0.41574	CGG	.	.		0.552	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
GMPR2	51292	hgsc.bcm.edu	37	14	24702442	24702442	+	5'UTR	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:24702442A>G	ENST00000355299.4	+	0	444				NEDD8_ENST00000533242.1_5'Flank|NEDD8_ENST00000524927.1_5'Flank|GMPR2_ENST00000559836.1_5'UTR|NEDD8-MDP1_ENST00000604306.1_5'Flank|GMPR2_ENST00000456667.3_5'UTR|NEDD8_ENST00000250495.5_5'Flank|GMPR2_ENST00000559910.1_5'UTR|GMPR2_ENST00000559104.1_Missense_Mutation_p.T13A|GMPR2_ENST00000420554.2_Missense_Mutation_p.T13A|GMPR2_ENST00000557854.1_Missense_Mutation_p.T13A|GMPR2_ENST00000348719.7_5'UTR|GMPR2_ENST00000399440.2_5'UTR|NEDD8-MDP1_ENST00000534348.1_5'Flank	NM_001002000.1	NP_001002000.1	Q9P2T1	GMPR2_HUMAN	guanosine monophosphate reductase 2						GMP metabolic process (GO:0046037)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)			large_intestine(4)|lung(3)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(265;0.0181)		ATTCATCGCTACCCCGAGGCT	0.522																																					p.T13A		Atlas-SNP	.											.	GMPR2	37	.	0			c.A37G						.						270.0	261.0	264.0					14																	24702442		2016	4184	6200	SO:0001623	5_prime_UTR_variant	51292	exon1			ATCGCTACCCCGA		CCDS41935.1, CCDS45087.1, CCDS61419.1, CCDS73624.1	14q11.2	2006-11-24							4377	protein-coding gene	gene with protein product		610781					Standard	XM_005267742		Approved		uc001wnw.3	Q9P2T1		ENST00000355299.4:c.-18A>G	chr14.hg19:g.24702442A>G		132.0	0.0		105.0	5.0	NM_016576	D3DS66|Q567T0|Q6IAJ8|Q86T14	Missense_Mutation	SNP	ENST00000355299.4	hg19	CCDS41935.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.528398	0.85706	.	.	ENSG00000100938	ENST00000420554	T	0.16597	2.33	4.37	3.21	0.36854	.	.	.	.	.	T	0.10165	0.0249	N	0.14661	0.345	0.24973	N	0.991653	B	0.02656	0.0	B	0.04013	0.001	T	0.23547	-1.0185	9	0.72032	D	0.01	.	6.7426	0.23445	0.892:0.0:0.108:0.0	.	13	Q9P2T1-2	.	A	13	ENSP00000392859:T13A	ENSP00000392859:T13A	T	+	1	0	GMPR2	23772282	0.000000	0.05858	0.016000	0.15963	0.951000	0.60555	0.083000	0.14871	0.813000	0.34350	0.460000	0.39030	ACC	.	.		0.522	GMPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415821.2	NM_016576	
HEATR5A	25938	hgsc.bcm.edu	37	14	31819853	31819853	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:31819853A>G	ENST00000389961.3	-	16	2463	c.2464T>C	c.(2464-2466)Tta>Cta	p.L822L	HEATR5A_ENST00000439348.1_Silent_p.L822L|HEATR5A_ENST00000404677.3_Silent_p.L828L|HEATR5A_ENST00000439727.1_Silent_p.L535L|HEATR5A_ENST00000543095.2_Silent_p.L828L			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	822										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		ACAACATGTAACTGAACCACT	0.313																																					p.L828L		Atlas-SNP	.											.	HEATR5A	181	.	0			c.T2482C						.						78.0	74.0	75.0					14																	31819853		1818	4074	5892	SO:0001819	synonymous_variant	25938	exon17			CATGTAACTGAAC	AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 125"""	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.2464T>C	chr14.hg19:g.31819853A>G		68.0	0.0		61.0	4.0	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Silent	SNP	ENST00000389961.3	hg19		.	.	.	.	.	.	.	.	.	.	A	9.185	1.024644	0.19433	.	.	ENSG00000129493	ENST00000550366	.	.	.	5.41	4.26	0.50523	.	.	.	.	.	T	0.59418	0.2192	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55398	-0.8147	4	.	.	.	.	9.1952	0.37224	0.847:0.0:0.153:0.0	.	.	.	.	A	470	.	.	V	-	2	0	HEATR5A	30889604	0.995000	0.38212	1.000000	0.80357	0.998000	0.95712	2.547000	0.45786	0.890000	0.36211	0.533000	0.62120	GTT	.	.		0.313	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473	
FANCM	57697	hgsc.bcm.edu	37	14	45644488	45644488	+	Missense_Mutation	SNP	A	A	G	rs113630826		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:45644488A>G	ENST00000267430.5	+	14	2616	c.2531A>G	c.(2530-2532)cAt>cGt	p.H844R	FANCM_ENST00000542564.2_Missense_Mutation_p.H818R	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	844					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AAACAAACTCATATCAAACCT	0.274								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.H844R		Atlas-SNP	.											.	FANCM	225	.	0			c.A2531G						.						43.0	42.0	42.0					14																	45644488		2203	4296	6499	SO:0001583	missense	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAACTCATATCAA	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.2531A>G	chr14.hg19:g.45644488A>G	ENSP00000267430:p.His844Arg	113.0	0.0		97.0	4.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	A	0.016	-1.520158	0.00967	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.16457	2.93;2.93;2.34	4.8	-4.44	0.03557	.	1.545420	0.03339	N	0.194534	T	0.09642	0.0237	L	0.34521	1.04	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.23762	-1.0179	10	0.15066	T	0.55	.	0.7073	0.00918	0.3496:0.246:0.245:0.1594	.	818;844	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	R	844;818;360	ENSP00000267430:H844R;ENSP00000442493:H818R;ENSP00000452033:H360R	ENSP00000267430:H844R	H	+	2	0	FANCM	44714238	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.438000	0.06905	-0.653000	0.05401	-0.446000	0.05623	CAT	.	A|0.500;G|0.500		0.274	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
SYNE2	23224	hgsc.bcm.edu	37	14	64630261	64630261	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:64630261T>C	ENST00000344113.4	+	89	16653	c.16441T>C	c.(16441-16443)Ttg>Ctg	p.L5481L	SYNE2_ENST00000394768.2_Silent_p.L1866L|SYNE2_ENST00000357395.3_Silent_p.L1866L|SYNE2_ENST00000358025.3_Silent_p.L5481L|SYNE2_ENST00000555002.1_Silent_p.L2115L|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000554584.1_Silent_p.L5398L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5481					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GGCTGCTTATTTGGAAAAGAT	0.483																																					p.L5481L		Atlas-SNP	.											.	SYNE2	577	.	0			c.T16441C						.						59.0	59.0	59.0					14																	64630261		2203	4300	6503	SO:0001819	synonymous_variant	23224	exon89			GCTTATTTGGAAA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.16441T>C	chr14.hg19:g.64630261T>C		120.0	0.0		94.0	4.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.483	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68029351	68029351	+	Missense_Mutation	SNP	C	C	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:68029351C>G	ENST00000329153.5	+	7	1135	c.1003C>G	c.(1003-1005)Ccc>Gcc	p.P335A		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	335						cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		CCACAGCCAGCCCCAGGTGGG	0.647																																					p.P335A		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.C1003G						.						20.0	22.0	21.0					14																	68029351		1985	4159	6144	SO:0001583	missense	57475	exon7			AGCCAGCCCCAGG	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.1003C>G	chr14.hg19:g.68029351C>G	ENSP00000330278:p.Pro335Ala	139.0	0.0		97.0	4.0	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	hg19	CCDS45128.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.920511	0.73213	.	.	ENSG00000054690	ENST00000329153	T	0.21932	1.98	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.45796	0.1360	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.44667	-0.9313	10	0.72032	D	0.01	.	14.8139	0.70017	0.0:1.0:0.0:0.0	.	335	Q9ULM0	PKHH1_HUMAN	A	335	ENSP00000330278:P335A	ENSP00000330278:P335A	P	+	1	0	PLEKHH1	67099104	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	6.610000	0.74178	2.467000	0.83353	0.491000	0.48974	CCC	.	.		0.647	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
EXD2	55218	hgsc.bcm.edu	37	14	69704317	69704317	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:69704317C>A	ENST00000409018.3	+	8	1446	c.1318C>A	c.(1318-1320)Cgg>Agg	p.R440R	EXD2_ENST00000409242.1_Silent_p.R315R|EXD2_ENST00000409014.1_Silent_p.R315R|EXD2_ENST00000409675.1_Silent_p.R315R|EXD2_ENST00000492815.1_3'UTR|RP11-363J20.2_ENST00000556316.1_lincRNA|EXD2_ENST00000312994.5_Silent_p.R440R|EXD2_ENST00000409949.1_Silent_p.R315R|EXD2_ENST00000449989.1_Silent_p.R315R	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	440							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						ACATGAGTACCGGAAGCACTT	0.527																																					p.R440R		Atlas-SNP	.											.	EXD2	43	.	0			c.C1318A						.						77.0	71.0	73.0					14																	69704317		2203	4300	6503	SO:0001819	synonymous_variant	55218	exon8			GAGTACCGGAAGC	AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177			20217	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 114"", ""exonuclease 3'-5' domain-like 2"""	C14orf114, EXDL2			Standard	NM_018199		Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.1318C>A	chr14.hg19:g.69704317C>A		92.0	0.0		99.0	4.0	NM_001193361	B4DIH6|G5E947|Q6AWB6|Q8N3D3	Silent	SNP	ENST00000409018.3	hg19	CCDS53902.1																																																																																			.	.		0.527	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000335504.1		
SIPA1L1	26037	hgsc.bcm.edu	37	14	72138015	72138015	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:72138015A>G	ENST00000555818.1	+	8	2783	c.2435A>G	c.(2434-2436)tAc>tGc	p.Y812C	SIPA1L1_ENST00000537413.1_Missense_Mutation_p.Y287C|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.Y812C|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.Y812C	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	812	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CGCCAGGAATACCTGAAAGAT	0.478																																					p.Y812C		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.A2435G						.						92.0	90.0	90.0					14																	72138015		2203	4300	6503	SO:0001583	missense	26037	exon8			AGGAATACCTGAA	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.2435A>G	chr14.hg19:g.72138015A>G	ENSP00000450832:p.Tyr812Cys	145.0	0.0		149.0	6.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	hg19	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.288094	0.80803	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	6.05	6.05	0.98169	Rap/ran-GAP (2);	0.000000	0.85682	D	0.000000	T	0.81083	0.4749	M	0.89840	3.065	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.997;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.988;1.0;1.0;0.998	D	0.84991	0.0894	10	0.87932	D	0	-23.2157	16.5932	0.84781	1.0:0.0:0.0:0.0	.	287;812;287;812;812	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	C	812;812;812;287	ENSP00000370630:Y812C;ENSP00000450832:Y812C;ENSP00000351352:Y812C;ENSP00000440682:Y287C	ENSP00000351352:Y812C	Y	+	2	0	SIPA1L1	71207768	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.307000	0.96226	2.320000	0.78422	0.528000	0.53228	TAC	.	.		0.478	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	
ISCA2	122961	hgsc.bcm.edu	37	14	74960541	74960541	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:74960541A>G	ENST00000556816.1	+	1	119	c.64A>G	c.(64-66)Agg>Ggg	p.R22G	NPC2_ENST00000541064.1_5'Flank|NPC2_ENST00000434013.2_5'Flank|ISCA2_ENST00000298818.8_Missense_Mutation_p.R22G|NPC2_ENST00000238633.2_5'Flank|NPC2_ENST00000557510.1_5'Flank|ISCA2_ENST00000554924.1_Missense_Mutation_p.R22G|NPC2_ENST00000555619.1_5'Flank			Q86U28	ISCA2_HUMAN	iron-sulfur cluster assembly 2	22					iron-sulfur cluster assembly (GO:0016226)	mitochondrion (GO:0005739)	iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			lung(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00146)		TCCCTGGCCGAGGGGCAGGTA	0.632																																					p.R22G		Atlas-SNP	.											.	ISCA2	4	.	0			c.A64G						.						11.0	13.0	12.0					14																	74960541		2174	4251	6425	SO:0001583	missense	122961	exon1			TGGCCGAGGGGCA		CCDS32122.1, CCDS61504.1	14q24.2	2013-08-06	2013-08-06	2007-01-18	ENSG00000165898	ENSG00000165898			19857	protein-coding gene	gene with protein product		615317	"""HesB like domain containing 1"", ""iron-sulfur cluster assembly 2 homolog (S. cerevisiae)"""	HBLD1		22323289	Standard	NM_194279		Approved	ISA2	uc001xpz.3	Q86U28		ENST00000556816.1:c.64A>G	chr14.hg19:g.74960541A>G	ENSP00000452007:p.Arg22Gly	94.0	0.0		79.0	5.0	NM_001272007	A6NFF1|A8K3W3|G3V291|Q8IYZ0|Q96BB2	Missense_Mutation	SNP	ENST00000556816.1	hg19	CCDS32122.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.154748	0.38021	.	.	ENSG00000165898	ENST00000556816;ENST00000298818;ENST00000554924	.	.	.	4.99	1.23	0.21249	.	1.050110	0.07419	N	0.893737	T	0.19327	0.0464	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27739	-1.0065	9	0.27785	T	0.31	0.0	0.3984	0.00422	0.4127:0.1458:0.1606:0.2809	.	22	Q86U28	ISCA2_HUMAN	G	22	.	ENSP00000298818:R22G	R	+	1	2	ISCA2	74030294	0.005000	0.15991	0.000000	0.03702	0.008000	0.06430	0.209000	0.17435	0.110000	0.17919	0.533000	0.62120	AGG	.	.		0.632	ISCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412354.1	NM_194279	
AREL1	9870	hgsc.bcm.edu	37	14	75130431	75130431	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:75130431T>C	ENST00000356357.4	-	20	2979	c.2464A>G	c.(2464-2466)Atg>Gtg	p.M822V	AREL1_ENST00000557401.1_Intron	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	822	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)										GGTCAGAGCATGCCAAAGCCC	0.522																																					p.M822V		Atlas-SNP	.											.	KIAA0317	68	.	0			c.A2464G						.						133.0	139.0	137.0					14																	75130431		2174	4263	6437	SO:0001583	missense	9870	exon20			AGAGCATGCCAAA	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.2464A>G	chr14.hg19:g.75130431T>C	ENSP00000348714:p.Met822Val	71.0	0.0		70.0	5.0	NM_001039479	B4E2C7|Q7LDY1|Q8IYY9	Missense_Mutation	SNP	ENST00000356357.4	hg19	CCDS41971.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.587795	0.46110	.	.	ENSG00000119682	ENST00000356357	T	0.55413	0.52	5.73	4.57	0.56435	HECT (3);	0.065915	0.85682	D	0.000000	T	0.57989	0.2091	L	0.46819	1.47	0.58432	D	0.999999	P	0.50710	0.938	P	0.53102	0.718	T	0.60449	-0.7261	10	0.72032	D	0.01	.	13.0212	0.58789	0.0:0.0:0.1347:0.8652	.	822	O15033	K0317_HUMAN	V	822	ENSP00000348714:M822V	ENSP00000348714:M822V	M	-	1	0	KIAA0317	74200184	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	4.967000	0.63722	0.981000	0.38548	-0.323000	0.08544	ATG	.	.		0.522	AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821	
TGFB3	7043	hgsc.bcm.edu	37	14	76437504	76437504	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:76437504A>G	ENST00000238682.3	-	3	908	c.611T>C	c.(610-612)gTc>gCc	p.V204A	RP11-270M14.5_ENST00000553732.1_lincRNA|TGFB3_ENST00000556285.1_Missense_Mutation_p.V204A	NM_003239.2	NP_003230.1	P10600	TGFB3_HUMAN	transforming growth factor, beta 3	204					activation of MAPK activity (GO:0000187)|aging (GO:0007568)|blood coagulation (GO:0007596)|cell growth (GO:0016049)|cell-cell junction organization (GO:0045216)|detection of hypoxia (GO:0070483)|digestive tract development (GO:0048565)|embryonic neurocranium morphogenesis (GO:0048702)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|female pregnancy (GO:0007565)|frontal suture morphogenesis (GO:0060364)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|lung alveolus development (GO:0048286)|mammary gland development (GO:0030879)|menstrual cycle phase (GO:0022601)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of macrophage cytokine production (GO:0010936)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|odontogenesis (GO:0042476)|ossification involved in bone remodeling (GO:0043932)|palate development (GO:0060021)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell division (GO:0051781)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein secretion (GO:0050714)|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, DNA-templated (GO:0045893)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to laminar fluid shear stress (GO:0034616)|response to progesterone (GO:0032570)|salivary gland morphogenesis (GO:0007435)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|T-tubule (GO:0030315)	identical protein binding (GO:0042802)|transforming growth factor beta binding (GO:0050431)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)			NS(1)|breast(1)|endometrium(4)|kidney(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	11				BRCA - Breast invasive adenocarcinoma(234;0.0169)		AGTGTCAGTGACATCAAAGGA	0.522																																					p.V204A		Atlas-SNP	.											.	TGFB3	25	.	0			c.T611C						.						110.0	94.0	99.0					14																	76437504		2203	4300	6503	SO:0001583	missense	7043	exon3			TCAGTGACATCAA		CCDS9846.1	14q24	2014-09-17				ENSG00000119699		"""Endogenous ligands"""	11769	protein-coding gene	gene with protein product	"""prepro-transforming growth factor beta-3"""	190230	"""arrhythmogenic right ventricular dysplasia 1"""	ARVD1, ARVD		16549496, 15639475	Standard	XM_005268028		Approved		uc001xsc.2	P10600		ENST00000238682.3:c.611T>C	chr14.hg19:g.76437504A>G	ENSP00000238682:p.Val204Ala	62.0	0.0		53.0	4.0	NM_003239	Q8WV88	Missense_Mutation	SNP	ENST00000238682.3	hg19	CCDS9846.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.614681	0.87359	.	.	ENSG00000119699	ENST00000238682;ENST00000556285	T;T	0.74842	-0.88;-0.88	5.55	5.55	0.83447	Transforming growth factor-beta, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84202	0.5420	M	0.86178	2.8	0.80722	D	1	P	0.52463	0.953	P	0.53593	0.73	D	0.87247	0.2270	10	0.87932	D	0	-11.4624	15.6992	0.77528	1.0:0.0:0.0:0.0	.	204	P10600	TGFB3_HUMAN	A	204	ENSP00000238682:V204A;ENSP00000451110:V204A	ENSP00000238682:V204A	V	-	2	0	TGFB3	75507257	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	8.962000	0.93254	2.122000	0.65172	0.459000	0.35465	GTC	.	.		0.522	TGFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413685.1	NM_003239	
VASH1	22846	hgsc.bcm.edu	37	14	77237533	77237533	+	Splice_Site	SNP	G	G	A	rs202147705		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:77237533G>A	ENST00000167106.4	+	3	1032	c.399G>A	c.(397-399)caG>caA	p.Q133Q	VASH1_ENST00000554237.1_Splice_Site_p.Q133Q|VASH1_ENST00000556038.1_3'UTR	NM_014909.4	NP_055724.1	Q7L8A9	VASH1_HUMAN	vasohibin 1	133					angiogenesis (GO:0001525)|cell cycle arrest (GO:0007050)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of lymphangiogenesis (GO:1901491)|regulation of cellular senescence (GO:2000772)|response to wounding (GO:0009611)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)		p.Q133H(2)		breast(2)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|urinary_tract(3)	10			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0283)		GTGCCCACAGGTACAATCACA	0.552																																					p.Q133Q		Atlas-SNP	.											VASH1_ENST00000554237,NS,carcinoma,0,2	VASH1	57	.	2	Substitution - Missense(2)	breast(2)	c.G399A						.						119.0	107.0	111.0					14																	77237533		2203	4300	6503	SO:0001630	splice_region_variant	22846	exon3			CCACAGGTACAAT	AB028959	CCDS9851.1	14q24.3	2006-09-25	2005-08-16	2005-08-16		ENSG00000071246			19964	protein-coding gene	gene with protein product		609011	"""KIAA1036"""	KIAA1036			Standard	NM_014909		Approved		uc001xst.2	Q7L8A9		ENST00000167106.4:c.399-1G>A	chr14.hg19:g.77237533G>A		452.0	0.0		357.0	98.0	NM_014909	Q96H02|Q9UBF4|Q9Y629	Silent	SNP	ENST00000167106.4	hg19	CCDS9851.1																																																																																			.	.		0.552	VASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413706.1	NM_014909	Silent
CIPC	85457	hgsc.bcm.edu	37	14	77580248	77580248	+	Missense_Mutation	SNP	G	G	T	rs201665496		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:77580248G>T	ENST00000361786.2	+	4	1104	c.787G>T	c.(787-789)Gcc>Tcc	p.A263S	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.A263S		Atlas-SNP	.											KIAA1737,NS,carcinoma,0,1	KIAA1737	26	.	0			c.G787T						.						86.0	73.0	78.0					14																	77580248		2203	4300	6503	SO:0001583	missense	85457	exon4			TCCCCCGCCAGTC																												ENST00000361786.2:c.787G>T	chr14.hg19:g.77580248G>T	ENSP00000355319:p.Ala263Ser	83.0	0.0		71.0	3.0	NM_033426	B2RCI1|Q8N389|Q8NDZ1	Missense_Mutation	SNP	ENST00000361786.2	hg19	CCDS9855.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.712699	0.48517	.	.	ENSG00000198894	ENST00000361786	T	0.32023	1.47	5.58	4.63	0.57726	.	0.505693	0.21867	N	0.067941	T	0.32912	0.0845	L	0.51422	1.61	0.40028	D	0.975499	D;D	0.53312	0.959;0.959	P;P	0.51385	0.668;0.668	T	0.01956	-1.1240	10	0.14252	T	0.57	-22.2881	8.9275	0.35650	0.0:0.1491:0.6748:0.1761	.	263;165	Q9C0C6;B3KU75	K1737_HUMAN;.	S	263	ENSP00000355319:A263S	ENSP00000355319:A263S	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		
POMT2	29954	hgsc.bcm.edu	37	14	77746806	77746806	+	Splice_Site	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:77746806C>A	ENST00000261534.4	-	16	1856	c.1654G>T	c.(1654-1656)Ggg>Tgg	p.G552W		NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	552						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	14			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		CCACTGTTCCCCTGCATGAAG	0.537																																					p.G552W		Atlas-SNP	.											.	POMT2	47	.	0			c.G1654T						.						156.0	137.0	143.0					14																	77746806		2203	4300	6503	SO:0001630	splice_region_variant	29954	exon16			TGTTCCCCTGCAT	AF105020	CCDS9857.1	14q24	2014-09-17			ENSG00000009830	ENSG00000009830	2.4.1.109	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	19743	protein-coding gene	gene with protein product		607439				11162531, 12460945	Standard	NM_013382		Approved	LGMD2N	uc001xti.2	Q9UKY4	OTTHUMG00000171556	ENST00000261534.4:c.1654-1G>T	chr14.hg19:g.77746806C>A		256.0	0.0		166.0	83.0	NM_013382	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	hg19	CCDS9857.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.085253	0.76642	.	.	ENSG00000009830	ENST00000261534	D	0.92348	-3.02	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.95890	0.8662	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94854	0.8016	10	0.38643	T	0.18	-13.1538	19.3746	0.94503	0.0:1.0:0.0:0.0	.	552	Q9UKY4	POMT2_HUMAN	W	552	ENSP00000261534:G552W	ENSP00000261534:G552W	G	-	1	0	POMT2	76816559	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	4.756000	0.62205	2.584000	0.87258	0.563000	0.77884	GGG	.	.		0.537	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382	Missense_Mutation
STON2	85439	hgsc.bcm.edu	37	14	81744156	81744156	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:81744156C>A	ENST00000267540.2	-	4	1699	c.1499G>T	c.(1498-1500)cGg>cTg	p.R500L	STON2_ENST00000556280.1_5'Flank|STON2_ENST00000555447.1_Missense_Mutation_p.R500L	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	500	SHD. {ECO:0000255|PROSITE- ProRule:PRU00403}.				hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		ACGGTCTATCCGCAAGCTGTG	0.488																																					p.R500L		Atlas-SNP	.											.	STON2	94	.	0			c.G1499T						.						96.0	101.0	99.0					14																	81744156		2203	4300	6503	SO:0001583	missense	85439	exon6			TCTATCCGCAAGC	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"""stoned B homolog 2 (Drosophila)"""	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.1499G>T	chr14.hg19:g.81744156C>A	ENSP00000267540:p.Arg500Leu	131.0	0.0		113.0	5.0	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Missense_Mutation	SNP	ENST00000267540.2	hg19	CCDS9875.1	.	.	.	.	.	.	.	.	.	.	C	19.88	3.908774	0.72868	.	.	ENSG00000140022	ENST00000555447;ENST00000546306;ENST00000267540	T;T	0.14640	2.49;2.49	6.17	6.17	0.99709	Stonin homology (1);	0.059063	0.64402	D	0.000004	T	0.33760	0.0874	L	0.44542	1.39	0.50313	D	0.999862	D;D	0.76494	0.998;0.999	D;D	0.72075	0.946;0.976	T	0.00380	-1.1776	10	0.87932	D	0	-21.9223	20.8794	0.99867	0.0:1.0:0.0:0.0	.	500;500	Q8WXE9;G3V2T7	STON2_HUMAN;.	L	500;512;500	ENSP00000450857:R500L;ENSP00000267540:R500L	ENSP00000267540:R500L	R	-	2	0	STON2	80813909	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.938000	0.70170	2.941000	0.99782	0.655000	0.94253	CGG	.	.		0.488	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104	
CPSF2	53981	hgsc.bcm.edu	37	14	92624221	92624221	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:92624221T>C	ENST00000298875.4	+	13	2099	c.1814T>C	c.(1813-1815)aTc>aCc	p.I605T		NM_017437.2	NP_059133.1	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2, 100kDa	605					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	24		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		GAAACTCACATCTACCAGGTA	0.423																																					p.I605T	Ovarian(78;28 1788 18702 44111)	Atlas-SNP	.											.	CPSF2	63	.	0			c.T1814C						.						62.0	63.0	62.0					14																	92624221		2203	4300	6503	SO:0001583	missense	53981	exon13			CTCACATCTACCA	AB037788	CCDS9902.1	14q31.1	2008-07-28	2002-08-29			ENSG00000165934			2325	protein-coding gene	gene with protein product		606028	"""cleavage and polyadenylation specific factor 2, 100kD subunit"""			7969155, 11124543	Standard	NM_017437		Approved	KIAA1367	uc001yah.2	Q9P2I0		ENST00000298875.4:c.1814T>C	chr14.hg19:g.92624221T>C	ENSP00000298875:p.Ile605Thr	99.0	0.0		87.0	4.0	NM_017437	B3KME1|Q6NSJ1|Q9H3W7	Missense_Mutation	SNP	ENST00000298875.4	hg19	CCDS9902.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.64|19.64	3.865938|3.865938	0.71949|0.71949	.|.	.|.	ENSG00000165934|ENSG00000165934	ENST00000298875|ENST00000555244	T|.	0.46063|.	0.88|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75406|0.75406	0.3845|0.3845	M|M	0.74647|0.74647	2.275|2.275	0.80722|0.80722	D|D	1|1	P|.	0.46457|.	0.878|.	P|.	0.51079|.	0.658|.	T|T	0.75693|0.75693	-0.3229|-0.3229	10|5	0.38643|.	T|.	0.18|.	.|.	16.0499|16.0499	0.80749|0.80749	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	605|.	Q9P2I0|.	CPSF2_HUMAN|.	T|P	605|122	ENSP00000298875:I605T|.	ENSP00000298875:I605T|.	I|S	+|+	2|1	0|0	CPSF2|CPSF2	91693974|91693974	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.836000|0.836000	0.47400|0.47400	7.946000|7.946000	0.87746|0.87746	2.193000|2.193000	0.70182|0.70182	0.533000|0.533000	0.62120|0.62120	ATC|TCT	.	.		0.423	CPSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412123.1		
CYP46A1	10858	hgsc.bcm.edu	37	14	100192567	100192567	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:100192567T>C	ENST00000261835.3	+	14	1410	c.1306T>C	c.(1306-1308)Tcc>Ccc	p.S436P	CYP46A1_ENST00000423126.2_Missense_Mutation_p.S339P|CYP46A1_ENST00000554176.1_Missense_Mutation_p.S273P	NM_006668.1	NP_006659.1	Q9Y6A2	CP46A_HUMAN	cytochrome P450, family 46, subfamily A, polypeptide 1	436					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|nervous system development (GO:0007399)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol 24-hydroxylase activity (GO:0033781)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)			breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)	25		Melanoma(154;0.0866)|all_epithelial(191;0.179)				GGGCCACCGCTCCTGCATCGG	0.642																																					p.S436P		Atlas-SNP	.											.	CYP46A1	62	.	0			c.T1306C						.						64.0	60.0	61.0					14																	100192567		2203	4300	6503	SO:0001583	missense	10858	exon14			CACCGCTCCTGCA	AF094480	CCDS9954.1	14q32.2	2013-05-03	2003-02-14	2003-02-28	ENSG00000036530	ENSG00000036530		"""Cytochrome P450s"""	2641	protein-coding gene	gene with protein product		604087	"""cytochrome P450, subfamily 46 (cholesterol 24-hydroxylase)"""	CYP46		10377398	Standard	NM_006668		Approved		uc001ygo.3	Q9Y6A2	OTTHUMG00000171510	ENST00000261835.3:c.1306T>C	chr14.hg19:g.100192567T>C	ENSP00000261835:p.Ser436Pro	125.0	0.0		74.0	4.0	NM_006668	B4DHP8|E7EQG9|Q8N2B0	Missense_Mutation	SNP	ENST00000261835.3	hg19	CCDS9954.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.00|19.00	3.741777|3.741777	0.69304|0.69304	.|.	.|.	ENSG00000036530|ENSG00000036530	ENST00000380228|ENST00000261835;ENST00000423126;ENST00000554176	.|T;T;T	.|0.69685	.|-0.42;-0.42;-0.42	3.68|3.68	3.68|3.68	0.42216|0.42216	.|Cytochrome P450, conserved site (1);	.|0.127312	.|0.53938	.|D	.|0.000044	T|T	0.79034|0.79034	0.4378|0.4378	M|M	0.78916|0.78916	2.43|2.43	0.44181|0.44181	D|D	0.996997|0.996997	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.79784	.|0.993;0.991	T|T	0.80580|0.80580	-0.1319|-0.1319	5|10	.|0.72032	.|D	.|0.01	.|.	9.2929|9.2929	0.37797|0.37797	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|273;436	.|Q8N2B0;Q9Y6A2	.|.;CP46A_HUMAN	P|P	422|436;339;273	.|ENSP00000261835:S436P;ENSP00000405779:S339P;ENSP00000450553:S273P	.|ENSP00000261835:S436P	L|S	+|+	2|1	0|0	CYP46A1|CYP46A1	99262320|99262320	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	1.246000|1.246000	0.32803|0.32803	1.623000|1.623000	0.50342|0.50342	0.459000|0.459000	0.35465|0.35465	CTC|TCC	.	.		0.642	CYP46A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413814.1		
DLK1	8788	hgsc.bcm.edu	37	14	101201179	101201179	+	Silent	SNP	C	C	A	rs150069528	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:101201179C>A	ENST00000341267.4	+	5	1340	c.1098C>A	c.(1096-1098)ccC>ccA	p.P366P	RP11-566J3.4_ENST00000608876.1_lincRNA|DLK1_ENST00000331224.6_Silent_p.P293P	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	366					cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				TCATCTTCCCCGAGAAGATCG	0.577																																					p.P366P		Atlas-SNP	.											DLK1,NS,carcinoma,0,1	DLK1	57	.	0			c.C1098A						.						97.0	94.0	95.0					14																	101201179		2203	4300	6503	SO:0001819	synonymous_variant	8788	exon5			CTTCCCCGAGAAG	U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"""delta-like homolog (Drosophila)"""			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.1098C>A	chr14.hg19:g.101201179C>A		32.0	0.0		25.0	2.0	NM_003836	P15803|Q96DW5	Silent	SNP	ENST00000341267.4	hg19	CCDS9963.1																																																																																			.	C|0.999;T|0.001		0.577	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
DYNC1H1	1778	hgsc.bcm.edu	37	14	102452814	102452814	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:102452814G>T	ENST00000360184.4	+	8	2416	c.2252G>T	c.(2251-2253)cGg>cTg	p.R751L		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	751	Interaction with DYNC1LI2. {ECO:0000250}.|Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						AAAGAAGTCCGGAACCTCAAA	0.483																																					p.R751L		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.G2252T						.						94.0	86.0	89.0					14																	102452814		2203	4300	6503	SO:0001583	missense	1778	exon8			AAGTCCGGAACCT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.2252G>T	chr14.hg19:g.102452814G>T	ENSP00000348965:p.Arg751Leu	93.0	0.0		92.0	4.0	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.025019	0.93518	.	.	ENSG00000197102	ENST00000360184	T	0.61742	0.08	5.6	5.6	0.85130	Dynein heavy chain, domain-1 (1);	0.000000	0.85682	D	0.000000	D	0.83248	0.5213	M	0.93720	3.45	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87242	0.2267	10	0.87932	D	0	.	19.6087	0.95589	0.0:0.0:1.0:0.0	.	751	Q14204	DYHC1_HUMAN	L	751	ENSP00000348965:R751L	ENSP00000348965:R751L	R	+	2	0	DYNC1H1	101522567	1.000000	0.71417	0.984000	0.44739	0.992000	0.81027	9.471000	0.97696	2.639000	0.89480	0.655000	0.94253	CGG	.	.		0.483	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
BAG5	9529	hgsc.bcm.edu	37	14	104026834	104026834	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr14:104026834A>G	ENST00000445922.2	-	2	914	c.668T>C	c.(667-669)cTg>cCg	p.L223P	BAG5_ENST00000337322.4_Missense_Mutation_p.L264P|RP11-73M18.2_ENST00000472726.2_5'Flank|APOPT1_ENST00000556253.2_5'Flank|RP11-894P9.2_ENST00000556332.1_RNA|APOPT1_ENST00000247618.4_5'Flank|APOPT1_ENST00000409074.2_5'Flank|BAG5_ENST00000299204.4_Missense_Mutation_p.L223P	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5	223	BAG 3. {ECO:0000255|PROSITE- ProRule:PRU00369}.				negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			GTCAGCGATCAGCCCCGAGAG	0.488																																					p.L264P	NSCLC(171;1832 2055 18950 31566 41632)	Atlas-SNP	.											.	BAG5	47	.	0			c.T791C						.						117.0	109.0	112.0					14																	104026834		2203	4300	6503	SO:0001583	missense	9529	exon2			GCGATCAGCCCCG	AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.668T>C	chr14.hg19:g.104026834A>G	ENSP00000391713:p.Leu223Pro	146.0	0.0		98.0	4.0	NM_001015049	O94950|Q86W59	Missense_Mutation	SNP	ENST00000445922.2	hg19	CCDS9982.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.608216	0.46527	.	.	ENSG00000166170	ENST00000299204;ENST00000445922;ENST00000337322	D;D;D	0.89485	-2.52;-2.52;-2.52	5.76	5.76	0.90799	BAG domain (3);	0.224733	0.37219	N	0.002186	D	0.90277	0.6959	L	0.27053	0.805	0.80722	D	1	P;D	0.67145	0.921;0.996	P;D	0.65233	0.906;0.933	D	0.91816	0.5463	10	0.87932	D	0	-10.7038	16.0833	0.81020	1.0:0.0:0.0:0.0	.	223;264	Q9UL15;Q9UL15-2	BAG5_HUMAN;.	P	223;223;264	ENSP00000299204:L223P;ENSP00000391713:L223P;ENSP00000338814:L264P	ENSP00000299204:L223P	L	-	2	0	BAG5	103096587	1.000000	0.71417	0.322000	0.25334	0.016000	0.09150	8.158000	0.89649	2.202000	0.70862	0.533000	0.62120	CTG	.	.		0.488	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1		
THBS1	7057	hgsc.bcm.edu	37	15	39886308	39886308	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:39886308C>A	ENST00000260356.5	+	20	3441	c.3276C>A	c.(3274-3276)acC>acA	p.T1092T	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1092	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)		AGGTGCGCACCCTGTGGCATG	0.463																																					p.T1092T		Atlas-SNP	.											.	THBS1	106	.	0			c.C3276A						.						56.0	54.0	55.0					15																	39886308		2200	4297	6497	SO:0001819	synonymous_variant	7057	exon20			GCGCACCCTGTGG		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.3276C>A	chr15.hg19:g.39886308C>A		122.0	0.0		103.0	5.0	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	hg19	CCDS32194.1																																																																																			.	.		0.463	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
IVD	3712	hgsc.bcm.edu	37	15	40700141	40700141	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:40700141T>C	ENST00000249760.2	+	3	581	c.238T>C	c.(238-240)Ttt>Ctt	p.F80L	IVD_ENST00000479013.2_Missense_Mutation_p.F53L|IVD_ENST00000490194.1_3'UTR|IVD_ENST00000487418.2_Missense_Mutation_p.F83L	NM_002225.3	NP_002216.2	P26440	IVD_HUMAN	isovaleryl-CoA dehydrogenase	80					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	flavin adenine dinucleotide binding (GO:0050660)|isovaleryl-CoA dehydrogenase activity (GO:0008470)			kidney(1)|lung(5)|ovary(2)|prostate(1)	9		all_cancers(109;1.19e-18)|all_epithelial(112;1.52e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.65e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0808)	Flavin adenine dinucleotide(DB03147)	TTGGCAGGAATTTTGGAAGCA	0.488																																					p.F83L	GBM(31;293 617 7486 32527 34655)	Atlas-SNP	.											.	IVD	29	.	0			c.T247C						.						98.0	98.0	98.0					15																	40700141		2203	4300	6503	SO:0001583	missense	3712	exon3			CAGGAATTTTGGA	AF038317	CCDS10057.1, CCDS10057.2, CCDS53930.1	15q14-q15	2010-05-11	2010-05-11		ENSG00000128928	ENSG00000128928	1.3.99.10		6186	protein-coding gene	gene with protein product		607036	"""isovaleryl Coenzyme A dehydrogenase"", ""isovaleryl CoA dehydrogenase"""			2063866	Standard	NM_002225		Approved	ACAD2	uc001zls.3	P26440	OTTHUMG00000129984	ENST00000249760.2:c.238T>C	chr15.hg19:g.40700141T>C	ENSP00000249760:p.Phe80Leu	81.0	0.0		74.0	4.0	NM_002225	B2RCV5|B3KVI7|J3KR54|Q53XZ9|Q96AF6	Missense_Mutation	SNP	ENST00000249760.2	hg19		.	.	.	.	.	.	.	.	.	.	T	11.87	1.767821	0.31320	.	.	ENSG00000128928	ENST00000249760;ENST00000479013;ENST00000487418	D;D;D	0.98493	-4.96;-4.96;-4.96	5.8	5.8	0.92144	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.045148	0.85682	D	0.000000	D	0.97356	0.9135	L	0.28649	0.875	0.80722	D	1	D;B	0.63046	0.992;0.01	D;B	0.68192	0.956;0.03	D	0.95386	0.8477	10	0.02654	T	1	.	16.1549	0.81657	0.0:0.0:0.0:1.0	.	80;53	P26440;B3KVI7	IVD_HUMAN;.	L	80;53;83	ENSP00000249760:F80L;ENSP00000417990:F53L;ENSP00000418397:F83L	ENSP00000249760:F80L	F	+	1	0	IVD	38487433	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.375000	0.79646	2.209000	0.71365	0.533000	0.62120	TTT	.	.		0.488	IVD-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
GATM	2628	hgsc.bcm.edu	37	15	45658625	45658625	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:45658625A>G	ENST00000396659.3	-	5	1096	c.757T>C	c.(757-759)Ttt>Ctt	p.F253L	GATM_ENST00000558336.1_Missense_Mutation_p.F253L	NM_001482.2	NP_001473.1	P50440	GATM_HUMAN	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	253					cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|embryo development (GO:0009790)|response to mercury ion (GO:0046689)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	glycine amidinotransferase activity (GO:0015068)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines (GO:0016813)			biliary_tract(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	15		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Glycine(DB00145)|L-Ornithine(DB00129)	GCAGCATCAAAGCATGGCTCA	0.418																																					p.F253L		Atlas-SNP	.											.	GATM	34	.	0			c.T757C						.						80.0	75.0	77.0					15																	45658625		2198	4298	6496	SO:0001583	missense	2628	exon5			CATCAAAGCATGG	S68805	CCDS10122.1	15q15.1	2007-12-06			ENSG00000171766	ENSG00000171766	2.1.4.1		4175	protein-coding gene	gene with protein product		602360				8313955	Standard	NM_001482		Approved	AGAT	uc001zvc.3	P50440	OTTHUMG00000131427	ENST00000396659.3:c.757T>C	chr15.hg19:g.45658625A>G	ENSP00000379895:p.Phe253Leu	103.0	0.0		86.0	4.0	NM_001482	B4DH99|B4DPI3|Q53EQ4	Missense_Mutation	SNP	ENST00000396659.3	hg19	CCDS10122.1	.	.	.	.	.	.	.	.	.	.	A	32	5.128614	0.94473	.	.	ENSG00000171766	ENST00000396659	T	0.31247	1.5	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.64929	0.2643	M	0.93462	3.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.73059	-0.4102	10	0.49607	T	0.09	-13.2515	13.7457	0.62874	1.0:0.0:0.0:0.0	.	253;253	P50440-3;P50440	.;GATM_HUMAN	L	253	ENSP00000379895:F253L	ENSP00000379895:F253L	F	-	1	0	GATM	43445917	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.619000	0.90938	2.126000	0.65437	0.533000	0.62120	TTT	.	.		0.418	GATM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254220.2	NM_001482	
GATM	2628	hgsc.bcm.edu	37	15	45658705	45658705	+	Splice_Site	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:45658705T>C	ENST00000396659.3	-	5	1016	c.677A>G	c.(676-678)gAt>gGt	p.D226G	GATM_ENST00000558336.1_Splice_Site_p.D226G	NM_001482.2	NP_001473.1	P50440	GATM_HUMAN	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	226					cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|embryo development (GO:0009790)|response to mercury ion (GO:0046689)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	glycine amidinotransferase activity (GO:0015068)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines (GO:0016813)			biliary_tract(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	15		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Glycine(DB00145)|L-Ornithine(DB00129)	GATGGGATAATCCTAATTGGA	0.378																																					p.D226G		Atlas-SNP	.											.	GATM	34	.	0			c.A677G						.						65.0	62.0	63.0					15																	45658705		2198	4298	6496	SO:0001630	splice_region_variant	2628	exon5			GGATAATCCTAAT	S68805	CCDS10122.1	15q15.1	2007-12-06			ENSG00000171766	ENSG00000171766	2.1.4.1		4175	protein-coding gene	gene with protein product		602360				8313955	Standard	NM_001482		Approved	AGAT	uc001zvc.3	P50440	OTTHUMG00000131427	ENST00000396659.3:c.676-1A>G	chr15.hg19:g.45658705T>C		70.0	0.0		68.0	4.0	NM_001482	B4DH99|B4DPI3|Q53EQ4	Missense_Mutation	SNP	ENST00000396659.3	hg19	CCDS10122.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.499050	0.44455	.	.	ENSG00000171766	ENST00000396659	T	0.48836	0.8	5.61	4.48	0.54585	.	0.356955	0.35235	N	0.003355	T	0.35799	0.0944	L	0.28344	0.845	0.44085	D	0.996844	B;B	0.14438	0.01;0.0	B;B	0.23419	0.046;0.0	T	0.10474	-1.0628	10	0.42905	T	0.14	-3.9467	11.1585	0.48501	0.0:0.0:0.1546:0.8454	.	226;226	P50440-3;P50440	.;GATM_HUMAN	G	226	ENSP00000379895:D226G	ENSP00000379895:D226G	D	-	2	0	GATM	43445997	1.000000	0.71417	0.980000	0.43619	0.994000	0.84299	4.623000	0.61247	0.941000	0.37499	-0.291000	0.09656	GAT	.	.		0.378	GATM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254220.2	NM_001482	Missense_Mutation
MYEF2	50804	hgsc.bcm.edu	37	15	48441407	48441407	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:48441407T>C	ENST00000324324.7	-	15	1819	c.1540A>G	c.(1540-1542)Atg>Gtg	p.M514V	MYEF2_ENST00000267836.6_Missense_Mutation_p.M490V	NM_016132.3	NP_057216	Q9P2K5	MYEF2_HUMAN	myelin expression factor 2	514	Gly-rich.				myotube differentiation (GO:0014902)|neuron differentiation (GO:0030182)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)		CTCTCTCTCATTCCGCTTCCC	0.373																																					p.M514V		Atlas-SNP	.											.	MYEF2	67	.	0			c.A1540G						.						117.0	117.0	117.0					15																	48441407		2198	4296	6494	SO:0001583	missense	50804	exon15			CTCTCATTCCGCT	AB037762	CCDS32230.1, CCDS73722.1	15q15.1	2013-07-16				ENSG00000104177		"""RNA binding motif (RRM) containing"""	17940	protein-coding gene	gene with protein product						10718198, 2601707	Standard	XM_005254422		Approved	MEF-2, FLJ11213, KIAA1341, HsT18564	uc001zwi.4	Q9P2K5		ENST00000324324.7:c.1540A>G	chr15.hg19:g.48441407T>C	ENSP00000316950:p.Met514Val	132.0	0.0		121.0	5.0	NM_016132	A7MCZ9|C9J921|C9K0J4|Q6NUM5|Q7L388|Q7Z4B7|Q9H922|Q9NUQ1	Missense_Mutation	SNP	ENST00000324324.7	hg19	CCDS32230.1	.	.	.	.	.	.	.	.	.	.	T	9.310	1.055438	0.19907	.	.	ENSG00000104177	ENST00000324324;ENST00000267836;ENST00000454655	T;T	0.21361	2.62;2.01	4.69	3.53	0.40419	Nucleotide-binding, alpha-beta plait (1);	0.169530	0.64402	D	0.000005	T	0.12732	0.0309	L	0.29908	0.895	0.37790	D	0.927338	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.14309	-1.0477	10	0.16896	T	0.51	-2.7258	7.2769	0.26290	0.1445:0.0:0.1509:0.7046	.	490;514	Q9P2K5-2;Q9P2K5	.;MYEF2_HUMAN	V	514;490;102	ENSP00000316950:M514V;ENSP00000267836:M490V	ENSP00000267836:M490V	M	-	1	0	MYEF2	46228699	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.995000	0.40767	0.861000	0.35504	0.482000	0.46254	ATG	.	.		0.373	MYEF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416909.2	NM_016132	
FBN1	2200	hgsc.bcm.edu	37	15	48756205	48756205	+	Nonsense_Mutation	SNP	A	A	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:48756205A>T	ENST00000316623.5	-	41	5411	c.4956T>A	c.(4954-4956)tgT>tgA	p.C1652*		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1652	EGF-like 28; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CAGGAGTCTCACATTCATTCA	0.408																																					p.C1652X		Atlas-SNP	.											.	FBN1	310	.	0			c.T4956A						.						123.0	108.0	113.0					15																	48756205		2198	4296	6494	SO:0001587	stop_gained	2200	exon41			AGTCTCACATTCA	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.4956T>A	chr15.hg19:g.48756205A>T	ENSP00000325527:p.Cys1652*	103.0	0.0		98.0	4.0	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Nonsense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	a	28.1	4.887605	0.91814	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	.	.	.	5.73	2.17	0.27698	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.4485	0.38712	0.7952:0.0:0.2048:0.0	.	.	.	.	X	1652;220;542	.	ENSP00000325527:C1652X	C	-	3	2	FBN1	46543497	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.187000	0.50950	0.523000	0.28482	-0.378000	0.06908	TGT	.	.		0.408	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
ATP8B4	79895	hgsc.bcm.edu	37	15	50190396	50190396	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:50190396A>G	ENST00000284509.6	-	22	2483	c.2342T>C	c.(2341-2343)aTg>aCg	p.M781T	ATP8B4_ENST00000559829.1_Missense_Mutation_p.M781T	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	781						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)		AGTCTTACACATGCAAGCAAG	0.403																																					p.M781T		Atlas-SNP	.											.	ATP8B4	173	.	0			c.T2342C						.						131.0	116.0	121.0					15																	50190396		2196	4294	6490	SO:0001583	missense	79895	exon22			TTACACATGCAAG	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.2342T>C	chr15.hg19:g.50190396A>G	ENSP00000284509:p.Met781Thr	129.0	0.0		150.0	6.0	NM_024837	Q9H727	Missense_Mutation	SNP	ENST00000284509.6	hg19	CCDS32238.1	.	.	.	.	.	.	.	.	.	.	A	9.964	1.223493	0.22457	.	.	ENSG00000104043	ENST00000284509	D	0.82344	-1.6	5.92	5.92	0.95590	HAD-like domain (1);	0.325157	0.35407	N	0.003227	T	0.78065	0.4225	L	0.33624	1.015	0.34704	D	0.727	B;B	0.33940	0.38;0.433	B;B	0.40901	0.343;0.297	T	0.79077	-0.1951	10	0.15066	T	0.55	.	14.3151	0.66443	1.0:0.0:0.0:0.0	.	1;781	B3KVY8;Q8TF62	.;AT8B4_HUMAN	T	781	ENSP00000284509:M781T	ENSP00000284509:M781T	M	-	2	0	ATP8B4	47977688	0.001000	0.12720	1.000000	0.80357	0.992000	0.81027	0.871000	0.28023	2.266000	0.75297	0.533000	0.62120	ATG	.	.		0.403	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837	
UNC13C	440279	hgsc.bcm.edu	37	15	54305696	54305696	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:54305696A>G	ENST00000260323.11	+	1	596	c.596A>G	c.(595-597)gAg>gGg	p.E199G	UNC13C_ENST00000537900.1_Missense_Mutation_p.E199G|UNC13C_ENST00000545554.1_Missense_Mutation_p.E199G	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	199					exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TCAGACTCAGAGTTAAGCACC	0.453																																					p.E199G		Atlas-SNP	.											.	UNC13C	674	.	0			c.A596G						.						96.0	95.0	95.0					15																	54305696		1854	4084	5938	SO:0001583	missense	440279	exon1			ACTCAGAGTTAAG	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.596A>G	chr15.hg19:g.54305696A>G	ENSP00000260323:p.Glu199Gly	141.0	0.0		90.0	4.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	A	16.59	3.164540	0.57476	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.85258	-1.95;-1.96;-1.95	4.98	4.98	0.66077	.	.	.	.	.	D	0.87237	0.6127	L	0.32530	0.975	0.54753	D	0.999983	D	0.76494	0.999	D	0.80764	0.994	D	0.85496	0.1188	9	0.28530	T	0.3	.	13.8729	0.63631	1.0:0.0:0.0:0.0	.	199	Q8NB66	UN13C_HUMAN	G	199	ENSP00000260323:E199G;ENSP00000438156:E199G;ENSP00000442569:E199G	ENSP00000260323:E199G	E	+	2	0	UNC13C	52092988	1.000000	0.71417	0.998000	0.56505	0.592000	0.36648	9.261000	0.95576	1.854000	0.53819	0.533000	0.62120	GAG	.	.		0.453	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
NEDD4	4734	hgsc.bcm.edu	37	15	56125247	56125247	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:56125247C>T	ENST00000508342.1	-	23	4042	c.3743G>A	c.(3742-3744)gGc>gAc	p.G1248D	NEDD4_ENST00000338963.2_Missense_Mutation_p.G1176D|NEDD4_ENST00000506154.1_Missense_Mutation_p.G1232D|NEDD4_ENST00000435532.3_Missense_Mutation_p.G829D	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	1248	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		CCGAGATGTGCCAGTGACAAA	0.348																																					p.G1176D		Atlas-SNP	.											.	NEDD4	167	.	0			c.G3527A						.						103.0	103.0	103.0					15																	56125247		2193	4292	6485	SO:0001583	missense	4734	exon20			GATGTGCCAGTGA	D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"""receptor-potentiating factor 1"""	602278	"""neural precursor cell expressed, developmentally down-regulated 4"""			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.3743G>A	chr15.hg19:g.56125247C>T	ENSP00000424827:p.Gly1248Asp	82.0	0.0		82.0	5.0	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.263888|5.263888	0.95399|0.95399	.|.	.|.	ENSG00000069869|ENSG00000069869	ENST00000508871|ENST00000508342;ENST00000435532;ENST00000338963;ENST00000506154	.|T;T;T;T	.|0.73681	.|-0.77;-0.77;-0.77;-0.77	5.36|5.36	5.36|5.36	0.76844|0.76844	.|HECT (4);	.|0.049127	.|0.85682	.|D	.|0.000000	D|D	0.92743|0.92743	0.7693|0.7693	H|H	0.99726|0.99726	4.73|4.73	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.994;0.991;0.998;0.999	.|P;D;D;D	.|0.68353	.|0.759;0.957;0.922;0.957	D|D	0.96066|0.96066	0.9042|0.9042	5|10	.|0.87932	.|D	.|0	.|.	18.0708|18.0708	0.89405|0.89405	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1232;829;1248;1176	.|P46934-2;P46934-4;P46934;P46934-3	.|.;.;NEDD4_HUMAN;.	T|D	839|1248;829;1176;1232	.|ENSP00000424827:G1248D;ENSP00000410613:G829D;ENSP00000345530:G1176D;ENSP00000422705:G1232D	.|ENSP00000345530:G1176D	A|G	-|-	1|2	0|0	NEDD4|NEDD4	53912539|53912539	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.754000|7.754000	0.85163|0.85163	2.513000|2.513000	0.84729|0.84729	0.557000|0.557000	0.71058|0.71058	GCA|GGC	.	.		0.348	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400	
ZNF280D	54816	hgsc.bcm.edu	37	15	56924037	56924037	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:56924037T>C	ENST00000267807.7	-	22	2815	c.2599A>G	c.(2599-2601)Aaa>Gaa	p.K867E	RP11-1129I3.1_ENST00000562300.1_RNA|ZNF280D_ENST00000559237.1_Missense_Mutation_p.K854E	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	867					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(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		TTGTGATCTTTAATCTGATCA	0.323																																					p.K867E		Atlas-SNP	.											.	ZNF280D	82	.	0			c.A2599G						.						135.0	133.0	134.0					15																	56924037		2192	4291	6483	SO:0001583	missense	54816	exon22			GATCTTTAATCTG	AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 4 (Drosophila)"""	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.2599A>G	chr15.hg19:g.56924037T>C	ENSP00000267807:p.Lys867Glu	93.0	0.0		74.0	4.0	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Missense_Mutation	SNP	ENST00000267807.7	hg19	CCDS32245.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.732159	0.00687	.	.	ENSG00000137871	ENST00000267807;ENST00000455329	T	0.03065	4.06	5.58	0.757	0.18427	.	.	.	.	.	T	0.01976	0.0062	N	0.12182	0.205	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.48139	-0.9061	9	0.06236	T	0.91	-1.2374	8.4686	0.32971	0.0:0.3075:0.0:0.6925	.	867	Q6N043	Z280D_HUMAN	E	867;854	ENSP00000267807:K867E	ENSP00000267807:K867E	K	-	1	0	ZNF280D	54711329	0.006000	0.16342	0.002000	0.10522	0.052000	0.14988	-0.140000	0.10342	-0.098000	0.12285	0.460000	0.39030	AAA	.	.		0.323	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867	
CGNL1	84952	hgsc.bcm.edu	37	15	57754012	57754012	+	Missense_Mutation	SNP	T	T	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:57754012T>G	ENST00000281282.5	+	8	2403	c.2325T>G	c.(2323-2325)gaT>gaG	p.D775E		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	775						myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		CCAGCCATGATCAGGAGATGG	0.532																																					p.D775E		Atlas-SNP	.											.	CGNL1	125	.	0			c.T2325G						.						100.0	97.0	98.0					15																	57754012		2192	4292	6484	SO:0001583	missense	84952	exon8			CCATGATCAGGAG	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.2325T>G	chr15.hg19:g.57754012T>G	ENSP00000281282:p.Asp775Glu	136.0	0.0		89.0	21.0	NM_032866	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	hg19	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	T	18.62	3.663587	0.67700	.	.	ENSG00000128849	ENST00000281282	T	0.41065	1.01	5.52	1.63	0.23807	.	0.113301	0.39759	N	0.001278	T	0.41766	0.1173	M	0.79123	2.44	0.38341	D	0.94406	B	0.32731	0.382	B	0.31442	0.13	T	0.48091	-0.9065	10	0.46703	T	0.11	-27.512	11.03	0.47767	0.0:0.7455:0.0:0.2545	.	775	Q0VF96	CGNL1_HUMAN	E	775	ENSP00000281282:D775E	ENSP00000281282:D775E	D	+	3	2	CGNL1	55541304	0.993000	0.37304	1.000000	0.80357	0.687000	0.40016	0.335000	0.19806	0.509000	0.28195	0.368000	0.22195	GAT	.	.		0.532	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866	
LIPC	3990	hgsc.bcm.edu	37	15	58840664	58840664	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:58840664G>A	ENST00000356113.6	+	8	1559	c.944G>A	c.(943-945)aGc>aAc	p.S315N	LIPC_ENST00000299022.5_Missense_Mutation_p.S315N|LIPC_ENST00000414170.3_Missense_Mutation_p.S315N|LIPC_ENST00000433326.2_Missense_Mutation_p.S254N			P11150	LIPC_HUMAN	lipase, hepatic	315					cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		CTGTGCCTGAGCTGCAAGAAG	0.642																																					p.S315N		Atlas-SNP	.											.	LIPC	56	.	0			c.G944A						.						39.0	34.0	36.0					15																	58840664		2192	4292	6484	SO:0001583	missense	3990	exon6			GCCTGAGCTGCAA		CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3.1.1.3		6619	protein-coding gene	gene with protein product		151670					Standard	NM_000236		Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000356113.6:c.944G>A	chr15.hg19:g.58840664G>A	ENSP00000348425:p.Ser315Asn	172.0	0.0		135.0	64.0	NM_000236	A2RUB4|A8K9B6|O43571|P78529|Q99465	Missense_Mutation	SNP	ENST00000356113.6	hg19	CCDS10166.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.858592	0.51376	.	.	ENSG00000166035	ENST00000356113;ENST00000414170;ENST00000299022;ENST00000433326	D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83	5.18	-0.204	0.13200	Lipase, N-terminal (1);	0.368824	0.34291	N	0.004091	D	0.86041	0.5838	M	0.62209	1.925	0.39169	D	0.96255	B;B	0.20368	0.044;0.005	B;B	0.21151	0.033;0.015	T	0.77882	-0.2422	10	0.54805	T	0.06	.	6.9254	0.24412	0.2676:0.1146:0.6178:0.0	.	254;315	E7EUK6;P11150	.;LIPC_HUMAN	N	315;315;315;254	ENSP00000348425:S315N;ENSP00000395569:S315N;ENSP00000299022:S315N;ENSP00000395002:S254N	ENSP00000299022:S315N	S	+	2	0	LIPC	56627956	1.000000	0.71417	0.979000	0.43373	0.914000	0.54420	1.140000	0.31516	0.047000	0.15862	0.655000	0.94253	AGC	.	.		0.642	LIPC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416209.1		
HERC1	8925	hgsc.bcm.edu	37	15	63915040	63915040	+	Silent	SNP	G	G	T	rs560505113		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:63915040G>T	ENST00000443617.2	-	74	13749	c.13662C>A	c.(13660-13662)acC>acA	p.T4554T		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4554	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CCACTTCTGCGGTGGCATTGG	0.358																																					p.T4554T		Atlas-SNP	.											.	HERC1	624	.	0			c.C13662A						.						45.0	44.0	44.0					15																	63915040		1834	4087	5921	SO:0001819	synonymous_variant	8925	exon74			TTCTGCGGTGGCA	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13662C>A	chr15.hg19:g.63915040G>T		77.0	0.0		71.0	4.0	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	hg19	CCDS45277.1																																																																																			.	.		0.358	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
HERC1	8925	hgsc.bcm.edu	37	15	63920929	63920929	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:63920929C>T	ENST00000443617.2	-	70	13139	c.13052G>A	c.(13051-13053)gGc>gAc	p.G4351D		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4351					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						GTGGCAGCGGCCAGCCGAGAT	0.522																																					p.G4351D		Atlas-SNP	.											.	HERC1	624	.	0			c.G13052A						.						84.0	89.0	87.0					15																	63920929		1959	4170	6129	SO:0001583	missense	8925	exon70			CAGCGGCCAGCCG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13052G>A	chr15.hg19:g.63920929C>T	ENSP00000390158:p.Gly4351Asp	157.0	0.0		130.0	6.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	32	5.150691	0.94645	.	.	ENSG00000103657	ENST00000443617	D	0.98135	-4.74	5.89	5.89	0.94794	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.99254	0.9740	H	0.95982	3.75	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98880	1.0769	10	0.87932	D	0	.	20.2469	0.98398	0.0:1.0:0.0:0.0	.	4351	Q15751	HERC1_HUMAN	D	4351	ENSP00000390158:G4351D	ENSP00000390158:G4351D	G	-	2	0	HERC1	61707982	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	7.758000	0.85224	2.781000	0.95711	0.555000	0.69702	GGC	.	.		0.522	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
TRIP4	9325	hgsc.bcm.edu	37	15	64689807	64689807	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:64689807A>G	ENST00000261884.3	+	4	468	c.408A>G	c.(406-408)gcA>gcG	p.A136A	RN7SL595P_ENST00000582065.1_RNA|TRIP4_ENST00000559565.1_3'UTR	NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	136					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						TACGATAGGCACAAGAGAACA	0.393																																					p.A136A		Atlas-SNP	.											.	TRIP4	43	.	0			c.A408G						.						64.0	61.0	62.0					15																	64689807		2203	4300	6503	SO:0001819	synonymous_variant	9325	exon4			ATAGGCACAAGAG	L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"""-"""	12310	protein-coding gene	gene with protein product	"""zinc finger, C2HC5-type"""	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.408A>G	chr15.hg19:g.64689807A>G		128.0	0.0		94.0	5.0	NM_016213	B2RAS0|Q96ED7|Q9UKH0	Silent	SNP	ENST00000261884.3	hg19	CCDS10194.1																																																																																			.	.		0.393	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256635.2	NM_016213	
SPG21	51324	hgsc.bcm.edu	37	15	65261687	65261687	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:65261687C>A	ENST00000204566.2	-	7	869	c.574G>T	c.(574-576)Ggt>Tgt	p.G192C	SPG21_ENST00000559199.1_Missense_Mutation_p.G38C|SPG21_ENST00000433215.2_Missense_Mutation_p.G192C|SPG21_ENST00000416889.2_Missense_Mutation_p.G165C	NM_016630.3	NP_057714.1	Q9NZD8	SPG21_HUMAN	spastic paraplegia 21 (autosomal recessive, Mast syndrome)	192					antigen receptor-mediated signaling pathway (GO:0050851)|cell death (GO:0008219)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network transport vesicle (GO:0030140)	CD4 receptor binding (GO:0042609)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10						TCACTCTGACCCAAACTTTCT	0.333																																					p.G192C		Atlas-SNP	.											.	SPG21	29	.	0			c.G574T						.						97.0	100.0	99.0					15																	65261687		2202	4299	6501	SO:0001583	missense	51324	exon7			TCTGACCCAAACT	AF208861	CCDS10198.1, CCDS45279.1	15q21-q22	2008-02-05	2007-04-23		ENSG00000090487	ENSG00000090487			20373	protein-coding gene	gene with protein product	"""maspardin"""	608181				11113139, 14564668	Standard	XM_006720564		Approved	ACP33, GL010, BM-019, MAST	uc002aoe.3	Q9NZD8	OTTHUMG00000133098	ENST00000204566.2:c.574G>T	chr15.hg19:g.65261687C>A	ENSP00000204566:p.Gly192Cys	88.0	0.0		94.0	4.0	NM_001127889	B4DW44|Q6ZMB6	Missense_Mutation	SNP	ENST00000204566.2	hg19	CCDS10198.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.259264	0.80246	.	.	ENSG00000090487	ENST00000204566;ENST00000416889;ENST00000433215	T;T;T	0.67345	-0.26;-0.26;-0.26	5.96	5.96	0.96718	.	0.098210	0.85682	D	0.000000	T	0.64305	0.2586	N	0.22421	0.69	0.47584	D	0.999461	P;P	0.45396	0.857;0.808	P;P	0.52758	0.584;0.708	T	0.65393	-0.6179	10	0.52906	T	0.07	-12.482	12.307	0.54908	0.0:0.9226:0.0:0.0774	.	165;192	Q9NZD8-2;Q9NZD8	.;SPG21_HUMAN	C	192;165;192	ENSP00000204566:G192C;ENSP00000394846:G165C;ENSP00000404111:G192C	ENSP00000204566:G192C	G	-	1	0	SPG21	63048740	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.483000	0.60264	2.815000	0.96918	0.650000	0.86243	GGT	.	.		0.333	SPG21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256758.3	NM_016630	
IQCH	64799	hgsc.bcm.edu	37	15	67664646	67664646	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:67664646C>A	ENST00000335894.4	+	9	1017	c.951C>A	c.(949-951)gtC>gtA	p.V317V	IQCH_ENST00000358767.3_Silent_p.V144V|IQCH_ENST00000546225.1_Silent_p.V65V|IQCH_ENST00000360277.4_Silent_p.V69V	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	317										NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(2)|pancreas(2)|skin(5)|upper_aerodigestive_tract(1)	33				Colorectal(3;0.0856)		TACCAGAAGTCAAAATAAAAG	0.418																																					p.V317V		Atlas-SNP	.											.	IQCH	81	.	0			c.C951A						.						114.0	120.0	118.0					15																	67664646		2201	4299	6500	SO:0001819	synonymous_variant	64799	exon9			AGAAGTCAAAATA	AY014282	CCDS10223.1, CCDS32273.1, CCDS10223.2, CCDS61680.1, CCDS61681.1	15q23	2005-10-24			ENSG00000103599	ENSG00000103599			25721	protein-coding gene	gene with protein product		612523				12477932	Standard	NM_022784		Approved	FLJ12476	uc002aqo.2	Q86VS3	OTTHUMG00000133231	ENST00000335894.4:c.951C>A	chr15.hg19:g.67664646C>A		120.0	0.0		139.0	6.0	NM_001031715	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	Silent	SNP	ENST00000335894.4	hg19	CCDS32273.1																																																																																			.	.		0.418	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256969.1	NM_022784	
MAP2K5	5607	hgsc.bcm.edu	37	15	67835762	67835762	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:67835762A>G	ENST00000178640.5	+	1	716	c.89A>G	c.(88-90)gAc>gGc	p.D30G	RP11-502I4.3_ENST00000604760.1_lincRNA|MAP2K5_ENST00000395476.2_Missense_Mutation_p.D30G|MAP2K5_ENST00000560591.1_3'UTR	NM_145160.2	NP_660143.1	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5	30	OPR.				activation of MAPK activity (GO:0000187)|cellular response to growth factor stimulus (GO:0071363)|cellular response to laminar fluid shear stress (GO:0071499)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|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 interleukin-8 biosynthetic process (GO:0045415)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|skin(1)	16						GGCGCGGTGGACTGGACAGTG	0.562																																					p.D30G		Atlas-SNP	.											.	MAP2K5	70	.	0			c.A89G						.						122.0	105.0	111.0					15																	67835762		2201	4298	6499	SO:0001583	missense	5607	exon1			CGGTGGACTGGAC	U25265	CCDS10224.1, CCDS42051.1, CCDS55970.1	15q22.31	2011-06-09			ENSG00000137764	ENSG00000137764		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6845	protein-coding gene	gene with protein product		602520		PRKMK5		7759517	Standard	NM_002757		Approved	MEK5, MAPKK5, HsT17454	uc002aqu.3	Q13163	OTTHUMG00000133264	ENST00000178640.5:c.89A>G	chr15.hg19:g.67835762A>G	ENSP00000178640:p.Asp30Gly	191.0	0.0		120.0	5.0	NM_145160	B4DE43|Q92961|Q92962	Missense_Mutation	SNP	ENST00000178640.5	hg19	CCDS10224.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.710827	0.89112	.	.	ENSG00000137764	ENST00000541298;ENST00000395476;ENST00000178640	T;T	0.21543	2.0;2.0	4.95	4.95	0.65309	Phox/Bem1p (2);	0.000000	0.85682	D	0.000000	T	0.32010	0.0815	L	0.29908	0.895	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.67103	0.915;0.949;0.949	T	0.03231	-1.1058	10	0.36615	T	0.2	-16.0225	14.2868	0.66251	1.0:0.0:0.0:0.0	.	30;30;30	Q13163-2;Q13163;B2RD76	.;MP2K5_HUMAN;.	G	30	ENSP00000378859:D30G;ENSP00000178640:D30G	ENSP00000178640:D30G	D	+	2	0	MAP2K5	65622816	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.066000	0.71185	1.852000	0.53769	0.533000	0.62120	GAC	.	.		0.562	MAP2K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257041.1	NM_145162	
CLN6	54982	hgsc.bcm.edu	37	15	68504132	68504132	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:68504132C>T	ENST00000249806.5	-	4	524	c.367G>A	c.(367-369)Ggt>Agt	p.G123S	CLN6_ENST00000418702.2_Intron|CLN6_ENST00000566347.1_Intron|CLN6_ENST00000538696.1_Missense_Mutation_p.G155S|CLN6_ENST00000565471.1_Intron|RP11-315D16.2_ENST00000562767.1_Intron|CLN6_ENST00000564752.1_Missense_Mutation_p.G123S	NM_017882.2	NP_060352.1	Q9NWW5	CLN6_HUMAN	ceroid-lipofuscinosis, neuronal 6, late infantile, variant	123			G -> D (in CLN6; dbSNP:rs28939384). {ECO:0000269|PubMed:11727201}.		cell death (GO:0008219)|cellular macromolecule catabolic process (GO:0044265)|cholesterol metabolic process (GO:0008203)|ganglioside metabolic process (GO:0001573)|glycosaminoglycan metabolic process (GO:0030203)|locomotion involved in locomotory behavior (GO:0031987)|lysosomal lumen acidification (GO:0007042)|positive regulation of proteolysis (GO:0045862)|protein catabolic process (GO:0030163)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						ATGCTGGCACCCATGATGAAG	0.592																																					p.G123S		Atlas-SNP	.											.	CLN6	16	.	0			c.G367A						.						126.0	117.0	120.0					15																	68504132		2200	4298	6498	SO:0001583	missense	54982	exon4			TGGCACCCATGAT	AK000568	CCDS10227.1	15q23	2014-09-17			ENSG00000128973	ENSG00000128973			2077	protein-coding gene	gene with protein product		606725				9097964, 11727201	Standard	NM_017882		Approved	FLJ20561, HsT18960, nclf	uc002arf.3	Q9NWW5	OTTHUMG00000133286	ENST00000249806.5:c.367G>A	chr15.hg19:g.68504132C>T	ENSP00000249806:p.Gly123Ser	136.0	0.0		98.0	4.0	NM_017882	A8K560|B4DDH6|Q6IAB1|Q96SR0	Missense_Mutation	SNP	ENST00000249806.5	hg19	CCDS10227.1	.	.	.	.	.	.	.	.	.	.	C	35	5.510038	0.96386	.	.	ENSG00000128973	ENST00000249806;ENST00000538696	D;D	0.96774	-4.12;-4.12	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	D	0.97801	0.9278	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98784	1.0733	10	0.87932	D	0	-25.7851	18.6234	0.91328	0.0:1.0:0.0:0.0	.	155;123	B4DDH6;Q9NWW5	.;CLN6_HUMAN	S	123;155	ENSP00000249806:G123S;ENSP00000445770:G155S	ENSP00000249806:G123S	G	-	1	0	CLN6	66291186	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.369000	0.79578	2.388000	0.81334	0.511000	0.50034	GGT	.	.		0.592	CLN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257066.1	NM_017882	
GLCE	26035	hgsc.bcm.edu	37	15	69561466	69561466	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:69561466T>C	ENST00000261858.2	+	5	1965	c.1737T>C	c.(1735-1737)caT>caC	p.H579H	GLCE_ENST00000559420.2_Silent_p.H515H	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	579					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	heparosan-N-sulfate-glucuronate 5-epimerase activity (GO:0047464)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)|UDP-glucuronate 5'-epimerase activity (GO:0050379)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						GGGACTATCATACCACCCACA	0.493																																					p.H579H		Atlas-SNP	.											.	GLCE	48	.	0			c.T1737C						.						213.0	207.0	209.0					15																	69561466		2200	4298	6498	SO:0001819	synonymous_variant	26035	exon5			CTATCATACCACC	AB020643	CCDS32277.1	15q23	2007-01-30	2007-01-30			ENSG00000138604	5.1.3.12		17855	protein-coding gene	gene with protein product	"""heparan sulfate epimerase"""	612134	"""D-glucuronyl C5-epimerase"", ""UDP-glucuronic acid epimerase"""			15853773	Standard	NM_015554		Approved	KIAA0836, HSEPI	uc002ary.1	O94923		ENST00000261858.2:c.1737T>C	chr15.hg19:g.69561466T>C		100.0	0.0		88.0	4.0	NM_015554	Q6GUQ2	Silent	SNP	ENST00000261858.2	hg19	CCDS32277.1																																																																																			.	.		0.493	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554	
MYO9A	4649	hgsc.bcm.edu	37	15	72152137	72152137	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:72152137A>G	ENST00000356056.5	-	34	6564	c.6092T>C	c.(6091-6093)tTa>tCa	p.L2031S	RNA5SP399_ENST00000364003.1_RNA|MYO9A_ENST00000424560.1_Splice_Site_p.L2102S|MYO9A_ENST00000444904.1_Splice_Site_p.L2012S|MYO9A_ENST00000564571.1_Splice_Site_p.L2031S	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	2031	Tail.				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						ATACTTGCATACTGAAAAATA	0.328																																					p.L2031S		Atlas-SNP	.											.	MYO9A	203	.	0			c.T6092C						.						98.0	95.0	96.0					15																	72152137		2199	4297	6496	SO:0001630	splice_region_variant	4649	exon34			TTGCATACTGAAA	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.6092-1T>C	chr15.hg19:g.72152137A>G		97.0	0.0		53.0	5.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.971708	0.74246	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	T;T;T	0.14391	2.51;2.51;2.51	5.02	5.02	0.67125	Protein kinase C-like, phorbol ester/diacylglycerol binding (3);	.	.	.	.	T	0.24586	0.0596	L	0.31476	0.935	0.58432	D	0.999997	D	0.76494	0.999	D	0.87578	0.998	T	0.03000	-1.1084	9	0.25106	T	0.35	.	14.7384	0.69434	1.0:0.0:0.0:0.0	.	2031	B2RTY4	MYO9A_HUMAN	S	2031;2102;2012	ENSP00000348349:L2031S;ENSP00000399162:L2102S;ENSP00000398250:L2012S	ENSP00000348349:L2031S	L	-	2	0	MYO9A	69939191	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.060000	0.76692	1.881000	0.54492	0.528000	0.53228	TTA	.	.		0.328	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	Missense_Mutation
ARIH1	25820	hgsc.bcm.edu	37	15	72859489	72859489	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:72859489A>G	ENST00000379887.4	+	9	1311	c.997A>G	c.(997-999)Acc>Gcc	p.T333A		NM_005744.3	NP_005735.2	Q9Y4X5	ARI1_HUMAN	ariadne RBR E3 ubiquitin protein ligase 1	333					cytokine-mediated signaling pathway (GO:0019221)|protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ubiquitin ligase complex (GO:0000151)	small conjugating protein ligase activity (GO:0019787)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	14						TGACAGTGAAACCTCCAATTG	0.333																																					p.T333A		Atlas-SNP	.											.	ARIH1	42	.	0			c.A997G						.						130.0	126.0	128.0					15																	72859489		2198	4297	6495	SO:0001583	missense	25820	exon9			AGTGAAACCTCCA	AF072832	CCDS10244.1	15q24	2013-10-03	2013-10-03		ENSG00000166233	ENSG00000166233			689	protein-coding gene	gene with protein product	"""ariadne, Drosophila, homolog of"""	605624	"""ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1"", ""ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila)"""			10521492, 24058416	Standard	NM_005744		Approved	HARI, HHARI, UBCH7BP, ARI	uc002aut.4	Q9Y4X5	OTTHUMG00000133474	ENST00000379887.4:c.997A>G	chr15.hg19:g.72859489A>G	ENSP00000369217:p.Thr333Ala	196.0	0.0		149.0	6.0	NM_005744	B2R6U3|O76026|Q9H3T6|Q9UEN0|Q9UP39	Missense_Mutation	SNP	ENST00000379887.4	hg19	CCDS10244.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.889666	0.91889	.	.	ENSG00000166233	ENST00000379887;ENST00000299305	D	0.87103	-2.21	5.83	5.83	0.93111	Zinc finger, C6HC-type (2);Zinc finger, RING-type (1);	0.000000	0.85682	D	0.000000	D	0.94640	0.8272	M	0.90082	3.085	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.95540	0.8611	10	0.87932	D	0	.	16.2506	0.82485	1.0:0.0:0.0:0.0	.	333	Q9Y4X5	ARI1_HUMAN	A	333;303	ENSP00000369217:T333A	ENSP00000299305:T303A	T	+	1	0	ARIH1	70646543	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.957000	0.93082	2.237000	0.73441	0.529000	0.55759	ACC	.	.		0.333	ARIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257350.1	NM_005744	
BBS4	585	hgsc.bcm.edu	37	15	73028183	73028183	+	Missense_Mutation	SNP	A	A	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:73028183A>C	ENST00000268057.4	+	14	1165	c.1124A>C	c.(1123-1125)aAc>aCc	p.N375T	BBS4_ENST00000539603.1_Missense_Mutation_p.N363T|BBS4_ENST00000395205.2_Missense_Mutation_p.N383T|BBS4_ENST00000542334.1_Missense_Mutation_p.N203T	NM_033028.4	NP_149017.2	Q96RK4	BBS4_HUMAN	Bardet-Biedl syndrome 4	375	Required for localization to centrosomes.				adult behavior (GO:0030534)|brain morphogenesis (GO:0048854)|centrosome organization (GO:0051297)|cerebral cortex development (GO:0021987)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|dendrite development (GO:0016358)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|hippocampus development (GO:0021766)|intracellular transport (GO:0046907)|maintenance of protein location in nucleus (GO:0051457)|melanosome transport (GO:0032402)|metabolic process (GO:0008152)|microtubule anchoring at centrosome (GO:0034454)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of systemic arterial blood pressure (GO:0003085)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of cilium assembly (GO:0045724)|positive regulation of multicellular organism growth (GO:0040018)|protein localization to centrosome (GO:0071539)|protein localization to organelle (GO:0033365)|protein transport (GO:0015031)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|regulation of cytokinesis (GO:0032465)|regulation of lipid metabolic process (GO:0019216)|retina homeostasis (GO:0001895)|retinal rod cell development (GO:0046548)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)|spermatid development (GO:0007286)|striatum development (GO:0021756)|visual perception (GO:0007601)	BBSome (GO:0034464)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary membrane (GO:0060170)|cilium (GO:0005929)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|pericentriolar material (GO:0000242)	alpha-tubulin binding (GO:0043014)|beta-tubulin binding (GO:0048487)|dynactin binding (GO:0034452)|microtubule motor activity (GO:0003777)|RNA polymerase II repressing transcription factor binding (GO:0001103)			autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(1)	19						CCTTTAGTAAACCTGAACTAT	0.463									Bardet-Biedl syndrome																												p.N375T		Atlas-SNP	.											.	BBS4	34	.	0			c.A1124C						.						156.0	153.0	154.0					15																	73028183		2198	4297	6495	SO:0001583	missense	585	exon14	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TAGTAAACCTGAA	AF090947	CCDS10246.1, CCDS58377.1	15q22.3-q23	2013-01-10			ENSG00000140463	ENSG00000140463		"""Tetratricopeptide (TTC) repeat domain containing"""	969	protein-coding gene	gene with protein product		600374				7711739, 11381270	Standard	NM_033028		Approved		uc002avb.3	Q96RK4	OTTHUMG00000133510	ENST00000268057.4:c.1124A>C	chr15.hg19:g.73028183A>C	ENSP00000268057:p.Asn375Thr	115.0	0.0		92.0	4.0	NM_033028	B4E178|Q53DZ5|Q8NHU9|Q96H45	Missense_Mutation	SNP	ENST00000268057.4	hg19	CCDS10246.1	.	.	.	.	.	.	.	.	.	.	A	16.09	3.025248	0.54683	.	.	ENSG00000140463	ENST00000542334;ENST00000268057;ENST00000539603;ENST00000395205	T;T;T;T	0.77750	0.69;-1.12;-1.12;-1.12	5.68	4.57	0.56435	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.045776	0.85682	D	0.000000	T	0.81903	0.4921	M	0.66939	2.045	0.52501	D	0.99995	D;D;D	0.57571	0.979;0.98;0.964	P;P;P	0.57009	0.74;0.811;0.554	T	0.79369	-0.1832	10	0.32370	T	0.25	-16.5762	10.1449	0.42758	0.9247:0.0:0.0753:0.0	.	363;383;375	F5H7I8;Q96RK4-2;Q96RK4	.;.;BBS4_HUMAN	T	203;375;363;383	ENSP00000445964:N203T;ENSP00000268057:N375T;ENSP00000442492:N363T;ENSP00000378631:N383T	ENSP00000268057:N375T	N	+	2	0	BBS4	70815236	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.976000	0.63785	0.999000	0.39023	0.528000	0.53228	AAC	.	.		0.463	BBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257473.2	NM_033028	
ISLR	3671	hgsc.bcm.edu	37	15	74468160	74468160	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:74468160G>A	ENST00000249842.3	+	2	1318	c.961G>A	c.(961-963)Gag>Aag	p.E321K	RP11-665J16.1_ENST00000561647.1_RNA|ISLR_ENST00000395118.1_Missense_Mutation_p.E321K	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	321	Ig-like.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						TGGCAAGCTGGAGGAAGGCAC	0.657																																					p.E321K		Atlas-SNP	.											.	ISLR	49	.	0			c.G961A						.						38.0	39.0	39.0					15																	74468160		2198	4296	6494	SO:0001583	missense	3671	exon2			AAGCTGGAGGAAG	AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"""Immunoglobulin superfamily / I-set domain containing"""	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.961G>A	chr15.hg19:g.74468160G>A	ENSP00000249842:p.Glu321Lys	67.0	0.0		36.0	16.0	NM_201526		Missense_Mutation	SNP	ENST00000249842.3	hg19	CCDS10260.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.580695	0.86748	.	.	ENSG00000129009	ENST00000249842;ENST00000395118	T;T	0.67698	-0.28;-0.28	4.37	4.37	0.52481	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.152349	0.29410	U	0.012229	T	0.71888	0.3393	M	0.70275	2.135	0.52501	D	0.999956	P	0.47484	0.896	P	0.50934	0.654	T	0.75687	-0.3231	10	0.72032	D	0.01	.	10.5949	0.45331	0.0896:0.0:0.9104:0.0	.	321	O14498	ISLR_HUMAN	K	321	ENSP00000249842:E321K;ENSP00000378550:E321K	ENSP00000249842:E321K	E	+	1	0	ISLR	72255213	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	7.846000	0.86887	1.987000	0.57996	0.313000	0.20887	GAG	.	.		0.657	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545	
CCDC33	80125	hgsc.bcm.edu	37	15	74573035	74573035	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:74573035A>G	ENST00000398814.3	+	9	1347	c.916A>G	c.(916-918)Aac>Gac	p.N306D	CCDC33_ENST00000321288.5_Missense_Mutation_p.N509D	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	509	C2.									breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GTGGACCCTCAACCAGCCCCT	0.597																																					p.N306D		Atlas-SNP	.											.	CCDC33	160	.	0			c.A916G						.						82.0	93.0	90.0					15																	74573035		1916	4134	6050	SO:0001583	missense	80125	exon9			ACCCTCAACCAGC	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.916A>G	chr15.hg19:g.74573035A>G	ENSP00000381795:p.Asn306Asp	97.0	0.0		87.0	4.0	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	hg19	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	A	1.459	-0.562826	0.03939	.	.	ENSG00000140481	ENST00000321288;ENST00000398814	T;T	0.23147	1.92;2.25	5.28	-6.73	0.01749	.	1.336340	0.04936	N	0.457774	T	0.15046	0.0363	L	0.47716	1.5	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.31166	-0.9953	10	0.08599	T	0.76	.	3.1067	0.06344	0.4846:0.1094:0.2974:0.1085	.	509;306	C9JFX2;Q8N5R6-6	.;.	D	509;306	ENSP00000325012:N509D;ENSP00000381795:N306D	ENSP00000325012:N509D	N	+	1	0	CCDC33	72360088	0.000000	0.05858	0.002000	0.10522	0.098000	0.18820	-0.360000	0.07622	-0.847000	0.04168	-1.235000	0.01560	AAC	.	.		0.597	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791	
MPI	4351	hgsc.bcm.edu	37	15	75183814	75183814	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:75183814A>G	ENST00000352410.4	+	3	306	c.239A>G	c.(238-240)gAc>gGc	p.D80G	MPI_ENST00000563422.1_Missense_Mutation_p.D80G|MPI_ENST00000323744.6_Missense_Mutation_p.D80G|MPI_ENST00000563786.1_Missense_Mutation_p.D60G|MPI_ENST00000564003.1_Missense_Mutation_p.D30G|MPI_ENST00000535694.1_Missense_Mutation_p.D30G|MPI_ENST00000562606.1_Missense_Mutation_p.D60G|MPI_ENST00000565576.1_Missense_Mutation_p.D80G|MPI_ENST00000566377.1_Missense_Mutation_p.D80G			P34949	MPI_HUMAN	mannose phosphate isomerase	80					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	mannose-6-phosphate isomerase activity (GO:0004476)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						GAGAACCAGGACAGCTTGGGC	0.542																																					p.D80G		Atlas-SNP	.											.	MPI	32	.	0			c.A239G						.						204.0	172.0	183.0					15																	75183814		2197	4295	6492	SO:0001583	missense	4351	exon3			ACCAGGACAGCTT		CCDS10272.1, CCDS73756.1, CCDS73757.1, CCDS73758.1	15q24.1	2013-09-19			ENSG00000178802	ENSG00000178802	5.3.1.8		7216	protein-coding gene	gene with protein product	"""mannose-6-phosphate isomerase"""	154550					Standard	NM_002435		Approved		uc002azc.1	P34949	OTTHUMG00000142826	ENST00000352410.4:c.239A>G	chr15.hg19:g.75183814A>G	ENSP00000318318:p.Asp80Gly	130.0	0.0		111.0	6.0	NM_002435	A8K8K9|Q96AB0	Missense_Mutation	SNP	ENST00000352410.4	hg19	CCDS10272.1	.	.	.	.	.	.	.	.	.	.	A	10.84	1.464264	0.26335	.	.	ENSG00000178802	ENST00000352410;ENST00000535694;ENST00000379693;ENST00000323744	D;D;D	0.95821	-3.82;-3.82;-3.82	4.86	2.31	0.28768	Cupin, RmlC-type (1);RmlC-like jelly roll fold (1);	0.528034	0.21846	N	0.068258	D	0.88945	0.6575	N	0.26162	0.8	0.24222	N	0.995434	B;B;B;B;B	0.10296	0.003;0.002;0.002;0.0;0.0	B;B;B;B;B	0.15052	0.006;0.012;0.003;0.002;0.005	T	0.77523	-0.2556	10	0.29301	T	0.29	.	6.4655	0.21980	0.6758:0.2345:0.0897:0.0	.	30;80;80;60;80	B4DYB8;B4DFC4;P34949-2;Q8NHZ6;P34949	.;.;.;.;MPI_HUMAN	G	80;30;60;80	ENSP00000318318:D80G;ENSP00000440447:D30G;ENSP00000318192:D80G	ENSP00000318192:D80G	D	+	2	0	MPI	72970867	0.945000	0.32115	0.999000	0.59377	0.965000	0.64279	1.729000	0.38115	1.826000	0.53198	0.379000	0.24179	GAC	.	.		0.542	MPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286418.4		
RCN2	5955	hgsc.bcm.edu	37	15	77241444	77241444	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:77241444G>T	ENST00000394885.3	+	7	1058	c.835G>T	c.(835-837)Ggt>Tgt	p.G279C	RCN2_ENST00000394883.3_Missense_Mutation_p.G178C|RCN2_ENST00000320963.5_Missense_Mutation_p.G297C	NM_002902.2	NP_002893.1	Q14257	RCN2_HUMAN	reticulocalbin 2, EF-hand calcium binding domain	279	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(2)|large_intestine(2)|lung(1)	7						GGATTTGAATGGTGACAAAAA	0.363																																					p.G297C		Atlas-SNP	.											.	RCN2	16	.	0			c.G889T						.						124.0	135.0	131.0					15																	77241444		2196	4294	6490	SO:0001583	missense	5955	exon8			TTGAATGGTGACA	X78669	CCDS10291.1, CCDS61719.1	15q22.33-q24.1	2013-01-10			ENSG00000117906	ENSG00000117906		"""EF-hand domain containing"""	9935	protein-coding gene	gene with protein product	"""Reticulocalbin 2, EF-hand calcium binding domain (endoplasmic reticulum calcium-binding protein, 55kD)"""	602584				9533013, 7624774	Standard	NM_002902		Approved	ERC-55, E6BP, ERC55, TCBP49	uc002bcd.3	Q14257	OTTHUMG00000143730	ENST00000394885.3:c.835G>T	chr15.hg19:g.77241444G>T	ENSP00000378349:p.Gly279Cys	62.0	0.0		74.0	5.0	NM_001271837	A8MTG6|F8WCY5|Q53XN8	Missense_Mutation	SNP	ENST00000394885.3	hg19	CCDS10291.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.531715	0.64972	.	.	ENSG00000117906	ENST00000394885;ENST00000320963;ENST00000394883	T;T;T	0.75050	-0.9;-0.9;-0.9	6.05	1.74	0.24563	EF-hand-like domain (1);	0.397599	0.32736	N	0.005703	T	0.81173	0.4767	M	0.79614	2.46	0.36877	D	0.889217	D;P;P	0.63880	0.993;0.929;0.78	P;P;P	0.60173	0.87;0.599;0.526	T	0.82360	-0.0496	10	0.72032	D	0.01	-4.3565	8.1976	0.31407	0.3611:0.0:0.6389:0.0	.	178;297;279	A8MXP8;F8WCY5;Q14257	.;.;RCN2_HUMAN	C	279;297;178	ENSP00000378349:G279C;ENSP00000319739:G297C;ENSP00000378347:G178C	ENSP00000319739:G297C	G	+	1	0	RCN2	75028499	1.000000	0.71417	0.433000	0.26760	0.997000	0.91878	4.217000	0.58547	0.324000	0.23333	0.650000	0.86243	GGT	.	.		0.363	RCN2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289795.1	NM_002902	
SH2D7	646892	hgsc.bcm.edu	37	15	78386536	78386536	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:78386536T>C	ENST00000328828.5	+	2	259	c.259T>C	c.(259-261)Tcc>Ccc	p.S87P	SNORA63_ENST00000362763.1_RNA|SH2D7_ENST00000409568.2_5'UTR	NM_001101404.1	NP_001094874.1	A6NKC9	SH2D7_HUMAN	SH2 domain containing 7	87	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.									endometrium(2)|kidney(2)|lung(3)	7						CTACATCTTGTCCTACAGGTA	0.557																																					p.S87P		Atlas-SNP	.											.	SH2D7	26	.	0			c.T259C						.						41.0	45.0	44.0					15																	78386536		2003	4172	6175	SO:0001583	missense	646892	exon2			ATCTTGTCCTACA		CCDS45315.1	15q25.1	2013-02-14			ENSG00000183476	ENSG00000183476		"""SH2 domain containing"""	34549	protein-coding gene	gene with protein product							Standard	NM_001101404		Approved	LOC646892	uc010blb.1	A6NKC9	OTTHUMG00000154271	ENST00000328828.5:c.259T>C	chr15.hg19:g.78386536T>C	ENSP00000327846:p.Ser87Pro	80.0	0.0		63.0	4.0	NM_001101404		Missense_Mutation	SNP	ENST00000328828.5	hg19	CCDS45315.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.373491	0.82573	.	.	ENSG00000183476	ENST00000328828	D	0.93426	-3.22	5.57	5.57	0.84162	SH2 motif (4);	.	.	.	.	D	0.98027	0.9350	H	0.98542	4.26	0.25221	N	0.989907	D	0.89917	1.0	D	0.91635	0.999	D	0.93691	0.7007	9	0.87932	D	0	.	12.1183	0.53878	0.0:0.0:0.0:1.0	.	87	A6NKC9	SH2D7_HUMAN	P	87	ENSP00000327846:S87P	ENSP00000327846:S87P	S	+	1	0	SH2D7	76173591	1.000000	0.71417	0.985000	0.45067	0.984000	0.73092	5.665000	0.68052	2.115000	0.64714	0.454000	0.30748	TCC	.	.		0.557	SH2D7-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000334660.2	NM_001101404	
AP3B2	8120	hgsc.bcm.edu	37	15	83358199	83358199	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:83358199A>G	ENST00000261722.3	-	2	327	c.120T>C	c.(118-120)gaT>gaC	p.D40D	RP11-752G15.3_ENST00000560650.1_RNA|AP3B2_ENST00000542200.1_Silent_p.D40D|AP3B2_ENST00000535359.1_Silent_p.D40D|AP3B2_ENST00000535348.1_Silent_p.D40D|AP3B2_ENST00000561455.1_5'UTR	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	40					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)			CCTTCAGGTCATCATGCCTGG	0.572																																					p.D40D		Atlas-SNP	.											.	AP3B2	103	.	0			c.T120C						.						62.0	58.0	59.0					15																	83358199		2029	4191	6220	SO:0001819	synonymous_variant	8120	exon2			CAGGTCATCATGC	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.120T>C	chr15.hg19:g.83358199A>G		136.0	0.0		95.0	4.0	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Silent	SNP	ENST00000261722.3	hg19	CCDS45331.1																																																																																			.	.		0.572	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1		
HDGFRP3	50810	hgsc.bcm.edu	37	15	83832817	83832817	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:83832817A>G	ENST00000299633.4	-	2	698	c.95T>C	c.(94-96)cTc>cCc	p.L32P		NM_016073.3	NP_057157.1	Q9Y3E1	HDGR3_HUMAN		32	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.L32P(1)		kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7						GCCCTCTGGGAGTTCATCAAT	0.363																																					p.L32P		Atlas-SNP	.											HDGFRP3,NS,carcinoma,0,1	HDGFRP3	17	.	1	Substitution - Missense(1)	kidney(1)	c.T95C						.						116.0	111.0	113.0					15																	83832817		2203	4300	6503	SO:0001583	missense	0	exon2			TCTGGGAGTTCAT																												ENST00000299633.4:c.95T>C	chr15.hg19:g.83832817A>G	ENSP00000299633:p.Leu32Pro	109.0	0.0		107.0	5.0	NM_016073		Missense_Mutation	SNP	ENST00000299633.4	hg19	CCDS32314.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.780179	0.90195	.	.	ENSG00000166503	ENST00000299633	T	0.69175	-0.38	5.19	5.19	0.71726	PWWP (3);	0.219879	0.40640	N	0.001060	T	0.69043	0.3067	N	0.25890	0.77	0.80722	D	1	P	0.52463	0.953	P	0.62649	0.905	T	0.65010	-0.6272	10	0.22109	T	0.4	.	15.5098	0.75772	1.0:0.0:0.0:0.0	.	32	Q9Y3E1	HDGR3_HUMAN	P	32	ENSP00000299633:L32P	ENSP00000299633:L32P	L	-	2	0	AC024270.1	81623821	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.010000	0.93611	2.304000	0.77564	0.528000	0.53228	CTC	.	.		0.363	HDGFRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419898.1		
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84694002	84694002	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:84694002T>C	ENST00000286744.5	+	27	4694	c.4470T>C	c.(4468-4470)agT>agC	p.S1490S	ADAMTSL3_ENST00000567476.1_Silent_p.S1490S	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	1490	TSP type-1 9. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			GGTTCACAAGTGTGTGGTCAC	0.502																																					p.S1490S		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.T4470C						.						166.0	133.0	144.0					15																	84694002		2203	4299	6502	SO:0001819	synonymous_variant	57188	exon27			CACAAGTGTGTGG	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.4470T>C	chr15.hg19:g.84694002T>C		106.0	0.0		54.0	5.0	NM_207517	A1A566|A1A567|Q9ULI7	Silent	SNP	ENST00000286744.5	hg19	CCDS10326.1																																																																																			.	.		0.502	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
GOLGA6L4	643707	hgsc.bcm.edu	37	15	84909434	84909434	+	Missense_Mutation	SNP	G	G	A	rs202197056	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:84909434G>A	ENST00000510439.2	+	6	1390	c.1328G>A	c.(1327-1329)cGg>cAg	p.R443Q	GOLGA6L4_ENST00000424966.1_Missense_Mutation_p.R24Q|GOLGA6L4_ENST00000422563.2_Missense_Mutation_p.R119Q	NM_001267536.1	NP_001254465.1	A6NEF3	GG6L4_HUMAN	golgin A6 family-like 4	443								p.R443Q(6)									GAGAGGCTGCGGGAGCTGGAG	0.667																																					p.R307Q		Atlas-SNP	.											RP11-671M22.1_ENST00000510439,NS,carcinoma,0,20	.	.	.	6	Substitution - Missense(6)	endometrium(4)|breast(2)	c.G920A						.																																			SO:0001583	missense	0	exon9			GGCTGCGGGAGCT	BC101294	CCDS73774.1	15q25.2	2012-11-16	2010-02-12		ENSG00000184206	ENSG00000184206			27256	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 4"""			12477932	Standard	NG_006151		Approved		uc021stn.2	A6NEF3	OTTHUMG00000163050	ENST00000510439.2:c.1328G>A	chr15.hg19:g.84909434G>A	ENSP00000421586:p.Arg443Gln	0.0	0.0		3.0	2.0	NM_001267536	D6REZ9	Missense_Mutation	SNP	ENST00000510439.2	hg19		.	.	.	.	.	.	.	.	.	.	.	2.055	-0.416809	0.04766	.	.	ENSG00000184206	ENST00000510439;ENST00000424966;ENST00000422563	T	0.18174	2.23	.	.	.	.	.	.	.	.	T	0.11922	0.0290	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.31364	-0.9946	5	0.42905	T	0.14	.	1.7695	0.03009	0.2735:0.0:0.4134:0.3131	.	.	.	.	Q	443;24;119	ENSP00000421586:R443Q	ENSP00000389305:R119Q	R	+	2	0	GOLGA6L4	82700438	0.000000	0.05858	0.006000	0.13384	0.018000	0.09664	-0.440000	0.06888	-0.347000	0.08299	-0.582000	0.04134	CGG	.	.		0.667	GOLGA6L4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000371478.2	NM_001267536	
ZNF592	9640	hgsc.bcm.edu	37	15	85341254	85341254	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:85341254A>G	ENST00000560079.2	+	6	2842	c.2554A>G	c.(2554-2556)Acc>Gcc	p.T852A	ZNF592_ENST00000299927.3_Missense_Mutation_p.T852A	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	852					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CCAGCACCCCACCCAGCCCCA	0.632																																					p.T852A		Atlas-SNP	.											.	ZNF592	95	.	0			c.A2554G						.						49.0	44.0	45.0					15																	85341254		2203	4299	6502	SO:0001583	missense	9640	exon6			CACCCCACCCAGC	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.2554A>G	chr15.hg19:g.85341254A>G	ENSP00000452877:p.Thr852Ala	97.0	0.0		76.0	4.0	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	hg19	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	A	3.959	-0.010658	0.07727	.	.	ENSG00000166716	ENST00000299927	T	0.28069	1.63	5.67	-1.31	0.09230	.	0.690424	0.15642	N	0.251852	T	0.11965	0.0291	N	0.12471	0.22	0.21627	N	0.999612	B	0.02656	0.0	B	0.08055	0.003	T	0.32903	-0.9889	10	0.10636	T	0.68	-8.4707	5.714	0.17950	0.5543:0.0:0.3211:0.1246	.	852	Q92610	ZN592_HUMAN	A	852	ENSP00000299927:T852A	ENSP00000299927:T852A	T	+	1	0	ZNF592	83142258	0.008000	0.16893	0.963000	0.40424	0.145000	0.21501	0.403000	0.20982	-0.124000	0.11724	0.459000	0.35465	ACC	.	.		0.632	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630	
AGBL1	123624	hgsc.bcm.edu	37	15	87097688	87097688	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:87097688G>T	ENST00000441037.2	+	20	2871	c.2776G>T	c.(2776-2778)Gtg>Ttg	p.V926L	AGBL1_ENST00000389298.3_Missense_Mutation_p.V657L|AGBL1_ENST00000421325.2_Missense_Mutation_p.V926L	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	926					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						GGCCCGGGTGGTGGTGTGGAG	0.542																																					p.V926L		Atlas-SNP	.											.	AGBL1	151	.	0			c.G2776T						.						29.0	31.0	31.0					15																	87097688		1910	4124	6034	SO:0001583	missense	123624	exon20			CGGGTGGTGGTGT	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2776G>T	chr15.hg19:g.87097688G>T	ENSP00000413001:p.Val926Leu	133.0	0.0		103.0	5.0	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	hg19	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.374134	0.82573	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	T;T	0.10382	2.88;2.88	4.97	4.05	0.47172	Peptidase M14, carboxypeptidase A (1);	0.199496	0.22238	U	0.062729	T	0.21674	0.0522	M	0.81341	2.54	0.33073	D	0.5356	P	0.41475	0.751	P	0.45167	0.472	T	0.39099	-0.9630	10	0.72032	D	0.01	-10.6475	12.5513	0.56227	0.0799:0.0:0.9201:0.0	.	926	Q96MI9	CBPC4_HUMAN	L	961;926;657	ENSP00000397173:V926L;ENSP00000373949:V657L	ENSP00000373949:V657L	V	+	1	0	AGBL1	84898692	1.000000	0.71417	0.977000	0.42913	0.847000	0.48162	9.477000	0.97925	1.337000	0.45525	-0.145000	0.13849	GTG	.	.		0.542	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
ZNF774	342132	hgsc.bcm.edu	37	15	90903883	90903883	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:90903883C>A	ENST00000354377.3	+	4	1006	c.820C>A	c.(820-822)Cga>Aga	p.R274R	ZNF774_ENST00000379090.5_Intron	NM_001004309.2	NP_001004309.2	Q6NX45	ZN774_HUMAN	zinc finger protein 774	274					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)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AAGCTTCAGTCGAAGCTCAAA	0.507																																					p.R274R		Atlas-SNP	.											.	ZNF774	35	.	0			c.C820A						.						56.0	57.0	56.0					15																	90903883		2199	4298	6497	SO:0001819	synonymous_variant	342132	exon4			TTCAGTCGAAGCT	BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391		"""Zinc fingers, C2H2-type"""	33108	protein-coding gene	gene with protein product							Standard	NM_001004309		Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000354377.3:c.820C>A	chr15.hg19:g.90903883C>A		86.0	0.0		84.0	5.0	NM_001004309	A8K020	Silent	SNP	ENST00000354377.3	hg19	CCDS32330.1																																																																																			.	.		0.507	ZNF774-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418048.1	NM_001004309	
IQGAP1	8826	hgsc.bcm.edu	37	15	90999516	90999516	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:90999516C>T	ENST00000268182.5	+	15	1869	c.1745C>T	c.(1744-1746)aCg>aTg	p.T582M	IQGAP1_ENST00000560738.1_Intron	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	582					cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TACCAAGACACGCTGATTAGA	0.507																																					p.T582M		Atlas-SNP	.											.	IQGAP1	140	.	0			c.C1745T						.						104.0	93.0	97.0					15																	90999516		2198	4298	6496	SO:0001583	missense	8826	exon15			AAGACACGCTGAT	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"""RasGAP-like with IQ motifs"""	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.1745C>T	chr15.hg19:g.90999516C>T	ENSP00000268182:p.Thr582Met	107.0	0.0		90.0	4.0	NM_003870	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	hg19	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.406495	0.42715	.	.	ENSG00000140575	ENST00000268182	T	0.08193	3.12	4.94	4.01	0.46588	.	0.120762	0.56097	D	0.000030	T	0.09598	0.0236	L	0.47716	1.5	0.80722	D	1	P	0.39809	0.689	B	0.37650	0.255	T	0.09228	-1.0684	10	0.52906	T	0.07	-7.9908	12.7561	0.57336	0.0:0.92:0.0:0.08	.	582	P46940	IQGA1_HUMAN	M	582	ENSP00000268182:T582M	ENSP00000268182:T582M	T	+	2	0	IQGAP1	88800520	0.606000	0.26949	0.880000	0.34516	0.955000	0.61496	1.169000	0.31871	1.289000	0.44618	0.650000	0.86243	ACG	.	.		0.507	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870	
FURIN	5045	hgsc.bcm.edu	37	15	91420416	91420416	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:91420416C>A	ENST00000268171.3	+	6	832	c.553C>A	c.(553-555)Cgg>Agg	p.R185R		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	185	Peptidase S8.				cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CCCCCAGCCTCGGTACACACA	0.547																																					p.R185R		Atlas-SNP	.											.	FURIN	85	.	0			c.C553A						.						63.0	64.0	64.0					15																	91420416		2198	4298	6496	SO:0001819	synonymous_variant	5045	exon6			CAGCCTCGGTACA	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"""paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"""	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.553C>A	chr15.hg19:g.91420416C>A		133.0	0.0		82.0	4.0	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	hg19	CCDS10364.1																																																																																			.	.		0.547	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	
SV2B	9899	hgsc.bcm.edu	37	15	91769904	91769904	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:91769904G>A	ENST00000394232.1	+	2	881	c.411G>A	c.(409-411)gaG>gaA	p.E137E	SV2B_ENST00000545111.2_Intron|SV2B_ENST00000557291.1_Intron|SV2B_ENST00000330276.4_Silent_p.E137E	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	137					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			CCAGTGCAGAGAAGGACATGT	0.478																																					p.E137E		Atlas-SNP	.											.	SV2B	98	.	0			c.G411A						.						101.0	77.0	85.0					15																	91769904		2198	4298	6496	SO:0001819	synonymous_variant	9899	exon3			TGCAGAGAAGGAC	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.411G>A	chr15.hg19:g.91769904G>A		76.0	0.0		80.0	26.0	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Silent	SNP	ENST00000394232.1	hg19	CCDS10370.1																																																																																			.	.		0.478	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
CHD2	1106	hgsc.bcm.edu	37	15	93522390	93522390	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr15:93522390A>G	ENST00000394196.4	+	22	3821	c.2753A>G	c.(2752-2754)aAg>aGg	p.K918R	CHD2_ENST00000557381.1_Missense_Mutation_p.K918R	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	918	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TTAGTTACAAAGGGGACTGTG	0.478																																					p.K918R		Atlas-SNP	.											.	CHD2	280	.	0			c.A2753G						.						182.0	183.0	183.0					15																	93522390		2197	4298	6495	SO:0001583	missense	1106	exon22			TTACAAAGGGGAC	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.2753A>G	chr15.hg19:g.93522390A>G	ENSP00000377747:p.Lys918Arg	90.0	0.0		71.0	4.0	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	A	13.70	2.314556	0.40996	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.96232	-3.95;-3.95	5.82	5.82	0.92795	Helicase, C-terminal (1);	0.000000	0.35677	U	0.003046	D	0.91429	0.7295	N	0.10972	0.075	0.80722	D	1	B;B;B	0.30664	0.083;0.005;0.289	B;B;B	0.36845	0.111;0.013;0.234	D	0.89958	0.4084	10	0.52906	T	0.07	-29.9084	10.5235	0.44934	0.9282:0.0:0.0718:0.0	.	918;918;918	A8K9Y5;O14647;O14647-2	.;CHD2_HUMAN;.	R	918	ENSP00000377747:K918R;ENSP00000451366:K918R	ENSP00000377747:K918R	K	+	2	0	CHD2	91323394	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.331000	0.72929	2.227000	0.72691	0.455000	0.32223	AAG	.	.		0.478	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
AXIN1	8312	hgsc.bcm.edu	37	16	396448	396448	+	Missense_Mutation	SNP	A	A	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:396448A>T	ENST00000262320.3	-	2	949	c.578T>A	c.(577-579)aTg>aAg	p.M193K	AXIN1_ENST00000481769.1_Intron|AXIN1_ENST00000354866.3_Missense_Mutation_p.M193K	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	193	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GTTTTCCTCCATAGTGGCCTG	0.502											OREG0003698	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.M193K		Atlas-SNP	.											.	AXIN1	290	.	0			c.T578A						.						96.0	98.0	97.0					16																	396448		2203	4300	6503	SO:0001583	missense	8312	exon2			TCCTCCATAGTGG	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	903	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 49"""	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.578T>A	chr16.hg19:g.396448A>T	ENSP00000262320:p.Met193Lys	192.0	0.0	588	114.0	20.0	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.579039	0.86645	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	T;T	0.33865	1.39;1.39	5.39	5.39	0.77823	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.038095	0.85682	D	0.000000	T	0.68769	0.3037	H	0.94925	3.6	0.80722	D	1	D;D	0.63880	0.991;0.993	P;D	0.63488	0.861;0.915	T	0.79252	-0.1880	10	0.87932	D	0	-4.3395	15.431	0.75099	1.0:0.0:0.0:0.0	.	193;193	O15169-2;O15169	.;AXIN1_HUMAN	K	193	ENSP00000262320:M193K;ENSP00000346935:M193K	ENSP00000262320:M193K	M	-	2	0	AXIN1	336449	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.206000	0.95056	2.047000	0.60756	0.533000	0.62120	ATG	.	.		0.502	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		
WDR90	197335	hgsc.bcm.edu	37	16	711769	711769	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:711769G>T	ENST00000293879.4	+	31	3846	c.3846G>T	c.(3844-3846)ggG>ggT	p.G1282G	WDR90_ENST00000549091.1_Silent_p.G1282G			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1282										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				AGCAGCGTGGGGCAGACATCA	0.657																																					p.G1282G		Atlas-SNP	.											.	WDR90	107	.	0			c.G3846T						.						44.0	52.0	49.0					16																	711769		2129	4244	6373	SO:0001819	synonymous_variant	197335	exon31			GCGTGGGGCAGAC	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.3846G>T	chr16.hg19:g.711769G>T		220.0	0.0		87.0	4.0	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	hg19	CCDS42092.1																																																																																			.	.		0.657	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
MSLN	10232	hgsc.bcm.edu	37	16	818713	818713	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:818713C>A	ENST00000382862.3	+	17	1968	c.1873C>A	c.(1873-1875)Cta>Ata	p.L625I	MIR662_ENST00000384847.1_RNA|MSLN_ENST00000545450.2_Missense_Mutation_p.L617I|MSLN_ENST00000566549.1_Missense_Mutation_p.L617I|MSLN_ENST00000563941.1_Missense_Mutation_p.L617I	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	625					cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				GGCACTGCTCCTAGCCTCCAC	0.697																																					p.L625I		Atlas-SNP	.											.	MSLN	109	.	0			c.C1873A						.						66.0	55.0	59.0					16																	818713		2194	4294	6488	SO:0001583	missense	10232	exon17			CTGCTCCTAGCCT	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.1873C>A	chr16.hg19:g.818713C>A	ENSP00000372313:p.Leu625Ile	149.0	0.0		59.0	4.0	NM_013404	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	hg19	CCDS32356.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.301512	0.23736	.	.	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.12255	2.7;2.7	2.84	-5.01	0.02991	.	0.284179	0.23268	N	0.050054	T	0.07324	0.0185	L	0.38175	1.15	0.09310	N	1	P;P;P	0.39862	0.642;0.692;0.642	B;B;B	0.35510	0.129;0.204;0.129	T	0.09773	-1.0659	10	0.87932	D	0	-2.3097	5.4485	0.16550	0.0:0.2956:0.156:0.5483	.	616;625;617	Q13421-4;Q13421;Q13421-3	.;MSLN_HUMAN;.	I	625;617;617;625	ENSP00000442965:L617I;ENSP00000372313:L625I	ENSP00000372313:L625I	L	+	1	2	MSLN	758714	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.840000	0.04363	-1.243000	0.02519	0.407000	0.27541	CTA	.	.		0.697	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
MEIOB	254528	hgsc.bcm.edu	37	16	1884289	1884289	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:1884289T>C	ENST00000397344.3	-	13	1491	c.1297A>G	c.(1297-1299)Agc>Ggc	p.S433G	MEIOB_ENST00000452149.2_Missense_Mutation_p.S433G|FAHD1_ENST00000382666.4_Intron|MEIOB_ENST00000470044.1_Missense_Mutation_p.S255G|MEIOB_ENST00000412554.2_Missense_Mutation_p.S462G|FAHD1_ENST00000382668.4_Intron|MEIOB_ENST00000325962.3_Missense_Mutation_p.S462G	NM_152764.2	NP_689977.2	Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	433					double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)										AAGTTTCTGCTTGCCTCAGTA	0.373																																					p.S462G		Atlas-SNP	.											.	.	.	.	0			c.A1384G						.						105.0	99.0	101.0					16																	1884289		2199	4300	6499	SO:0001583	missense	254528	exon14			TTCTGCTTGCCTC	BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039			28569	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 73"""	C16orf73		12477932	Standard	NM_152764		Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000397344.3:c.1297A>G	chr16.hg19:g.1884289T>C	ENSP00000380504:p.Ser433Gly	173.0	0.0		90.0	4.0	NM_001163560	B1AK39|C9J0S1|Q96RY0	Missense_Mutation	SNP	ENST00000397344.3	hg19	CCDS10449.2	.	.	.	.	.	.	.	.	.	.	T	11.37	1.617258	0.28801	.	.	ENSG00000162039	ENST00000412554;ENST00000452149;ENST00000325962;ENST00000397344	T;T;T;T	0.09817	2.94;2.94;2.94;2.94	5.72	4.56	0.56223	.	0.147993	0.64402	D	0.000009	T	0.15782	0.0380	L	0.54323	1.7	0.21325	N	0.99972	P;P	0.51791	0.948;0.933	P;P	0.48982	0.547;0.597	T	0.07481	-1.0770	10	0.46703	T	0.11	.	9.7866	0.40679	0.1532:0.0:0.0:0.8468	.	462;433	C9J0S1;Q8N635	.;CP073_HUMAN	G	462;433;462;433	ENSP00000390778:S462G;ENSP00000391033:S433G;ENSP00000314484:S462G;ENSP00000380504:S433G	ENSP00000314484:S462G	S	-	1	0	C16orf73	1824290	0.944000	0.32072	0.281000	0.24762	0.077000	0.17291	2.286000	0.43496	2.193000	0.70182	0.477000	0.44152	AGC	.	.		0.373	MEIOB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250580.1	NM_152764	
SLC9A3R2	9351	hgsc.bcm.edu	37	16	2079608	2079608	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:2079608A>G	ENST00000424542.2	+	2	377	c.239A>G	c.(238-240)gAg>gGg	p.E80G	SLC9A3R2_ENST00000432365.2_Missense_Mutation_p.E80G|SLC9A3R2_ENST00000563587.1_5'UTR	NM_001130012.2|NM_004785.5	NP_001123484.1|NP_004776.3	Q15599	NHRF2_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 2	80	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|protein complex assembly (GO:0006461)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatase binding (GO:0019902)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)	2						AAGGCTGTGGAGGGGCAGACT	0.662																																					p.E80G	Ovarian(69;105 1552 17724 23473)	Atlas-SNP	.											.	SLC9A3R2	24	.	0			c.A239G						.						30.0	41.0	37.0					16																	2079608		2105	4209	6314	SO:0001583	missense	9351	exon2			CTGTGGAGGGGCA	AF004900	CCDS45382.1, CCDS45383.1, CCDS58407.1	16p13.3	2014-09-04	2012-03-22		ENSG00000065054	ENSG00000065054			11076	protein-coding gene	gene with protein product		606553	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 2"", ""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulator 2"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2"""			9054412, 9671706	Standard	NM_001130012		Approved	SIP-1, TKA-1, NHERF-2, E3KARP	uc002coi.3	Q15599	OTTHUMG00000176956	ENST00000424542.2:c.239A>G	chr16.hg19:g.2079608A>G	ENSP00000408005:p.Glu80Gly	191.0	0.0		108.0	5.0	NM_004785	D3DU84|D3DU85|H3BSV6|O00272|O00556|Q3KQY7	Missense_Mutation	SNP	ENST00000424542.2	hg19	CCDS45382.1	.	.	.	.	.	.	.	.	.	.	A	11.08	1.534723	0.27475	.	.	ENSG00000065054	ENST00000424542;ENST00000432365	T;T	0.41400	1.0;1.0	4.61	3.52	0.40303	PDZ/DHR/GLGF (4);	0.122780	0.53938	D	0.000045	T	0.13114	0.0318	N	0.00666	-1.275	0.80722	D	1	B;B	0.19935	0.002;0.04	B;B	0.26969	0.006;0.075	T	0.07947	-1.0746	10	0.19590	T	0.45	-17.7268	7.529	0.27672	0.9012:0.0:0.0988:0.0	.	80;80	D3DU85;Q15599	.;NHRF2_HUMAN	G	80	ENSP00000408005:E80G;ENSP00000402857:E80G	ENSP00000408005:E80G	E	+	2	0	SLC9A3R2	2019609	1.000000	0.71417	0.995000	0.50966	0.912000	0.54170	4.297000	0.59061	1.728000	0.51552	0.454000	0.30748	GAG	.	.		0.662	SLC9A3R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434448.1		
CEMP1	752014	hgsc.bcm.edu	37	16	2580390	2580390	+	Missense_Mutation	SNP	T	T	C	rs375591203		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:2580390T>C	ENST00000567119.1	-	1	1019	c.685A>G	c.(685-687)Atg>Gtg	p.M229V	AMDHD2_ENST00000302956.4_3'UTR|CEMP1_ENST00000565480.1_Intron|AMDHD2_ENST00000565570.1_3'UTR|CEMP1_ENST00000382350.1_Missense_Mutation_p.M229V|AMDHD2_ENST00000413459.3_Missense_Mutation_p.M472T|MIR3178_ENST00000581887.1_RNA	NM_001048212.3	NP_001041677.1	Q6PRD7	CEMP1_HUMAN	cementum protein 1	229						cytoplasm (GO:0005737)				lung(1)|skin(1)	2						CACACACCCATGTGGCAAACA	0.627																																					p.M472T		Atlas-SNP	.											.	AMDHD2	33	.	0			c.T1415C						.	T	VAL/MET,THR/MET	1,4111		0,1,2055	55.0	58.0	57.0		685,1415	-3.0	0.0	16		57	0,8404		0,0,4202	no	missense,missense	AMDHD2,CEMP1	NM_001048212.3,NM_001145815.1	21,81	0,1,6257	CC,CT,TT		0.0,0.0243,0.0080	benign,benign	229/248,472/595	2580390	1,12515	2056	4202	6258	SO:0001583	missense	51005	exon11			CACCCATGTGGCA	AY584596	CCDS42108.1	16p13.3	2006-09-22							32553	protein-coding gene	gene with protein product	"""cementum protein-23"""	611113				16263347	Standard	NM_001048212		Approved	CP-23	uc002cqr.3	Q6PRD7		ENST00000567119.1:c.685A>G	chr16.hg19:g.2580390T>C	ENSP00000457380:p.Met229Val	167.0	0.0		78.0	4.0	NM_001145815	B2RUY1	Missense_Mutation	SNP	ENST00000567119.1	hg19	CCDS42108.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.146|3.146	-0.175183|-0.175183	0.06421|0.06421	2.43E-4|2.43E-4	0.0|0.0	ENSG00000162066|ENSG00000205923	ENST00000413459|ENST00000382350	.|T	.|0.48522	.|0.81	2.1|2.1	-2.95|-2.95	0.05564|0.05564	.|.	.|.	.|.	.|.	.|.	T|T	0.22399|0.22399	0.0540|0.0540	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|B	0.02656|0.10296	0.0|0.003	B|B	0.01281|0.13407	0.0|0.009	T|T	0.16012|0.16012	-1.0417|-1.0417	8|9	0.87932|0.87932	D|D	0|0	.|.	3.4838|3.4838	0.07611|0.07611	0.0:0.3012:0.2137:0.485|0.0:0.3012:0.2137:0.485	.|.	472|229	Q9Y303-3|Q6PRD7	.|CEMP1_HUMAN	T|V	472|229	.|ENSP00000371787:M229V	ENSP00000391596:M472T|ENSP00000371787:M229V	M|M	+|-	2|1	0|0	AMDHD2|CEMP1	2520391|2520391	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.856000|-0.856000	0.04290|0.04290	-0.752000|-0.752000	0.04728|0.04728	-0.366000|-0.366000	0.07423|0.07423	ATG|ATG	.	.		0.627	CEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435686.1	NM_001048212	
CREBBP	1387	hgsc.bcm.edu	37	16	3778015	3778015	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:3778015A>G	ENST00000262367.5	-	31	7842	c.7033T>C	c.(7033-7035)Tct>Cct	p.S2345P	CREBBP_ENST00000382070.3_Missense_Mutation_p.S2307P	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2345					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|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 transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		GGGGCTGGAGACCGCACCTGG	0.647			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.S2345P		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.T7033C						.						89.0	87.0	88.0					16																	3778015		2197	4300	6497	SO:0001583	missense	1387	exon31			CTGGAGACCGCAC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.7033T>C	chr16.hg19:g.3778015A>G	ENSP00000262367:p.Ser2345Pro	223.0	0.0		108.0	5.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	a	12.31	1.900600	0.33535	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.88354	-2.37;-2.31	5.35	5.35	0.76521	.	0.149672	0.47852	D	0.000203	D	0.90827	0.7119	L	0.34521	1.04	0.80722	D	1	D;D	0.65815	0.995;0.995	D;D	0.72982	0.979;0.979	D	0.90892	0.4762	10	0.45353	T	0.12	-8.416	14.8194	0.70059	1.0:0.0:0.0:0.0	.	2375;2345	Q4LE28;Q92793	.;CBP_HUMAN	P	2345;2375;2307;880	ENSP00000262367:S2345P;ENSP00000371502:S2307P	ENSP00000262367:S2345P	S	-	1	0	CREBBP	3718016	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.185000	0.94900	2.156000	0.67533	0.533000	0.62120	TCT	.	.		0.647	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
C16orf96	342346	hgsc.bcm.edu	37	16	4626475	4626475	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:4626475A>G	ENST00000444310.4	+	5	1994	c.1994A>G	c.(1993-1995)cAg>cGg	p.Q665R		NM_001145011.1	NP_001138483.1			chromosome 16 open reading frame 96											NS(1)|breast(1)|endometrium(6)|kidney(1)|skin(3)	12						GCCCTGTCCCAGGCCATGGTG	0.552																																					p.Q665R		Atlas-SNP	.											.	C16orf96	28	.	0			c.A1994G						.						32.0	33.0	33.0					16																	4626475		692	1591	2283	SO:0001583	missense	342346	exon5			TGTCCCAGGCCAT		CCDS53986.1	16p13.3	2012-10-10			ENSG00000205832	ENSG00000205832			40031	protein-coding gene	gene with protein product							Standard	NM_001145011		Approved		uc010uxn.2	A6NNT2	OTTHUMG00000176519	ENST00000444310.4:c.1994A>G	chr16.hg19:g.4626475A>G	ENSP00000415027:p.Gln665Arg	143.0	0.0		93.0	5.0	NM_001145011		Missense_Mutation	SNP	ENST00000444310.4	hg19	CCDS53986.1	.	.	.	.	.	.	.	.	.	.	A	15.13	2.741294	0.49151	.	.	ENSG00000205832	ENST00000444310	.	.	.	4.29	-2.37	0.06643	.	.	.	.	.	T	0.19046	0.0457	L	0.27053	0.805	0.09310	N	1	B	0.29432	0.244	B	0.31547	0.132	T	0.24584	-1.0156	8	0.28530	T	0.3	.	1.0857	0.01652	0.3259:0.3383:0.1889:0.1469	.	665	A6NNT2	CP096_HUMAN	R	665	.	ENSP00000415027:Q665R	Q	+	2	0	C16orf96	4566476	0.000000	0.05858	0.000000	0.03702	0.107000	0.19398	0.068000	0.14531	-0.454000	0.07066	0.260000	0.18958	CAG	.	.		0.552	C16orf96-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432384.1	NM_001145011	
ZC3H7A	29066	hgsc.bcm.edu	37	16	11862325	11862325	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:11862325C>A	ENST00000396516.2	-	11	1403	c.1206G>T	c.(1204-1206)gaG>gaT	p.E402D	ZC3H7A_ENST00000355758.4_Missense_Mutation_p.E402D			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	402						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2)	25						CCAGGAAATTCTCTGAAGCAA	0.368																																					p.E402D		Atlas-SNP	.											ZC3H7A,NS,carcinoma,0,2	ZC3H7A	72	.	0			c.G1206T						.						70.0	73.0	72.0					16																	11862325		2197	4300	6497	SO:0001583	missense	29066	exon12			GAAATTCTCTGAA	AF161540	CCDS10550.1	16p13-p12	2013-01-11	2005-06-02	2005-06-08	ENSG00000122299	ENSG00000122299		"""Zinc fingers, CCCH-type domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30959	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 7"", ""zinc finger CCCH-type containing 7"""	ZC3HDC7, ZC3H7		11042152	Standard	NM_014153		Approved	HSPC055, FLJ20318	uc002dbl.3	Q8IWR0	OTTHUMG00000129825	ENST00000396516.2:c.1206G>T	chr16.hg19:g.11862325C>A	ENSP00000379773:p.Glu402Asp	81.0	0.0		60.0	3.0	NM_014153	D3DUG5|Q9NPE9	Missense_Mutation	SNP	ENST00000396516.2	hg19	CCDS10550.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.358598	0.24598	.	.	ENSG00000122299	ENST00000355758;ENST00000396516	T;T	0.10477	2.87;2.87	5.74	1.54	0.23209	.	0.427763	0.29376	N	0.012323	T	0.04182	0.0116	N	0.11427	0.14	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.002	T	0.44174	-0.9345	10	0.22706	T	0.39	.	2.564	0.04778	0.1315:0.5168:0.1277:0.2241	.	123;402	Q9NXC8;Q8IWR0	.;Z3H7A_HUMAN	D	402	ENSP00000347999:E402D;ENSP00000379773:E402D	ENSP00000347999:E402D	E	-	3	2	ZC3H7A	11769826	0.999000	0.42202	0.811000	0.32455	0.778000	0.44026	0.502000	0.22594	0.064000	0.16427	-0.137000	0.14449	GAG	.	.		0.368	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153	
RRN3	54700	hgsc.bcm.edu	37	16	15168676	15168676	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:15168676C>T	ENST00000198767.6	-	11	984	c.901G>A	c.(901-903)Gaa>Aaa	p.E301K	RRN3_ENST00000540462.1_Missense_Mutation_p.E119K|PDXDC1_ENST00000535621.2_Intron|RRN3_ENST00000563559.1_Missense_Mutation_p.E301K|RRN3_ENST00000429751.2_Missense_Mutation_p.E271K|RRN3_ENST00000327307.7_Missense_Mutation_p.E268K	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	301					cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						TCGAGCCGTTCAGGACCAGCC	0.408																																					p.E301K		Atlas-SNP	.											.	RRN3	36	.	0			c.G901A						.						117.0	87.0	97.0					16																	15168676		2197	4300	6497	SO:0001583	missense	54700	exon11			GCCGTTCAGGACC	AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721			30346	protein-coding gene	gene with protein product		605121	"""RRN3 RNA polymerase I transcription factor homolog (yeast)"""			10758157, 11250903	Standard	XM_005255375		Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.901G>A	chr16.hg19:g.15168676C>T	ENSP00000198767:p.Glu301Lys	119.0	0.0		71.0	4.0	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Missense_Mutation	SNP	ENST00000198767.6	hg19	CCDS10559.1	.	.	.	.	.	.	.	.	.	.	.	0.242	-1.013088	0.02095	.	.	ENSG00000085721	ENST00000198767;ENST00000429751;ENST00000327307;ENST00000540462	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.52	-0.359	0.12571	.	1.706890	0.03358	N	0.197154	T	0.33469	0.0864	L	0.46157	1.445	0.09310	N	1	B;B;B	0.12630	0.006;0.001;0.0	B;B;B	0.15870	0.014;0.002;0.001	T	0.09552	-1.0669	10	0.15499	T	0.54	.	5.1958	0.15236	0.1117:0.2372:0.5061:0.145	.	271;202;301	F5H148;B4DZL9;Q9NYV6	.;.;RRN3_HUMAN	K	301;271;268;119	ENSP00000198767:E301K;ENSP00000402027:E271K;ENSP00000318484:E268K;ENSP00000437963:E119K	ENSP00000198767:E301K	E	-	1	0	RRN3	15076177	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.120000	0.15647	0.005000	0.14708	-0.254000	0.11334	GAA	.	.		0.408	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427	
SMG1	23049	hgsc.bcm.edu	37	16	18846414	18846414	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:18846414C>T	ENST00000446231.2	-	49	8542	c.8130G>A	c.(8128-8130)ctG>ctA	p.L2710L	SMG1_ENST00000389467.3_Silent_p.L2710L			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2710					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						CGTATCGCTGCAGGGTCATTT	0.453																																					p.L2710L		Atlas-SNP	.											.	SMG1	401	.	0			c.G8130A						.						139.0	134.0	135.0					16																	18846414		1946	4155	6101	SO:0001819	synonymous_variant	23049	exon49			TCGCTGCAGGGTC	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.8130G>A	chr16.hg19:g.18846414C>T		243.0	0.0		203.0	116.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	hg19	CCDS45430.1																																																																																			.	.		0.453	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
PALB2	79728	hgsc.bcm.edu	37	16	23641766	23641766	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:23641766T>C	ENST00000261584.4	-	5	1861	c.1709A>G	c.(1708-1710)gAg>gGg	p.E570G		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	570	DNA-binding (with the preference D loop > dsDNA > ssDNA).				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		AAGGGAATCCTCTTTTTGATG	0.358			"""F, N, Mis"""			"""Wilms tumor, medulloblastoma, AML ,breast"""		Involved in tolerance or repair of DNA crosslinks																													p.E570G		Atlas-SNP	.	yes	Rec		"""Fanconi anaemia N, breast cancer susceptibility """	16	16p12.1	79728	partner and localizer of BRCA2		"""L, O, E"""	.	PALB2	108	.	0			c.A1709G						.						38.0	34.0	35.0					16																	23641766		2197	4300	6497	SO:0001583	missense	79728	exon5			GAATCCTCTTTTT		CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"""Fanconi anemia, complementation groups"""	26144	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group N"""	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.1709A>G	chr16.hg19:g.23641766T>C	ENSP00000261584:p.Glu570Gly	189.0	0.0		93.0	4.0	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	hg19	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	T	12.53	1.966291	0.34659	.	.	ENSG00000083093	ENST00000261584	T	0.16743	2.32	5.05	3.88	0.44766	.	0.563831	0.17191	N	0.183487	T	0.21227	0.0511	M	0.63428	1.95	0.09310	N	1	P	0.46784	0.884	P	0.46253	0.509	T	0.07252	-1.0782	10	0.30854	T	0.27	-4.9817	8.2211	0.31541	0.0:0.0:0.2023:0.7977	.	570	Q86YC2	PALB2_HUMAN	G	570	ENSP00000261584:E570G	ENSP00000261584:E570G	E	-	2	0	PALB2	23549267	0.000000	0.05858	0.347000	0.25668	0.119000	0.20118	0.136000	0.15974	1.885000	0.54596	0.533000	0.62120	GAG	.	.		0.358	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675	
ERN2	10595	hgsc.bcm.edu	37	16	23707249	23707249	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:23707249G>A	ENST00000457008.2	-	13	1458	c.1420C>T	c.(1420-1422)Ctg>Ttg	p.L474L	ERN2_ENST00000256797.4_Silent_p.L574L					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		CCGCGGCCCAGCACGTCCTTG	0.642																																					p.L574L		Atlas-SNP	.											.	ERN2	131	.	0			c.C1720T						.						45.0	42.0	43.0					16																	23707249		2197	4300	6497	SO:0001819	synonymous_variant	10595	exon14			GGCCCAGCACGTC	AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"""ER to nucleus signalling 2"""			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.1420C>T	chr16.hg19:g.23707249G>A		96.0	0.0		75.0	22.0	NM_033266		Silent	SNP	ENST00000457008.2	hg19																																																																																				.	.		0.642	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1		
TNRC6A	27327	hgsc.bcm.edu	37	16	24834848	24834848	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:24834848C>A	ENST00000395799.3	+	25	5738	c.5609C>A	c.(5608-5610)cCc>cAc	p.P1870H	TNRC6A_ENST00000432286.2_Missense_Mutation_p.P348H|TNRC6A_ENST00000315183.7_Missense_Mutation_p.P1821H	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1870	Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|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)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ACCCCTTCTCCCGGCTGGCAG	0.557																																					p.P1870H		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C5609A						.						97.0	103.0	101.0					16																	24834848		2197	4300	6497	SO:0001583	missense	27327	exon25			CTTCTCCCGGCTG	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.5609C>A	chr16.hg19:g.24834848C>A	ENSP00000379144:p.Pro1870His	104.0	0.0		61.0	4.0	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	c	17.76	3.469269	0.63625	.	.	ENSG00000090905	ENST00000315183;ENST00000395799;ENST00000432286	T;T	0.12879	2.65;2.64	5.64	5.64	0.86602	.	0.059955	0.64402	D	0.000002	T	0.32466	0.0830	L	0.44542	1.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.70935	0.971;0.956	T	0.01235	-1.1410	10	0.87932	D	0	-4.6991	19.7099	0.96094	0.0:1.0:0.0:0.0	.	1821;1870	Q8NDV7-6;Q8NDV7	.;TNR6A_HUMAN	H	1821;1870;348	ENSP00000326900:P1821H;ENSP00000379144:P1870H	ENSP00000326900:P1821H	P	+	2	0	TNRC6A	24742349	0.999000	0.42202	0.998000	0.56505	0.993000	0.82548	5.619000	0.67729	2.638000	0.89438	0.651000	0.88453	CCC	.	.		0.557	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
GTF3C1	2975	hgsc.bcm.edu	37	16	27499733	27499733	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:27499733T>C	ENST00000356183.4	-	23	3530	c.3515A>G	c.(3514-3516)aAc>aGc	p.N1172S	GTF3C1_ENST00000561623.1_Missense_Mutation_p.N1172S	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1172					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CAACCTGCTGTTGCCTAGACA	0.542																																					p.N1172S		Atlas-SNP	.											.	GTF3C1	210	.	0			c.A3515G						.						108.0	109.0	109.0					16																	27499733		2197	4300	6497	SO:0001583	missense	2975	exon23			CTGCTGTTGCCTA	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.3515A>G	chr16.hg19:g.27499733T>C	ENSP00000348510:p.Asn1172Ser	105.0	0.0		60.0	4.0	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	T	1.419	-0.573316	0.03882	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.21932	1.98	4.9	-6.65	0.01795	.	0.943286	0.08892	N	0.878477	T	0.08403	0.0209	N	0.16066	0.365	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.001;0.004	T	0.43507	-0.9387	10	0.02654	T	1	-19.0721	10.3697	0.44046	0.0:0.5609:0.1161:0.323	.	1172;1172	Q12789;Q12789-3	TF3C1_HUMAN;.	S	1172;1168	ENSP00000348510:N1172S	ENSP00000348510:N1172S	N	-	2	0	GTF3C1	27407234	0.000000	0.05858	0.000000	0.03702	0.895000	0.52256	-0.690000	0.05138	-1.774000	0.01288	0.459000	0.35465	AAC	.	.		0.542	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
SEZ6L2	26470	hgsc.bcm.edu	37	16	29891258	29891258	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:29891258A>G	ENST00000308713.5	-	9	2027	c.1500T>C	c.(1498-1500)ccT>ccC	p.P500P	SEZ6L2_ENST00000350527.3_Silent_p.P430P|SEZ6L2_ENST00000537485.1_Silent_p.P456P|SEZ6L2_ENST00000346932.5_Silent_p.P386P	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	500	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGGGGGGCCCAGGGGGCTCCA	0.612																																					p.P500P		Atlas-SNP	.											.	SEZ6L2	137	.	0			c.T1500C						.						114.0	114.0	114.0					16																	29891258		2197	4300	6497	SO:0001819	synonymous_variant	26470	exon9			GGGCCCAGGGGGC	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"""type I transmembrane receptor (seizure related protein)"""					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.1500T>C	chr16.hg19:g.29891258A>G		95.0	0.0		70.0	4.0	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Silent	SNP	ENST00000308713.5	hg19	CCDS10659.1																																																																																			.	.		0.612	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410	
ITGAL	3683	hgsc.bcm.edu	37	16	30500452	30500452	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:30500452C>T	ENST00000356798.6	+	10	1236	c.1056C>T	c.(1054-1056)agC>agT	p.S352S	RP11-297C4.2_ENST00000569459.1_RNA|ITGAL_ENST00000433423.2_Intron|ITGAL_ENST00000358164.5_Silent_p.S269S|ITGAL_ENST00000568012.1_3'UTR	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	352					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	TGTCCTCCAGCGGCATCAGTG	0.597																																					p.S352S	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.C1056T						.						68.0	62.0	64.0					16																	30500452		2197	4300	6497	SO:0001819	synonymous_variant	3683	exon10			CTCCAGCGGCATC		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"""CD molecules"", ""Integrins"""	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.1056C>T	chr16.hg19:g.30500452C>T		124.0	0.0		100.0	4.0	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	hg19	CCDS32433.1																																																																																			.	.		0.597	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2		
ITGAX	3687	hgsc.bcm.edu	37	16	31373480	31373480	+	Missense_Mutation	SNP	A	A	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:31373480A>T	ENST00000268296.4	+	11	1292	c.1171A>T	c.(1171-1173)Atc>Ttc	p.I391F	ITGAX_ENST00000562522.1_Missense_Mutation_p.I391F	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	391					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CCCTACCTTCATCAACATGTC	0.582																																					p.I391F		Atlas-SNP	.											.	ITGAX	198	.	0			c.A1171T						.						100.0	100.0	100.0					16																	31373480		2197	4300	6497	SO:0001583	missense	3687	exon11			ACCTTCATCAACA	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1171A>T	chr16.hg19:g.31373480A>T	ENSP00000268296:p.Ile391Phe	170.0	0.0		86.0	4.0	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	hg19	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	a	18.06	3.539840	0.65085	.	.	ENSG00000140678	ENST00000268296	T	0.71698	-0.59	4.5	4.5	0.54988	.	.	.	.	.	T	0.79793	0.4507	M	0.68593	2.085	0.34780	D	0.734667	D	0.89917	1.0	D	0.91635	0.999	D	0.84522	0.0628	9	0.72032	D	0.01	.	7.0718	0.25183	0.8953:0.0:0.1047:0.0	.	391	P20702	ITAX_HUMAN	F	391	ENSP00000268296:I391F	ENSP00000268296:I391F	I	+	1	0	ITGAX	31280981	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	1.392000	0.34486	1.798000	0.52647	0.473000	0.43528	ATC	.	.		0.582	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
NETO2	81831	hgsc.bcm.edu	37	16	47163230	47163230	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:47163230C>T	ENST00000562435.1	-	3	521	c.137G>A	c.(136-138)gGc>gAc	p.G46D	NETO2_ENST00000303155.5_Missense_Mutation_p.G46D	NM_018092.4	NP_060562.3	Q8NC67	NETO2_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 2	46	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				regulation of kainate selective glutamate receptor activity (GO:2000312)	kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)				breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	29		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)				AACCCAAATGCCACACTGGGT	0.393										HNSCC(25;0.065)																											p.G46D		Atlas-SNP	.											.	NETO2	67	.	0			c.G137A						.						163.0	153.0	156.0					16																	47163230		2202	4300	6502	SO:0001583	missense	81831	exon3			CAAATGCCACACT	AK001292	CCDS10727.1, CCDS58460.1	16q11.2	2008-08-04			ENSG00000171208	ENSG00000171208			14644	protein-coding gene	gene with protein product		607974				11943477	Standard	NM_018092		Approved	FLJ10430, NEOT2	uc002eer.2	Q8NC67	OTTHUMG00000133101	ENST00000562435.1:c.137G>A	chr16.hg19:g.47163230C>T	ENSP00000455169:p.Gly46Asp	138.0	0.0		79.0	4.0	NM_018092	J3KNF1|Q7Z381|Q8ND51|Q96SP4|Q9NVY8	Missense_Mutation	SNP	ENST00000562435.1	hg19	CCDS10727.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.882055	0.72294	.	.	ENSG00000171208	ENST00000303155	T	0.37411	1.2	6.03	6.03	0.97812	CUB (5);	0.048111	0.85682	D	0.000000	T	0.56171	0.1967	H	0.96430	3.82	0.54753	D	0.999983	B;B	0.19331	0.035;0.035	B;B	0.26094	0.066;0.066	T	0.61950	-0.6957	10	0.59425	D	0.04	.	14.1385	0.65303	0.0:0.9235:0.0:0.0765	.	46;46	Q32NC3;Q8NC67	.;NETO2_HUMAN	D	46	ENSP00000306726:G46D	ENSP00000306726:G46D	G	-	2	0	NETO2	45720731	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.816000	0.62642	2.854000	0.98071	0.655000	0.94253	GGC	.	.		0.393	NETO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256766.2	NM_018092	
N4BP1	9683	hgsc.bcm.edu	37	16	48596338	48596338	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:48596338G>T	ENST00000262384.3	-	2	452	c.216C>A	c.(214-216)atC>atA	p.I72I	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	72					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				CAGGTTCACAGATTCCTTTAA	0.343																																					p.I72I		Atlas-SNP	.											N4BP1_ENST00000262384,NS,carcinoma,0,2	N4BP1	121	.	0			c.C216A						.						37.0	37.0	37.0					16																	48596338		1827	4077	5904	SO:0001819	synonymous_variant	9683	exon2			TTCACAGATTCCT	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.216C>A	chr16.hg19:g.48596338G>T		126.0	0.0		72.0	3.0	NM_153029	A7MD49|Q2YDX1	Silent	SNP	ENST00000262384.3	hg19	CCDS45479.1																																																																																			.	.		0.343	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664	
SALL1	6299	hgsc.bcm.edu	37	16	51175284	51175284	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:51175284G>T	ENST00000251020.4	-	2	882	c.849C>A	c.(847-849)tcC>tcA	p.S283S	SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.S186S	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	283					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)			AACTTAGCGTGGACAAGGGGT	0.498																																					p.S283S	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C849A						.						91.0	91.0	91.0					16																	51175284		2198	4300	6498	SO:0001819	synonymous_variant	6299	exon2			TAGCGTGGACAAG	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.849C>A	chr16.hg19:g.51175284G>T		110.0	0.0		69.0	4.0	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	hg19	CCDS10747.1																																																																																			.	.		0.498	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53636067	53636067	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:53636067C>T	ENST00000379925.3	-	27	3919	c.3869G>A	c.(3868-3870)gGc>gAc	p.G1290D	RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.G1256D|RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.G1210D	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1290					camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)			endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				CCTGAGCTTGCCAATACCTTC	0.453																																					p.G1290D		Atlas-SNP	.											.	RPGRIP1L	118	.	0			c.G3869A						.						118.0	94.0	102.0					16																	53636067		2198	4300	6498	SO:0001583	missense	23322	exon27			AGCTTGCCAATAC		CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"""fantom homolog"", ""Meckel syndrome, type 5"", ""protein phosphatase 1, regulatory subunit 134"""	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.3869G>A	chr16.hg19:g.53636067C>T	ENSP00000369257:p.Gly1290Asp	154.0	0.0		95.0	4.0	NM_015272	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	hg19	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.772027	0.90108	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	D;D	0.84442	-1.85;-1.85	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.91590	0.7343	M	0.72894	2.215	0.80722	D	1	P;D;D	0.62365	0.94;0.991;0.964	P;D;D	0.65233	0.858;0.91;0.933	D	0.91894	0.5526	10	0.87932	D	0	-10.8324	18.3801	0.90448	0.0:1.0:0.0:0.0	.	1244;1290;1210	B7ZKJ9;Q68CZ1;Q68CZ1-2	.;FTM_HUMAN;.	D	1290;1210	ENSP00000369257:G1290D;ENSP00000262135:G1210D	ENSP00000262135:G1210D	G	-	2	0	RPGRIP1L	52193568	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.287000	0.65645	2.776000	0.95493	0.650000	0.86243	GGC	.	.		0.453	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272	
SLC6A2	6530	hgsc.bcm.edu	37	16	55690842	55690842	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:55690842T>C	ENST00000379906.2	+	1	491	c.236T>C	c.(235-237)gTg>gCg	p.V79A	SLC6A2_ENST00000561820.1_Missense_Mutation_p.V79A|SLC6A2_ENST00000414754.3_Missense_Mutation_p.V79A|SLC6A2_ENST00000568943.1_Missense_Mutation_p.V79A|SLC6A2_ENST00000566163.1_Missense_Mutation_p.V79A|SLC6A2_ENST00000219833.8_Missense_Mutation_p.V79A	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	79					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)			breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	CTGGCCAACGTGTGGCGCTTC	0.667																																					p.V79A		Atlas-SNP	.											.	SLC6A2	189	.	0			c.T236C						.						80.0	85.0	83.0					16																	55690842		2198	4300	6498	SO:0001583	missense	6530	exon2			CCAACGTGTGGCG		CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"""Solute carriers"""	11048	protein-coding gene	gene with protein product	"""norepinephrine transporter"""	163970	"""solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"""	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.236T>C	chr16.hg19:g.55690842T>C	ENSP00000369237:p.Val79Ala	178.0	0.0		87.0	5.0	NM_001172501	B2R707|B4DX48|Q96KH8	Missense_Mutation	SNP	ENST00000379906.2	hg19	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	T	16.67	3.187653	0.57909	.	.	ENSG00000103546	ENST00000414754;ENST00000379906;ENST00000219833	T;T;T	0.80480	-1.38;-1.38;-1.38	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.91885	0.7431	M	0.92169	3.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.995;0.996	D	0.93831	0.7128	10	0.87932	D	0	.	15.4969	0.75662	0.0:0.0:0.0:1.0	.	79;79	Q96KH8;P23975	.;SC6A2_HUMAN	A	79	ENSP00000394956:V79A;ENSP00000369237:V79A;ENSP00000219833:V79A	ENSP00000219833:V79A	V	+	2	0	SLC6A2	54248343	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.930000	0.87610	2.117000	0.64856	0.460000	0.39030	GTG	.	.		0.667	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2		
NUP93	9688	hgsc.bcm.edu	37	16	56868679	56868679	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:56868679G>T	ENST00000308159.5	+	16	1892	c.1771G>T	c.(1771-1773)Gga>Tga	p.G591*	NUP93_ENST00000569842.1_Nonsense_Mutation_p.G591*|NUP93_ENST00000542526.1_Nonsense_Mutation_p.G468*|NUP93_ENST00000564887.1_Nonsense_Mutation_p.G468*	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	591					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						AGAGAATGACGGAAGTAGAAA	0.318																																					p.G591X	Colon(33;610 796 1305 1705 38917)	Atlas-SNP	.											.	NUP93	75	.	0			c.G1771T						.						82.0	82.0	82.0					16																	56868679		2198	4300	6498	SO:0001587	stop_gained	9688	exon16			AATGACGGAAGTA	D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.1771G>T	chr16.hg19:g.56868679G>T	ENSP00000310668:p.Gly591*	171.0	0.0		94.0	5.0	NM_014669	B3KPQ8|Q14705	Nonsense_Mutation	SNP	ENST00000308159.5	hg19	CCDS10769.1	.	.	.	.	.	.	.	.	.	.	G	45	11.378068	0.99554	.	.	ENSG00000102900	ENST00000308159;ENST00000542526	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-15.6325	20.04	0.97581	0.0:0.0:1.0:0.0	.	.	.	.	X	591;468	.	ENSP00000310668:G591X	G	+	1	0	NUP93	55426180	1.000000	0.71417	0.893000	0.35052	0.986000	0.74619	9.312000	0.96287	2.733000	0.93635	0.655000	0.94253	GGA	.	.		0.318	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669	
CX3CL1	6376	hgsc.bcm.edu	37	16	57416825	57416825	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:57416825A>G	ENST00000006053.6	+	3	1186	c.1075A>G	c.(1075-1077)Atg>Gtg	p.M359V	CX3CL1_ENST00000563383.1_Missense_Mutation_p.M365V|CX3CL1_ENST00000565912.1_Missense_Mutation_p.M321V	NM_002996.3	NP_002987.1	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	359					angiogenesis involved in wound healing (GO:0060055)|cell adhesion (GO:0007155)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|immune response (GO:0006955)|leukocyte adhesive activation (GO:0050902)|leukocyte chemotaxis (GO:0030595)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcium-independent cell-cell adhesion (GO:0051041)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transforming growth factor beta1 production (GO:0032914)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chemokine activity (GO:0008009)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GGGGGTGGCCATGTTCACCTA	0.637																																					p.M359V		Atlas-SNP	.											.	CX3CL1	27	.	0			c.A1075G						.						65.0	69.0	67.0					16																	57416825		2198	4300	6498	SO:0001583	missense	6376	exon3			GTGGCCATGTTCA	U84487	CCDS10779.1	16q13	2013-02-25	2002-08-22	2002-08-23	ENSG00000006210	ENSG00000006210		"""Endogenous ligands"""	10647	protein-coding gene	gene with protein product		601880	"""small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)"""	SCYD1		9177350, 9024663	Standard	NM_002996		Approved	NTN, C3Xkine, ABCD-3, CXC3C, CXC3, fractalkine, neurotactin	uc002eli.3	P78423	OTTHUMG00000133469	ENST00000006053.6:c.1075A>G	chr16.hg19:g.57416825A>G	ENSP00000006053:p.Met359Val	93.0	0.0		44.0	4.0	NM_002996	O00672	Missense_Mutation	SNP	ENST00000006053.6	hg19	CCDS10779.1	.	.	.	.	.	.	.	.	.	.	A	18.97	3.735506	0.69189	.	.	ENSG00000006210	ENST00000006053	T	0.09911	2.93	5.19	5.19	0.71726	.	0.585004	0.15417	N	0.263445	T	0.22475	0.0542	L	0.36672	1.1	0.36566	D	0.872705	D	0.63880	0.993	D	0.68192	0.956	T	0.07693	-1.0759	10	0.87932	D	0	-37.3436	11.4823	0.50333	1.0:0.0:0.0:0.0	.	359	P78423	X3CL1_HUMAN	V	359	ENSP00000006053:M359V	ENSP00000006053:M359V	M	+	1	0	CX3CL1	55974326	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	2.655000	0.46707	1.953000	0.56701	0.456000	0.33151	ATG	.	.		0.637	CX3CL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257345.3	NM_002996	
GOT2	2806	hgsc.bcm.edu	37	16	58743423	58743423	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:58743423A>G	ENST00000245206.5	-	9	1196	c.1068T>C	c.(1066-1068)acT>acC	p.T356T	GOT2_ENST00000434819.2_Silent_p.T313T	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	356					2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	AGACCAGTTGAGTCCGCATGC	0.498																																					p.T356T		Atlas-SNP	.											.	GOT2	42	.	0			c.T1068C						.						220.0	205.0	210.0					16																	58743423		2198	4300	6498	SO:0001819	synonymous_variant	2806	exon9			CAGTTGAGTCCGC		CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"""kynurenine aminotransferase IV"", ""aspartate aminotransferase 2"", ""aspartate transaminase 2"""	138150	"""glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"""			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.1068T>C	chr16.hg19:g.58743423A>G		58.0	0.0		34.0	4.0	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Silent	SNP	ENST00000245206.5	hg19	CCDS10801.1																																																																																			.	.		0.498	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
CDH5	1003	hgsc.bcm.edu	37	16	66426269	66426269	+	Silent	SNP	G	G	T	rs376087780		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:66426269G>T	ENST00000341529.3	+	7	1348	c.1200G>T	c.(1198-1200)gcG>gcT	p.A400A	CDH5_ENST00000563425.2_Silent_p.A400A	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	400	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel maturation (GO:0001955)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|negative regulation of cell proliferation (GO:0008285)|regulation of establishment of cell polarity (GO:2000114)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|receptor binding (GO:0005102)	p.A400A(1)		central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Lenalidomide(DB00480)	ACCCTGATGCGGCTAGGCATA	0.552																																					p.A400A		Atlas-SNP	.											CDH5,NS,carcinoma,0,1	CDH5	111	.	1	Substitution - coding silent(1)	endometrium(1)	c.G1200T						.						88.0	88.0	88.0					16																	66426269		2201	4300	6501	SO:0001819	synonymous_variant	1003	exon7			TGATGCGGCTAGG	X79981	CCDS10804.1	16q22.1	2010-01-26	2008-07-25		ENSG00000179776	ENSG00000179776		"""CD molecules"", ""Cadherins / Major cadherins"""	1764	protein-coding gene	gene with protein product	"""VE-cadherin"""	601120	"""cadherin 5, type 2, VE-cadherin (vascular epithelium)"""			2059658	Standard	NM_001795		Approved	7B4, CD144	uc002eom.4	P33151	OTTHUMG00000137495	ENST00000341529.3:c.1200G>T	chr16.hg19:g.66426269G>T		85.0	0.0		42.0	3.0	NM_001795	Q4VAI5|Q4VAI6	Silent	SNP	ENST00000341529.3	hg19	CCDS10804.1																																																																																			.	.		0.552	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795	
CMTM4	146223	hgsc.bcm.edu	37	16	66651253	66651253	+	Missense_Mutation	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:66651253T>A	ENST00000330687.4	-	5	813	c.632A>T	c.(631-633)tAc>tTc	p.Y211F		NM_178818.2|NM_181521.2	NP_848933.1|NP_852662.1	Q8IZR5	CKLF4_HUMAN	CKLF-like MARVEL transmembrane domain containing 4	211					chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)		GTTTGTGGAGTAGGAAAAACT	0.363																																					p.Y211F		Atlas-SNP	.											.	CMTM4	19	.	0			c.A632T						.						82.0	76.0	78.0					16																	66651253		2200	4300	6500	SO:0001583	missense	146223	exon5			GTGGAGTAGGAAA	AF479814	CCDS10817.1, CCDS42170.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000183723	ENSG00000183723			19175	protein-coding gene	gene with protein product		607887	"""chemokine-like factor super family 4"", ""chemokine-like factor superfamily 4"""	CKLFSF4		12782130	Standard	NM_178818		Approved		uc002epz.3	Q8IZR5	OTTHUMG00000137500	ENST00000330687.4:c.632A>T	chr16.hg19:g.66651253T>A	ENSP00000333833:p.Tyr211Phe	405.0	1.0		287.0	98.0	NM_178818	Q52M40|Q8IZR4|Q8IZV1	Missense_Mutation	SNP	ENST00000330687.4	hg19	CCDS10817.1	.	.	.	.	.	.	.	.	.	.	T	7.873	0.728630	0.15507	.	.	ENSG00000183723	ENST00000330687	T	0.23147	1.92	4.01	4.01	0.46588	.	0.712591	0.12721	N	0.444676	T	0.10165	0.0249	N	0.03608	-0.345	0.35073	D	0.762639	D	0.53885	0.963	B	0.41088	0.347	T	0.03898	-1.0994	10	0.09084	T	0.74	.	9.5874	0.39526	0.0:0.0:0.0:1.0	.	211	Q8IZR5	CKLF4_HUMAN	F	211	ENSP00000333833:Y211F	ENSP00000333833:Y211F	Y	-	2	0	CMTM4	65208754	0.256000	0.24012	0.005000	0.12908	0.003000	0.03518	2.529000	0.45632	2.031000	0.59945	0.459000	0.35465	TAC	.	.		0.363	CMTM4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268807.1		
PSKH1	5681	hgsc.bcm.edu	37	16	67942888	67942888	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:67942888G>T	ENST00000291041.5	+	2	406	c.236G>T	c.(235-237)cGc>cTc	p.R79L		NM_006742.2	NP_006733.1	P11801	KPSH1_HUMAN	protein serine kinase H1	79						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)		GAACCACCACGCAGGGCCAGG	0.612																																					p.R79L		Atlas-SNP	.											PSKH1,NS,carcinoma,0,1	PSKH1	28	.	0			c.G236T						.						64.0	58.0	60.0					16																	67942888		2198	4300	6498	SO:0001583	missense	5681	exon2			CACCACGCAGGGC	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.236G>T	chr16.hg19:g.67942888G>T	ENSP00000291041:p.Arg79Leu	163.0	0.0		89.0	4.0	NM_006742	Q9NY19	Missense_Mutation	SNP	ENST00000291041.5	hg19	CCDS10851.1	.	.	.	.	.	.	.	.	.	.	G	13.18	2.160033	0.38119	.	.	ENSG00000159792	ENST00000291041	T	0.37752	1.18	4.21	4.21	0.49690	.	0.107588	0.64402	D	0.000006	T	0.31167	0.0788	L	0.56769	1.78	0.49798	D	0.999828	B	0.16396	0.017	B	0.13407	0.009	T	0.10268	-1.0637	10	0.31617	T	0.26	-13.1757	8.1675	0.31235	0.1056:0.0:0.8944:0.0	.	79	P11801	KPSH1_HUMAN	L	79	ENSP00000291041:R79L	ENSP00000291041:R79L	R	+	2	0	PSKH1	66500389	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.920000	0.63390	2.645000	0.89757	0.655000	0.94253	CGC	.	.		0.612	PSKH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268882.3	NM_006742	
TANGO6	79613	hgsc.bcm.edu	37	16	68953121	68953121	+	Splice_Site	SNP	A	A	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:68953121A>T	ENST00000261778.1	+	12	2138	c.2126A>T	c.(2125-2127)cAg>cTg	p.Q709L		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	709						integral component of membrane (GO:0016021)											GGAGCTGTTCAGGTGAGTTGT	0.512																																					p.Q709L		Atlas-SNP	.											.	.	.	.	0			c.A2126T						.						59.0	58.0	58.0					16																	68953121		2111	4227	6338	SO:0001630	splice_region_variant	79613	exon12			CTGTTCAGGTGAG		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 7"""	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.2127+1A>T	chr16.hg19:g.68953121A>T		220.0	0.0		112.0	23.0	NM_024562	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	hg19	CCDS45516.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.152870	0.78001	.	.	ENSG00000103047	ENST00000261778	T	0.63580	-0.05	5.36	5.36	0.76844	Armadillo-type fold (1);	0.225081	0.47455	D	0.000229	T	0.54631	0.1870	M	0.64997	1.995	0.44927	D	0.997947	P	0.44090	0.826	B	0.36845	0.234	T	0.57642	-0.7776	10	0.36615	T	0.2	-16.9474	10.2972	0.43631	0.8528:0.0:0.0:0.1472	.	709	Q9C0B7	TMCO7_HUMAN	L	709	ENSP00000261778:Q709L	ENSP00000261778:Q709L	Q	+	2	0	TMCO7	67510622	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.909000	0.56363	2.028000	0.59812	0.533000	0.62120	CAG	.	.		0.512	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2	Missense_Mutation
AARS	16	hgsc.bcm.edu	37	16	70292100	70292100	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:70292100G>A	ENST00000261772.8	-	15	2156	c.2013C>T	c.(2011-2013)tgC>tgT	p.C671C	AARS_ENST00000564359.1_Intron	NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		CTGCCAGGGGGCAATCCTGGG	0.597																																					p.C671C		Atlas-SNP	.											.	AARS	62	.	0			c.C2013T						.						32.0	27.0	28.0					16																	70292100		2198	4300	6498	SO:0001819	synonymous_variant	16	exon15			CAGGGGGCAATCC	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	20	protein-coding gene	gene with protein product	"""alanine tRNA ligase 1, cytoplasmic"""	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.2013C>T	chr16.hg19:g.70292100G>A		117.0	0.0		70.0	4.0	NM_001605		Silent	SNP	ENST00000261772.8	hg19	CCDS32474.1																																																																																			.	.		0.597	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605	
CMTR2	55783	hgsc.bcm.edu	37	16	71319522	71319522	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:71319522T>C	ENST00000338099.5	-	3	638	c.302A>G	c.(301-303)cAt>cGt	p.H101R	CMTR2_ENST00000434935.2_Missense_Mutation_p.H101R			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	101					7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										TTTTCTAACATGAGAAATGAT	0.388																																					p.H101R		Atlas-SNP	.											.	FTSJD1	70	.	0			c.A302G						.						90.0	86.0	88.0					16																	71319522		2198	4300	6498	SO:0001583	missense	55783	exon3			CTAACATGAGAAA	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"""adrift homolog (Drosophila)"""		"""FtsJ methyltransferase domain containing 1"""	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.302A>G	chr16.hg19:g.71319522T>C	ENSP00000337512:p.His101Arg	131.0	0.0		79.0	6.0	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	hg19	CCDS10898.1	.	.	.	.	.	.	.	.	.	.	T	0.782	-0.761961	0.02996	.	.	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.13901	2.55;2.55	5.56	4.47	0.54385	.	0.255608	0.38217	N	0.001766	T	0.08714	0.0216	L	0.37630	1.12	0.41700	D	0.989398	P	0.43169	0.8	B	0.32289	0.143	T	0.30534	-0.9975	10	0.19147	T	0.46	-28.6195	10.7544	0.46228	0.0:0.0743:0.0:0.9257	.	101	Q8IYT2	FTSJ1_HUMAN	R	101	ENSP00000337512:H101R;ENSP00000411148:H101R	ENSP00000337512:H101R	H	-	2	0	FTSJD1	69877023	1.000000	0.71417	0.977000	0.42913	0.998000	0.95712	6.412000	0.73303	0.941000	0.37499	0.459000	0.35465	CAT	.	.		0.388	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
RFWD3	55159	hgsc.bcm.edu	37	16	74694849	74694849	+	Nonsense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:74694849G>A	ENST00000361070.4	-	2	596	c.499C>T	c.(499-501)Cag>Tag	p.Q167*	RFWD3_ENST00000571750.1_Nonsense_Mutation_p.Q167*	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	167					DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						TCTGTCCTCTGAGACCCTCCG	0.468																																					p.Q167X		Atlas-SNP	.											.	RFWD3	49	.	0			c.C499T						.						127.0	125.0	126.0					16																	74694849		2198	4300	6498	SO:0001587	stop_gained	55159	exon2			TCCTCTGAGACCC	AK001382	CCDS32486.1	16q22.3	2013-01-09						"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.499C>T	chr16.hg19:g.74694849G>A	ENSP00000354361:p.Gln167*	154.0	0.0		97.0	4.0	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Nonsense_Mutation	SNP	ENST00000361070.4	hg19	CCDS32486.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.820351	0.90873	.	.	ENSG00000168411	ENST00000361070	.	.	.	4.64	4.64	0.57946	.	0.345316	0.28114	N	0.016553	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-17.0351	14.7109	0.69232	0.0:0.0:1.0:0.0	.	.	.	.	X	167	.	ENSP00000354361:Q167X	Q	-	1	0	RFWD3	73252350	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.082000	0.57635	2.565000	0.86533	0.591000	0.81541	CAG	.	.		0.468	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124	
MON1B	22879	hgsc.bcm.edu	37	16	77225506	77225506	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:77225506G>T	ENST00000248248.3	+	2	474	c.124G>T	c.(124-126)Gaa>Taa	p.E42*	MON1B_ENST00000545553.1_Intron|MON1B_ENST00000439557.2_Nonsense_Mutation_p.E42*|MON1B_ENST00000320859.6_Nonsense_Mutation_p.E42*	NM_014940.2	NP_055755.1	Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	42										breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						GCCGGATCCCGAAGACGAGGG	0.622																																					p.E42X		Atlas-SNP	.											.	MON1B	55	.	0			c.G124T						.						31.0	34.0	33.0					16																	77225506		2198	4300	6498	SO:0001587	stop_gained	22879	exon2			GATCCCGAAGACG	BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111			25020	protein-coding gene	gene with protein product		608954	"""MON1 homolog B (yeast)"""			10048485	Standard	NM_014940		Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000248248.3:c.124G>T	chr16.hg19:g.77225506G>T	ENSP00000248248:p.Glu42*	154.0	0.0		82.0	4.0	NM_014940	B4DDZ0|O94949	Nonsense_Mutation	SNP	ENST00000248248.3	hg19	CCDS10925.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.005079	0.93287	.	.	ENSG00000103111	ENST00000248248;ENST00000320859;ENST00000439557	.	.	.	3.84	0.838	0.18902	.	0.917379	0.08990	N	0.864588	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	6.3037	0.21127	0.3107:0.0:0.6893:0.0	.	.	.	.	X	42	.	ENSP00000248248:E42X	E	+	1	0	MON1B	75783007	0.123000	0.22298	0.000000	0.03702	0.004000	0.04260	1.004000	0.29822	0.222000	0.20900	-0.717000	0.03617	GAA	.	.		0.622	MON1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269036.2	NM_014940	
SYCE1L	100130958	hgsc.bcm.edu	37	16	77243331	77243331	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:77243331C>A	ENST00000378644.4	+	6	377	c.322C>A	c.(322-324)Cag>Aag	p.Q108K	RP11-538I12.2_ENST00000569032.1_RNA	NM_001129979.1	NP_001123451.1	A8MT33	SYC1L_HUMAN	synaptonemal complex central element protein 1-like	108					synaptonemal complex assembly (GO:0007130)	synaptonemal complex (GO:0000795)				breast(1)|prostate(1)	2						gAGGATCCTCCAGATGCACTG	0.567																																					p.Q108K		Atlas-SNP	.											.	SYCE1L	10	.	0			c.C322A						.						75.0	83.0	81.0					16																	77243331		692	1591	2283	SO:0001583	missense	100130958	exon6			ATCCTCCAGATGC		CCDS45533.1	16q23.1	2009-10-06			ENSG00000205078	ENSG00000205078			37236	protein-coding gene	gene with protein product	"""meiosis-related protein"""					16328886	Standard	NM_001129979		Approved	MRP2	uc010vnh.1	A8MT33		ENST00000378644.4:c.322C>A	chr16.hg19:g.77243331C>A	ENSP00000367911:p.Gln108Lys	89.0	0.0		54.0	4.0	NM_001129979	A6NF23	Missense_Mutation	SNP	ENST00000378644.4	hg19	CCDS45533.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.763742	0.31228	.	.	ENSG00000205078	ENST00000378644	T	0.34275	1.37	3.64	2.66	0.31614	.	2.034340	0.04277	N	0.343087	T	0.27933	0.0688	L	0.42245	1.32	0.20821	N	0.999842	P	0.40107	0.703	B	0.35470	0.203	T	0.12344	-1.0551	10	0.07325	T	0.83	.	8.6793	0.34198	0.2252:0.7748:0.0:0.0	.	108	A8MT33	SYC1L_HUMAN	K	108	ENSP00000367911:Q108K	ENSP00000367911:Q108K	Q	+	1	0	SYCE1L	75800832	0.972000	0.33761	0.972000	0.41901	0.954000	0.61252	0.948000	0.29096	1.091000	0.41335	0.563000	0.77884	CAG	.	.		0.567	SYCE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433889.1	NM_001129979	
JPH3	57338	hgsc.bcm.edu	37	16	87723326	87723326	+	Nonsense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:87723326C>T	ENST00000284262.2	+	4	1602	c.1360C>T	c.(1360-1362)Cag>Tag	p.Q454*	JPH3_ENST00000563609.1_3'UTR	NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	454					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		GACACCCCTGCAGCAGGAGAG	0.677																																					p.Q454X		Atlas-SNP	.											.	JPH3	95	.	0			c.C1360T						.						39.0	30.0	33.0					16																	87723326		2195	4298	6493	SO:0001587	stop_gained	57338	exon4			CCCCTGCAGCAGG	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"""trinucleotide repeat containing 22"""	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.1360C>T	chr16.hg19:g.87723326C>T	ENSP00000284262:p.Gln454*	206.0	0.0		71.0	4.0	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Nonsense_Mutation	SNP	ENST00000284262.2	hg19	CCDS10962.1	.	.	.	.	.	.	.	.	.	.	C	40	8.062469	0.98635	.	.	ENSG00000154118	ENST00000537256;ENST00000284262	.	.	.	4.48	4.48	0.54585	.	0.152719	0.41823	D	0.000819	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	16.1715	0.81820	0.0:1.0:0.0:0.0	.	.	.	.	X	317;454	.	ENSP00000284262:Q454X	Q	+	1	0	JPH3	86280827	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	6.073000	0.71245	2.050000	0.60909	0.655000	0.94253	CAG	.	.		0.677	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2		
ZNF469	84627	hgsc.bcm.edu	37	16	88500010	88500010	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:88500010A>G	ENST00000437464.1	+	2	6048	c.6048A>G	c.(6046-6048)gcA>gcG	p.A2016A	ZNF469_ENST00000565624.1_Silent_p.A2044A	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2016					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)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						GAAGCAGGGCAGCCATGAGCC	0.647																																					p.A2016A		Atlas-SNP	.											.	ZNF469	121	.	0			c.A6048G						.						30.0	37.0	35.0					16																	88500010		692	1590	2282	SO:0001819	synonymous_variant	84627	exon2			CAGGGCAGCCATG	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.6048A>G	chr16.hg19:g.88500010A>G		160.0	0.0		60.0	4.0	NM_001127464		Silent	SNP	ENST00000437464.1	hg19	CCDS45544.1																																																																																			.	.		0.647	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
ZNF778	197320	hgsc.bcm.edu	37	16	89294364	89294364	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:89294364A>G	ENST00000433976.2	+	6	1916	c.1584A>G	c.(1582-1584)acA>acG	p.T528T	ZNF778_ENST00000306502.6_Silent_p.T486T|RP11-46C24.6_ENST00000563182.1_RNA	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	528					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(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		AAACTCACACAGAGGAGAAGC	0.438																																					p.T556T		Atlas-SNP	.											.	ZNF778	67	.	0			c.A1668G						.						75.0	83.0	80.0					16																	89294364		2182	4294	6476	SO:0001819	synonymous_variant	197320	exon7			TCACACAGAGGAG	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"""Zinc fingers, C2H2-type"", ""-"""	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.1584A>G	chr16.hg19:g.89294364A>G		135.0	0.0		87.0	4.0	NM_001201407	Q08AG0	Silent	SNP	ENST00000433976.2	hg19	CCDS45550.1																																																																																			.	.		0.438	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531	
VPS53	55275	hgsc.bcm.edu	37	17	526908	526908	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:526908T>C	ENST00000571805.1	-	11	1117	c.981A>G	c.(979-981)gaA>gaG	p.E327E	VPS53_ENST00000576149.1_5'UTR|VPS53_ENST00000446250.2_Silent_p.E129E|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000401468.3_Intron|VPS53_ENST00000291074.5_Silent_p.E298E|VPS53_ENST00000437048.2_Silent_p.E327E			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	327					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		TCTTGGCAAGTTCTGCCCTTC	0.348																																					p.E327E		Atlas-SNP	.											.	VPS53	109	.	0			c.A981G						.						70.0	64.0	66.0					17																	526908		2203	4300	6503	SO:0001819	synonymous_variant	55275	exon11			GGCAAGTTCTGCC		CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"""vacuolar protein sorting 53 (yeast)"""			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.981A>G	chr17.hg19:g.526908T>C		103.0	0.0		94.0	4.0	NM_001128159	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Silent	SNP	ENST00000571805.1	hg19																																																																																				.	.		0.348	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289	
SMG6	23293	hgsc.bcm.edu	37	17	1964865	1964865	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:1964865T>C	ENST00000263073.6	-	19	4231	c.4181A>G	c.(4180-4182)aAc>aGc	p.N1394S	SMG6_ENST00000354901.4_Missense_Mutation_p.N486S|SMG6_ENST00000544865.1_Missense_Mutation_p.N1363S|SMG6_ENST00000573166.1_5'UTR|SMG6_ENST00000536871.2_Missense_Mutation_p.N486S	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	1394	PINc.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CACACGCAGGTTCCGGTCATC	0.632																																					p.N1394S	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.A4181G						.						93.0	50.0	65.0					17																	1964865		2196	4296	6492	SO:0001583	missense	23293	exon19			CGCAGGTTCCGGT	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.4181A>G	chr17.hg19:g.1964865T>C	ENSP00000263073:p.Asn1394Ser	100.0	0.0		79.0	4.0	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	hg19	CCDS11016.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.756121	0.89843	.	.	ENSG00000070366	ENST00000263073;ENST00000544865;ENST00000354901;ENST00000536871	T;T;T	0.28255	2.33;2.32;1.62	4.95	4.95	0.65309	Nucleotide binding protein, PINc (1);	0.000000	0.85682	D	0.000000	T	0.62974	0.2472	M	0.91972	3.26	0.80722	D	1	D	0.71674	0.998	D	0.72338	0.977	T	0.72896	-0.4153	10	0.87932	D	0	-9.1547	14.4404	0.67311	0.0:0.0:0.0:1.0	.	1394	Q86US8	EST1A_HUMAN	S	1394;1363;305;486	ENSP00000263073:N1394S;ENSP00000443920:N1363S;ENSP00000440283:N486S	ENSP00000263073:N1394S	N	-	2	0	SMG6	1911615	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.078000	0.62432	0.533000	0.62120	AAC	.	.		0.632	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
PLD2	5338	hgsc.bcm.edu	37	17	4712848	4712848	+	Splice_Site	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:4712848T>C	ENST00000263088.6	+	7	745		c.e7+2		PLD2_ENST00000572940.1_Splice_Site|RP11-81A22.5_ENST00000571067.1_lincRNA	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2						cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	CAAAGGACTGTGAGTGTCTGG	0.572																																					.		Atlas-SNP	.											.	PLD2	138	.	0			c.614+2T>C						.						54.0	56.0	56.0					17																	4712848		2203	4300	6503	SO:0001630	splice_region_variant	5338	exon7			GGACTGTGAGTGT	AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"""choline phosphatase 2"""	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.614+2T>C	chr17.hg19:g.4712848T>C		114.0	0.0		110.0	6.0	NM_002663	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Splice_Site	SNP	ENST00000263088.6	hg19	CCDS11057.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.384349	0.61845	.	.	ENSG00000129219	ENST00000263088	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.8822	0.58024	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PLD2	4659812	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	5.590000	0.67530	2.148000	0.66965	0.459000	0.35465	.	.	.		0.572	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	Intron
DHX33	56919	hgsc.bcm.edu	37	17	5365718	5365718	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:5365718G>T	ENST00000225296.3	-	3	799	c.599C>A	c.(598-600)aCt>aAt	p.T200N	DHX33_ENST00000433302.3_Intron	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	200	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TGTGTGGATAGTCCGTTCGTG	0.463																																					p.T200N		Atlas-SNP	.											.	DHX33	41	.	0			c.C599A						.						96.0	85.0	89.0					17																	5365718		2203	4300	6503	SO:0001583	missense	56919	exon3			TGGATAGTCCGTT	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"""DEAH-boxes"""	16718	protein-coding gene	gene with protein product		614405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"""	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.599C>A	chr17.hg19:g.5365718G>T	ENSP00000225296:p.Thr200Asn	138.0	0.0		69.0	4.0	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	hg19	CCDS11072.1	.	.	.	.	.	.	.	.	.	.	G	34	5.390786	0.95988	.	.	ENSG00000005100	ENST00000225296	T	0.09255	3.0	5.78	5.78	0.91487	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.34978	0.0916	M	0.71036	2.16	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.01643	-1.1305	10	0.87932	D	0	.	19.1701	0.93574	0.0:0.0:1.0:0.0	.	200	Q9H6R0	DHX33_HUMAN	N	200	ENSP00000225296:T200N	ENSP00000225296:T200N	T	-	2	0	DHX33	5306442	1.000000	0.71417	0.982000	0.44146	0.978000	0.69477	7.862000	0.87013	2.769000	0.95229	0.638000	0.83543	ACT	.	.		0.463	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
POLR2A	5430	hgsc.bcm.edu	37	17	7404157	7404157	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:7404157G>T	ENST00000322644.6	+	11	2270	c.1871G>T	c.(1870-1872)gGg>gTg	p.G624V		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	624					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|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-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				ATCTCTCCTGGGGACACCAAG	0.527																																					p.G624V		Atlas-SNP	.											.	POLR2A	157	.	0			c.G1871T						.						135.0	122.0	126.0					17																	7404157		2203	4300	6503	SO:0001583	missense	5430	exon11			CTCCTGGGGACAC			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.1871G>T	chr17.hg19:g.7404157G>T	ENSP00000314949:p.Gly624Val	172.0	0.0		78.0	4.0	NM_000937	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	hg19	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.498307	0.85069	.	.	ENSG00000181222	ENST00000535204;ENST00000322644	T	0.68479	-0.33	5.96	5.96	0.96718	RNA polymerase Rpb1, domain 3 (1);	0.000000	0.85682	D	0.000000	D	0.86230	0.5883	H	0.96080	3.765	0.80722	D	1	D	0.54964	0.969	P	0.56788	0.806	D	0.89892	0.4038	10	0.87932	D	0	.	19.1654	0.93555	0.0:0.0:1.0:0.0	.	624	P24928	RPB1_HUMAN	V	580;624	ENSP00000314949:G624V	ENSP00000314949:G624V	G	+	2	0	SLC35G6	7344881	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	9.075000	0.94004	2.830000	0.97506	0.585000	0.79938	GGG	.	.		0.527	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
AURKB	9212	hgsc.bcm.edu	37	17	8110166	8110166	+	Silent	SNP	G	G	T	rs148133660	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:8110166G>T	ENST00000585124.1	-	6	532	c.439C>A	c.(439-441)Cgg>Agg	p.R147R	AURKB_ENST00000578549.1_Silent_p.R115R|AURKB_ENST00000535053.1_Intron|AURKB_ENST00000534871.1_Silent_p.R106R|AURKB_ENST00000316199.6_Silent_p.R148R	NM_004217.3	NP_004208.2	Q96GD4	AURKB_HUMAN	aurora kinase B	147	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				abscission (GO:0009838)|aging (GO:0007568)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|attachment of spindle microtubules to kinetochore (GO:0008608)|cell proliferation (GO:0008283)|cellular response to UV (GO:0034644)|cleavage furrow formation (GO:0036089)|cytokinesis checkpoint (GO:0031565)|histone H3-S28 phosphorylation (GO:0043988)|histone modification (GO:0016570)|mitotic cell cycle (GO:0000278)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytokinesis (GO:0032467)|protein autophosphorylation (GO:0046777)|protein localization to kinetochore (GO:0034501)|protein phosphorylation (GO:0006468)|regulation of chromosome segregation (GO:0051983)|spindle checkpoint (GO:0031577)|spindle midzone assembly involved in mitosis (GO:0051256)|spindle stabilization (GO:0043146)	chromocenter (GO:0010369)|chromosome passenger complex (GO:0032133)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.R147W(1)		breast(1)|central_nervous_system(1)|lung(2)	4						ATCCTCCTCCGGTCATAAAAA	0.527																																					p.R147R	NSCLC(134;1161 2470 43664 51568)	Atlas-SNP	.											AURKB_ENST00000316199,NS,haematopoietic_neoplasm,0,1	AURKB	47	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C439A						.						37.0	38.0	38.0					17																	8110166		2203	4300	6503	SO:0001819	synonymous_variant	9212	exon6			TCCTCCGGTCATA	AF004022	CCDS11134.1, CCDS58514.1, CCDS67162.1	17p13.1	2013-01-17	2003-07-21	2003-07-23	ENSG00000178999	ENSG00000178999		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	11390	protein-coding gene	gene with protein product	"""aurora-B"", ""aurora-1"", ""protein phosphatase 1, regulatory subunit 48"""	604970	"""serine/threonine kinase 12"""	STK12		9858806	Standard	NM_001256834		Approved	Aik2, IPL1, AurB, AIM-1, ARK2, STK5, PPP1R48	uc002gkm.4	Q96GD4	OTTHUMG00000108189	ENST00000585124.1:c.439C>A	chr17.hg19:g.8110166G>T		147.0	0.0		48.0	4.0	NM_004217	B4DNM4|C7G533|C7G534|C7G535|D3DTR4|J9JID1|O14630|O60446|O95083|Q96DV5|Q9UQ46	Silent	SNP	ENST00000585124.1	hg19	CCDS11134.1																																																																																			.	G|1.000;A|0.000		0.527	AURKB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000226995.2	NM_004217	
CTC1	80169	hgsc.bcm.edu	37	17	8131843	8131843	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:8131843T>C	ENST00000315684.8	-	22	3499	c.3492A>G	c.(3490-3492)aaA>aaG	p.K1164K		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	1164					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						TCTTCGACGGTTTCCTTTCCA	0.527																																					p.K1164K		Atlas-SNP	.											.	CTC1	75	.	0			c.A3492G						.						283.0	283.0	283.0					17																	8131843		1939	4141	6080	SO:0001819	synonymous_variant	80169	exon22			CGACGGTTTCCTT	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.3492A>G	chr17.hg19:g.8131843T>C		128.0	0.0		61.0	5.0	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	hg19	CCDS42259.1																																																																																			.	.		0.527	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
CTC1	80169	hgsc.bcm.edu	37	17	8133211	8133211	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:8133211G>T	ENST00000315684.8	-	18	3016	c.3009C>A	c.(3007-3009)atC>atA	p.I1003I		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	1003					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						GCACTGACCTGATGGTGGTCT	0.483																																					p.I1003I		Atlas-SNP	.											.	CTC1	75	.	0			c.C3009A						.						115.0	120.0	118.0					17																	8133211		1973	4147	6120	SO:0001819	synonymous_variant	80169	exon18			TGACCTGATGGTG	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.3009C>A	chr17.hg19:g.8133211G>T		97.0	0.0		43.0	4.0	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	hg19	CCDS42259.1																																																																																			.	.		0.483	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
RANGRF	29098	hgsc.bcm.edu	37	17	8192743	8192743	+	Intron	SNP	G	G	T	rs370613922		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:8192743G>T	ENST00000226105.6	+	3	643				SLC25A35_ENST00000579192.1_Intron|RANGRF_ENST00000407006.4_Intron|SLC25A35_ENST00000581320.1_5'Flank|SLC25A35_ENST00000396278.1_Intron|RANGRF_ENST00000439238.3_Missense_Mutation_p.R121L|SLC25A35_ENST00000380067.2_3'UTR|RANGRF_ENST00000580434.1_Intron|SLC25A35_ENST00000580340.1_3'UTR	NM_016492.4	NP_057576.2	Q9HD47	MOG1_HUMAN	RAN guanine nucleotide release factor						ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein localization to cell surface (GO:2000010)|protein exit from endoplasmic reticulum (GO:0032527)|regulation of heart rate (GO:0002027)|regulation of membrane depolarization (GO:0003254)|regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900825)|regulation of membrane potential (GO:0042391)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	guanyl-nucleotide exchange factor activity (GO:0005085)|ion channel binding (GO:0044325)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)|sodium channel regulator activity (GO:0017080)			endometrium(1)	1						GTGAGGGCCCGAGAGTGTGTA	0.572																																					p.R121L		Atlas-SNP	.											.	RANGRF	5	.	0			c.G362T						.						40.0	40.0	40.0					17																	8192743		2203	4300	6503	SO:0001627	intron_variant	29098	exon3			GGGCCCGAGAGTG	AF151070	CCDS11137.1, CCDS54086.1, CCDS54087.1	17p13	2014-05-09				ENSG00000108961			17679	protein-coding gene	gene with protein product	"""MOG1 homolog (S. cerevisiae)"""	607954				11290418	Standard	NM_016492		Approved	MOG1, HSPC165, HSPC236, RANGNRF	uc002gkv.3	Q9HD47		ENST00000226105.6:c.351+11G>T	chr17.hg19:g.8192743G>T		248.0	0.0		91.0	4.0	NM_001177802	D3DTR6|Q68DI3|Q9BR68|Q9HD48|Q9NRU9|Q9P001|Q9P0P2	Missense_Mutation	SNP	ENST00000226105.6	hg19	CCDS11137.1	.	.	.	.	.	.	.	.	.	.	G	6.581	0.475506	0.12521	.	.	ENSG00000108961	ENST00000439238	T	0.75821	-0.97	4.93	-3.59	0.04583	.	.	.	.	.	T	0.48892	0.1525	.	.	.	0.09310	N	1	B	0.18863	0.031	B	0.16289	0.015	T	0.25779	-1.0122	7	.	.	.	.	1.0577	0.01593	0.3286:0.262:0.2755:0.1339	.	121	Q9HD47-3	.	L	121	ENSP00000413190:R121L	.	R	+	2	0	RANGRF	8133468	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.541000	0.06099	-0.877000	0.04012	-0.253000	0.11424	CGA	.	.		0.572	RANGRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442127.1	NM_016492	
MYH10	4628	hgsc.bcm.edu	37	17	8455422	8455422	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:8455422A>G	ENST00000269243.4	-	8	969	c.831T>C	c.(829-831)gaT>gaC	p.D277D	MYH10_ENST00000379980.4_Silent_p.D293D|MYH10_ENST00000360416.3_Silent_p.D287D|MYH10_ENST00000396239.1_Silent_p.D277D	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	277	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						AAGTACGTTCATCTTTTGCTT	0.318																																					p.D287D		Atlas-SNP	.											.	MYH10	148	.	0			c.T861C						.						47.0	48.0	48.0					17																	8455422		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon9			ACGTTCATCTTTT	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.831T>C	chr17.hg19:g.8455422A>G		203.0	0.0		83.0	4.0	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	hg19	CCDS11144.1																																																																																			.	.		0.318	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
HS3ST3A1	9955	hgsc.bcm.edu	37	17	13504323	13504323	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:13504323G>T	ENST00000284110.1	-	1	921	c.124C>A	c.(124-126)Ctg>Atg	p.L42M		NM_006042.1	NP_006033.1	Q9Y663	HS3SA_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	42					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)|sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CGCTCGGCCAGGCAGTAGAAG	0.716																																					p.L42M		Atlas-SNP	.											.	HS3ST3A1	39	.	0			c.C124A						.						31.0	28.0	29.0					17																	13504323		2183	4291	6474	SO:0001583	missense	9955	exon1			CGGCCAGGCAGTA	AF105376	CCDS11165.1	17p12	2007-04-02			ENSG00000153976	ENSG00000153976	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5196	protein-coding gene	gene with protein product		604057				9988767	Standard	NM_006042		Approved	3OST3A1, 30ST3A1	uc002gob.1	Q9Y663	OTTHUMG00000058768	ENST00000284110.1:c.124C>A	chr17.hg19:g.13504323G>T	ENSP00000284110:p.Leu42Met	114.0	0.0		56.0	4.0	NM_006042	A8K7N2	Missense_Mutation	SNP	ENST00000284110.1	hg19	CCDS11165.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.213597	0.58452	.	.	ENSG00000153976	ENST00000284110	T	0.66638	-0.22	3.03	0.926	0.19430	.	.	.	.	.	T	0.50377	0.1612	L	0.34521	1.04	0.80722	D	1	B	0.21905	0.062	B	0.17979	0.02	T	0.42189	-0.9466	9	0.56958	D	0.05	.	6.5802	0.22589	0.1049:0.0:0.7169:0.1782	.	42	Q9Y663	HS3SA_HUMAN	M	42	ENSP00000284110:L42M	ENSP00000284110:L42M	L	-	1	2	HS3ST3A1	13445048	0.979000	0.34478	1.000000	0.80357	0.991000	0.79684	-0.014000	0.12656	0.279000	0.22186	-0.140000	0.14226	CTG	.	.		0.716	HS3ST3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129952.1	NM_006042	
PIGL	9487	hgsc.bcm.edu	37	17	16137378	16137378	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:16137378A>G	ENST00000225609.5	+	2	346	c.329A>G	c.(328-330)gAc>gGc	p.D110G	PIGL_ENST00000395844.4_Missense_Mutation_p.D110G|PIGL_ENST00000498772.2_Missense_Mutation_p.D110G|PIGL_ENST00000581006.1_Missense_Mutation_p.D110G	NM_004278.3	NP_004269.1	Q9Y2B2	PIGL_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class L	110					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	N-acetylglucosaminylphosphatidylinositol deacetylase activity (GO:0000225)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)		ATGATTATTGACAACAGGTAA	0.353																																					p.D110G		Atlas-SNP	.											.	PIGL	16	.	0			c.A329G						.						78.0	81.0	80.0					17																	16137378		2203	4300	6503	SO:0001583	missense	9487	exon2			TTATTGACAACAG	AB017165	CCDS11176.1	17p12-p11.2	2013-02-26	2006-06-28		ENSG00000108474	ENSG00000108474	3.5.1.89	"""Phosphatidylinositol glycan anchor biosynthesis"""	8966	protein-coding gene	gene with protein product	"""N-acetylglucosaminylphosphatidylinositol deacetylase"""	605947	"""phosphatidylinositol glycan, class L"""			10085243	Standard	NM_004278		Approved		uc002gpv.3	Q9Y2B2	OTTHUMG00000059346	ENST00000225609.5:c.329A>G	chr17.hg19:g.16137378A>G	ENSP00000225609:p.Asp110Gly	95.0	0.0		54.0	4.0	NM_004278	A8KA67|B4DYN4	Missense_Mutation	SNP	ENST00000225609.5	hg19	CCDS11176.1	.	.	.	.	.	.	.	.	.	.	A	13.60	2.285341	0.40394	.	.	ENSG00000108474	ENST00000225609;ENST00000395844	T;T	0.76448	-1.02;-1.02	5.78	5.78	0.91487	Putative deacetylase LmbE-like domain (2);	0.134522	0.64402	D	0.000003	T	0.80099	0.4561	L	0.47716	1.5	0.49213	D	0.999766	P;P	0.51537	0.946;0.892	P;P	0.53360	0.721;0.724	T	0.80881	-0.1184	10	0.51188	T	0.08	-11.6728	14.11	0.65115	1.0:0.0:0.0:0.0	.	110;110	B4DYN4;Q9Y2B2	.;PIGL_HUMAN	G	110	ENSP00000225609:D110G;ENSP00000379185:D110G	ENSP00000225609:D110G	D	+	2	0	PIGL	16078103	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.741000	0.74837	2.220000	0.72140	0.477000	0.44152	GAC	.	.		0.353	PIGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131881.1		
MYO15A	51168	hgsc.bcm.edu	37	17	18047030	18047030	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:18047030A>G	ENST00000205890.5	+	27	6304	c.5966A>G	c.(5965-5967)gAg>gGg	p.E1989G	snoU13_ENST00000459354.1_RNA	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	1989	Neck or regulatory domain.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					TCCCTCTAGGAGCTGAGCAAG	0.677																																					p.E1989G		Atlas-SNP	.											.	MYO15A	268	.	0			c.A5966G						.						31.0	37.0	35.0					17																	18047030		2154	4239	6393	SO:0001630	splice_region_variant	51168	exon26			TCTAGGAGCTGAG	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.5965-1A>G	chr17.hg19:g.18047030A>G		174.0	0.0		162.0	7.0	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	A	15.22	2.767788	0.49574	.	.	ENSG00000091536	ENST00000205890	D	0.89485	-2.52	5.0	2.7	0.31948	.	.	.	.	.	D	0.83142	0.5190	L	0.47716	1.5	0.80722	D	1	B	0.21753	0.06	B	0.17433	0.018	T	0.78145	-0.2318	9	0.62326	D	0.03	.	7.0293	0.24958	0.7946:0.0:0.0741:0.1313	.	1989	Q9UKN7	MYO15_HUMAN	G	1989	ENSP00000205890:E1989G	ENSP00000205890:E1989G	E	+	2	0	MYO15A	17987755	1.000000	0.71417	1.000000	0.80357	0.672000	0.39443	5.104000	0.64584	0.719000	0.32188	-0.490000	0.04691	GAG	.	.		0.677	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	Missense_Mutation
SUPT6H	6830	hgsc.bcm.edu	37	17	27014158	27014158	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:27014158G>T	ENST00000314616.6	+	22	3036	c.2753G>T	c.(2752-2754)cGg>cTg	p.R918L	SUPT6H_ENST00000347486.4_Missense_Mutation_p.R918L	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	918	Interaction with KDM6A. {ECO:0000250}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					TCCCTGGCCCGGCGCATCCAG	0.542																																					p.R918L		Atlas-SNP	.											.	SUPT6H	165	.	0			c.G2753T						.						94.0	106.0	102.0					17																	27014158		2203	4300	6503	SO:0001583	missense	6830	exon22			TGGCCCGGCGCAT	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.2753G>T	chr17.hg19:g.27014158G>T	ENSP00000319104:p.Arg918Leu	100.0	0.0		97.0	4.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	hg19	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	36	5.642353	0.96704	.	.	ENSG00000109111	ENST00000314616	.	.	.	5.82	5.82	0.92795	YqgF/RNase H-like domain (1);	0.000000	0.85682	D	0.000000	D	0.91164	0.7217	H	0.98446	4.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93996	0.7271	9	0.87932	D	0	-18.2791	19.7131	0.96103	0.0:0.0:1.0:0.0	.	918	Q7KZ85	SPT6H_HUMAN	L	918	.	ENSP00000319104:R918L	R	+	2	0	SUPT6H	24038285	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.499000	0.73683	2.760000	0.94817	0.551000	0.68910	CGG	.	.		0.542	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
MYO18A	399687	hgsc.bcm.edu	37	17	27437088	27437088	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:27437088T>C	ENST00000527372.1	-	19	3299	c.3119A>G	c.(3118-3120)aAg>aGg	p.K1040R	MYO18A_ENST00000533112.1_Missense_Mutation_p.K1040R|MYO18A_ENST00000354329.4_Missense_Mutation_p.K1040R|MYO18A_ENST00000531253.1_Missense_Mutation_p.K1040R	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1040	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			AAAATGCAGCTTTGACTTCTT	0.627																																					p.K1040R	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.A3119G						.						42.0	53.0	49.0					17																	27437088		2186	4279	6465	SO:0001583	missense	399687	exon19			TGCAGCTTTGACT	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"""Myosins / Myosin superfamily : Class XVIII"""	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.3119A>G	chr17.hg19:g.27437088T>C	ENSP00000437073:p.Lys1040Arg	77.0	0.0		64.0	4.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	T	9.421	1.082964	0.20309	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000458428	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	5.06	5.06	0.68205	Myosin head, motor domain (2);	0.093725	0.64402	D	0.000001	T	0.47432	0.1445	N	0.05306	-0.075	0.34569	D	0.713263	B;B;B;B;B	0.15719	0.001;0.009;0.009;0.009;0.014	B;B;B;B;B	0.16722	0.003;0.016;0.016;0.016;0.014	T	0.51395	-0.8711	10	0.07175	T	0.84	.	14.7537	0.69546	0.0:0.0:0.0:1.0	.	709;652;1040;1040;1040	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	R	1040;1040;1040;1040;1040;652	ENSP00000346291:K1040R;ENSP00000435932:K1040R;ENSP00000434228:K1040R;ENSP00000437073:K1040R	ENSP00000346291:K1040R	K	-	2	0	MYO18A	24461214	1.000000	0.71417	0.997000	0.53966	0.754000	0.42855	3.561000	0.53770	2.029000	0.59856	0.459000	0.35465	AAG	.	.		0.627	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
RAD51D	5892	hgsc.bcm.edu	37	17	33443890	33443890	+	Intron	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:33443890A>G	ENST00000345365.6	-	3	519				RAD51D_ENST00000590380.1_Intron|RAD51D_ENST00000360276.3_Intron|RAD51D_ENST00000335858.7_Intron|RAD51D_ENST00000460118.2_Intron|RAD51D_ENST00000590016.1_Missense_Mutation_p.V104A|RAD51L3-RFFL_ENST00000593039.1_Intron|RAD51D_ENST00000394589.4_Intron	NM_002878.3	NP_002869.3	O75771	RA51D_HUMAN	RAD51 paralog D						ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|reciprocal meiotic recombination (GO:0007131)|strand invasion (GO:0042148)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|gamma-tubulin binding (GO:0043015)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						tgaagtgctgaccgcagtgcc	0.502								Direct reversal of damage																													p.V104A		Atlas-SNP	.											.	RAD51D	53	.	0			c.T311C						.						83.0	76.0	78.0					17																	33443890		1559	3559	5118	SO:0001627	intron_variant	5892	exon3			GTGCTGACCGCAG	AF034956	CCDS11287.1, CCDS11288.1, CCDS45646.1	17q11	2014-09-17	2013-07-02	2011-07-01	ENSG00000185379	ENSG00000185379			9823	protein-coding gene	gene with protein product	"""recombination repair protein"", ""DNA repair protein RAD51 homolog 4"""	602954	"""RAD51 (S. cerevisiae)-like 3"", ""RAD51-like 3 (S. cerevisiae)"", ""RAD51 homolog D (S. cerevisiae)"""	RAD51L3		9570954	Standard	NM_001142571		Approved	R51H3, Trad, HsTRAD	uc010ctj.2	O75771	OTTHUMG00000132930	ENST00000345365.6:c.263+1629T>C	chr17.hg19:g.33443890A>G		103.0	0.0		114.0	5.0	NM_001142571	B4DJU7|E1P637|O43537|O60355|O75196|O75847|O75848|O76073|O76085|O94908|Q9UFU5	Missense_Mutation	SNP	ENST00000345365.6	hg19	CCDS11287.1	.	.	.	.	.	.	.	.	.	.	A	8.684	0.905906	0.17760	.	.	ENSG00000185379	ENST00000394589	.	.	.	2.38	-0.0313	0.13910	.	.	.	.	.	T	0.27384	0.0672	.	.	.	0.09310	N	1	B	0.19583	0.037	B	0.21151	0.033	T	0.29458	-1.0011	7	0.72032	D	0.01	.	2.7198	0.05197	0.5605:0.2754:0.1641:0.0	.	104	B4DJU7	.	A	104	.	ENSP00000378090:V104A	V	-	2	0	RAD51D	30468003	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.252000	0.18278	-0.044000	0.13491	0.397000	0.26171	GTC	.	.		0.502	RAD51D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256446.1	NM_002878	
C17orf78	284099	hgsc.bcm.edu	37	17	35736083	35736083	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:35736083A>G	ENST00000300618.4	+	3	204	c.154A>G	c.(154-156)Aca>Gca	p.T52A	ACACA_ENST00000353139.5_Intron|ACACA_ENST00000416895.1_Intron|C17orf78_ENST00000586700.1_Missense_Mutation_p.T52A	NM_173625.3	NP_775896.3	Q8N4C9	CQ078_HUMAN	chromosome 17 open reading frame 78	52						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(1)|lung(2)|stomach(1)	6		Breast(25;0.00295)|Ovarian(249;0.15)				AGAAACTCACACAGAAACCAA	0.418																																					p.T52A		Atlas-SNP	.											.	C17orf78	23	.	0			c.A154G						.						63.0	64.0	63.0					17																	35736083		1851	4087	5938	SO:0001583	missense	284099	exon3			ACTCACACAGAAA	BC034672	CCDS45655.1	17q12	2014-05-06			ENSG00000167230	ENSG00000278505			26831	protein-coding gene	gene with protein product						14702039	Standard	NM_173625		Approved	FLJ39647	uc002hns.3	Q8N4C9	OTTHUMG00000188467	ENST00000300618.4:c.154A>G	chr17.hg19:g.35736083A>G	ENSP00000300618:p.Thr52Ala	99.0	0.0		85.0	4.0	NM_173625	Q8N8D2	Missense_Mutation	SNP	ENST00000300618.4	hg19	CCDS45655.1	.	.	.	.	.	.	.	.	.	.	A	1.738	-0.492534	0.04322	.	.	ENSG00000167230	ENST00000300618;ENST00000321564	T	0.43294	0.95	4.27	2.16	0.27623	.	0.518519	0.16062	N	0.231453	T	0.14960	0.0361	N	0.05124	-0.11	0.23739	N	0.996977	B;B	0.09022	0.002;0.002	B;B	0.08055	0.003;0.003	T	0.31166	-0.9953	10	0.02654	T	1	-3.002	3.9095	0.09197	0.5801:0.0:0.4199:0.0	.	52;52	Q8N4C9-2;Q8N4C9	.;CQ078_HUMAN	A	52	ENSP00000300618:T52A	ENSP00000300618:T52A	T	+	1	0	C17orf78	32810196	0.569000	0.26643	0.998000	0.56505	0.977000	0.68977	0.838000	0.27572	0.298000	0.22638	0.482000	0.46254	ACA	.	.		0.418	C17orf78-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451570.2	NM_173625	
TOP2A	7153	hgsc.bcm.edu	37	17	38556308	38556308	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:38556308G>A	ENST00000423485.1	-	24	3170	c.3012C>T	c.(3010-3012)gaC>gaT	p.D1004D		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1004					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	AGCCTACGTGGTCAAAAAGCA	0.313																																					p.D1004D		Atlas-SNP	.											.	TOP2A	124	.	0			c.C3012T						.						38.0	37.0	37.0					17																	38556308		1804	4075	5879	SO:0001819	synonymous_variant	7153	exon24			TACGTGGTCAAAA		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.3012C>T	chr17.hg19:g.38556308G>A		57.0	0.0		57.0	4.0	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	hg19	CCDS45672.1																																																																																			.	.		0.313	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
KRTAP1-5	83895	hgsc.bcm.edu	37	17	39183240	39183240	+	Silent	SNP	G	G	A	rs367586882		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:39183240G>A	ENST00000361883.5	-	1	214	c.168C>T	c.(166-168)tgC>tgT	p.C56C		NM_031957.1	NP_114163.1	Q9BYS1	KRA15_HUMAN	keratin associated protein 1-5	56	15 X 5 AA repeats of C-C-[QEPVRC]- [TPIVLE]-[SRHVP].					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(2)|kidney(1)|lung(9)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	17		Breast(137;0.00043)	STAD - Stomach adenocarcinoma(17;0.000371)			AACTGGAGCTGCAGGTCCCAC	0.622													g|||	1	0.000199681	0.0	0.0014	5008	,	,		18155	0.0		0.0	False		,,,				2504	0.0				p.C56C		Atlas-SNP	.											.	KRTAP1-5	33	.	0			c.C168T						.	G		0,4046		0,0,2023	41.0	46.0	44.0		168	-3.4	0.0	17		44	6,8396		0,6,4195	no	coding-synonymous	KRTAP1-5	NM_031957.1		0,6,6218	AA,AG,GG		0.0714,0.0,0.0482		56/175	39183240	6,12442	2023	4201	6224	SO:0001819	synonymous_variant	83895	exon1			GGAGCTGCAGGTC	AJ406928	CCDS42321.1	17q21.2	2013-06-25			ENSG00000221852	ENSG00000221852		"""Keratin associated proteins"""	16777	protein-coding gene	gene with protein product		608822				11279113	Standard	NM_031957		Approved	KAP1.5	uc002hvu.3	Q9BYS1	OTTHUMG00000133587	ENST00000361883.5:c.168C>T	chr17.hg19:g.39183240G>A		154.0	0.0		132.0	9.0	NM_031957	A6NJW6|A6NLZ6|B6ZDR1|Q52LP6	Silent	SNP	ENST00000361883.5	hg19	CCDS42321.1																																																																																			.	.		0.622	KRTAP1-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257691.1		
KRT32	3882	hgsc.bcm.edu	37	17	39620667	39620667	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:39620667C>A	ENST00000225899.3	-	4	840	c.737G>T	c.(736-738)gGg>gTg	p.G246V		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	246	Linker 12.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				AAGGCGGTCCCCAAGCTGGCA	0.587																																					p.G246V		Atlas-SNP	.											.	KRT32	57	.	0			c.G737T						.						66.0	51.0	56.0					17																	39620667		2203	4300	6503	SO:0001583	missense	3882	exon4			CGGTCCCCAAGCT	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.737G>T	chr17.hg19:g.39620667C>A	ENSP00000225899:p.Gly246Val	98.0	0.0		96.0	4.0	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	hg19	CCDS11393.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.036808	0.75617	.	.	ENSG00000108759	ENST00000225899	T	0.80123	-1.34	5.13	5.13	0.70059	Filament (1);	0.000000	0.40064	N	0.001184	D	0.91499	0.7316	M	0.91406	3.205	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92786	0.6244	10	0.59425	D	0.04	.	15.6788	0.77352	0.0:1.0:0.0:0.0	.	246	Q14532	K1H2_HUMAN	V	246	ENSP00000225899:G246V	ENSP00000225899:G246V	G	-	2	0	KRT32	36874193	0.122000	0.22280	1.000000	0.80357	0.970000	0.65996	1.883000	0.39658	2.547000	0.85894	0.655000	0.94253	GGG	.	.		0.587	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
KRT35	3886	hgsc.bcm.edu	37	17	39637018	39637018	+	Missense_Mutation	SNP	T	T	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:39637018T>A	ENST00000393989.1	-	1	374	c.332A>T	c.(331-333)tAc>tTc	p.Y111F	KRT35_ENST00000246639.2_Missense_Mutation_p.Y81F	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	111	Coil 1A.|Rod.				anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				CTTCTCCAGGTAGCCGGCCAG	0.627																																					p.Y111F		Atlas-SNP	.											.	KRT35	58	.	0			c.A332T						.						68.0	74.0	72.0					17																	39637018		2203	4300	6503	SO:0001583	missense	3886	exon1			TCCAGGTAGCCGG	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6453	protein-coding gene	gene with protein product	"""hard keratin type I 5"""	602764	"""keratin, hair, acidic, 5"""	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.332A>T	chr17.hg19:g.39637018T>A	ENSP00000377558:p.Tyr111Phe	115.0	0.0		113.0	6.0	NM_002280	O76012|Q92651	Missense_Mutation	SNP	ENST00000393989.1	hg19	CCDS11394.2	.	.	.	.	.	.	.	.	.	.	T	19.49	3.837990	0.71373	.	.	ENSG00000197079	ENST00000246639;ENST00000393989	D;D	0.92446	-3.04;-3.04	5.24	4.16	0.48862	Filament (1);	0.000000	0.53938	D	0.000047	D	0.95468	0.8528	M	0.80028	2.48	0.41674	D	0.989258	D	0.89917	1.0	D	0.97110	1.0	D	0.95310	0.8411	10	0.87932	D	0	.	10.8643	0.46844	0.141:0.0:0.0:0.859	.	111	Q92764	KRT35_HUMAN	F	81;111	ENSP00000246639:Y81F;ENSP00000377558:Y111F	ENSP00000246639:Y81F	Y	-	2	0	KRT35	36890544	1.000000	0.71417	0.999000	0.59377	0.633000	0.38033	7.868000	0.87116	0.988000	0.38734	-0.496000	0.04628	TAC	.	.		0.627	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280	
NAGLU	4669	hgsc.bcm.edu	37	17	40695160	40695160	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:40695160T>C	ENST00000225927.2	+	6	1237	c.1136T>C	c.(1135-1137)cTg>cCg	p.L379P	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	379					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	GGCCGCCTCCTGGTTCTGGAC	0.647																																					p.L379P		Atlas-SNP	.											.	NAGLU	36	.	0			c.T1136C						.						52.0	57.0	55.0					17																	40695160		2203	4300	6503	SO:0001583	missense	4669	exon6			GCCTCCTGGTTCT		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"""Sanfilippo disease IIIB"""	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.1136T>C	chr17.hg19:g.40695160T>C	ENSP00000225927:p.Leu379Pro	88.0	0.0		92.0	4.0	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	hg19	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.254197	0.59212	.	.	ENSG00000108784	ENST00000225927;ENST00000377405	D	0.99399	-5.83	4.54	4.54	0.55810	Alpha-N-acetylglucosaminidase, tim-barrel domain (1);	0.069962	0.56097	D	0.000035	D	0.99521	0.9829	M	0.90309	3.105	0.80722	D	1	D	0.76494	0.999	D	0.70716	0.97	D	0.98237	1.0486	10	0.87932	D	0	-14.305	12.8389	0.57790	0.0:0.0:0.0:1.0	.	379	P54802	ANAG_HUMAN	P	379;55	ENSP00000225927:L379P	ENSP00000225927:L379P	L	+	2	0	NAGLU	37948686	1.000000	0.71417	0.998000	0.56505	0.547000	0.35210	7.732000	0.84908	1.906000	0.55180	0.260000	0.18958	CTG	.	.		0.647	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263	
ASB16	92591	hgsc.bcm.edu	37	17	42255627	42255627	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:42255627C>T	ENST00000293414.1	+	5	1315	c.1231C>T	c.(1231-1233)Ctg>Ttg	p.L411L	ASB16-AS1_ENST00000588785.1_RNA|ASB16-AS1_ENST00000585457.1_RNA|ASB16-AS1_ENST00000592897.1_RNA|ASB16-AS1_ENST00000591166.1_RNA	NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	411	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|liver(2)|lung(2)|prostate(1)	14		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		GCCAAGGCAGCTGCAGCACCT	0.652																																					p.L411L		Atlas-SNP	.											.	ASB16	34	.	0			c.C1231T						.						45.0	38.0	40.0					17																	42255627		2203	4300	6503	SO:0001819	synonymous_variant	92591	exon5			AGGCAGCTGCAGC	AK054727	CCDS11478.1	17q21.31	2013-01-10	2011-01-25		ENSG00000161664	ENSG00000161664		"""Ankyrin repeat domain containing"""	19768	protein-coding gene	gene with protein product		615056	"""ankyrin repeat and SOCS box-containing 16"""			12076535	Standard	NM_080863		Approved	FLJ30165	uc002ifl.1	Q96NS5	OTTHUMG00000181809	ENST00000293414.1:c.1231C>T	chr17.hg19:g.42255627C>T		77.0	0.0		54.0	4.0	NM_080863	B2RBC0|Q8WXK0	Silent	SNP	ENST00000293414.1	hg19	CCDS11478.1																																																																																			.	.		0.652	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1		
GOSR2	9570	hgsc.bcm.edu	37	17	45006918	45006918	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:45006918G>A	ENST00000393456.2	+	2	119	c.62G>A	c.(61-63)cGc>cAc	p.R21H	RP11-156P1.2_ENST00000571841.1_Missense_Mutation_p.R21H|GOSR2_ENST00000439730.2_Missense_Mutation_p.R21H|GOSR2_ENST00000225567.4_Missense_Mutation_p.R21H|GOSR2_ENST00000576910.2_Missense_Mutation_p.R21H|GOSR2_ENST00000575949.1_Missense_Mutation_p.R21H|GOSR2_ENST00000415811.2_Missense_Mutation_p.R21H	NM_004287.3	NP_004278.2	O14653	GOSR2_HUMAN	golgi SNAP receptor complex member 2	21					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)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|skin(1)	7			BRCA - Breast invasive adenocarcinoma(9;0.102)			TGCATGGGACGCCTGGAGACG	0.517																																					p.R21H		Atlas-SNP	.											.	GOSR2	38	.	0			c.G62A						.						100.0	82.0	88.0					17																	45006918		2203	4300	6503	SO:0001583	missense	9570	exon2			TGGGACGCCTGGA	AF007548	CCDS11507.1, CCDS42355.1, CCDS45719.1	17q21	2006-02-10				ENSG00000108433			4431	protein-coding gene	gene with protein product		604027				9349823, 10198168	Standard	XM_005257843		Approved	GS27, Bos1	uc002ikz.3	O14653		ENST00000393456.2:c.62G>A	chr17.hg19:g.45006918G>A	ENSP00000377101:p.Arg21His	70.0	0.0		49.0	23.0	NM_001012511	D3DXJ5|D3DXJ6|Q8N4B8|Q96DA5|Q9BZZ4	Missense_Mutation	SNP	ENST00000393456.2	hg19	CCDS42355.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.628916	0.46944	.	.	ENSG00000108433	ENST00000225567;ENST00000393456;ENST00000415811;ENST00000439730	T;T;T;T	0.47177	0.85;0.85;0.85;1.85	5.74	5.74	0.90152	.	0.265792	0.45126	D	0.000392	T	0.45034	0.1322	L	0.58810	1.83	0.54753	D	0.999986	B;B;B;B	0.28208	0.01;0.039;0.016;0.203	B;B;B;B	0.19148	0.003;0.003;0.006;0.024	T	0.40924	-0.9537	10	0.62326	D	0.03	-22.8506	14.6945	0.69110	0.0:0.0:0.8548:0.1452	.	21;21;21;21	E7EQ34;O14653;O14653-2;Q8N4B8	.;GOSR2_HUMAN;.;.	H	21	ENSP00000225567:R21H;ENSP00000377101:R21H;ENSP00000394559:R21H;ENSP00000390577:R21H	ENSP00000225567:R21H	R	+	2	0	GOSR2	42361917	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.817000	0.39002	2.873000	0.98535	0.561000	0.74099	CGC	.	.		0.517	GOSR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440438.1		
CDC27	996	hgsc.bcm.edu	37	17	45234463	45234463	+	Missense_Mutation	SNP	A	A	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:45234463A>C	ENST00000066544.3	-	7	751	c.658T>G	c.(658-660)Tcc>Gcc	p.S220A	CDC27_ENST00000527547.1_Missense_Mutation_p.S220A|CDC27_ENST00000531206.1_Missense_Mutation_p.S220A|CDC27_ENST00000446365.2_Missense_Mutation_p.S159A|CDC27_ENST00000528748.1_5'UTR	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	220					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TTTGAATTGGAAGATTCTAAA	0.323																																					p.S220A		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27	337	.	0			c.T658G						.						25.0	27.0	26.0					17																	45234463		2153	4281	6434	SO:0001583	missense	996	exon7			AATTGGAAGATTC	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.658T>G	chr17.hg19:g.45234463A>C	ENSP00000066544:p.Ser220Ala	53.0	0.0		49.0	4.0	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	hg19	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.291146	0.40494	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68331	-0.32;-0.27;-0.05;-0.32;0.81	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	N	0.19112	0.55	0.58432	D	0.999998	B;B;B;B	0.21225	0.013;0.023;0.053;0.031	B;B;B;B	0.15484	0.004;0.004;0.013;0.009	T	0.45086	-0.9285	10	0.07175	T	0.84	-13.9867	13.9377	0.64034	1.0:0.0:0.0:0.0	.	159;220;220;220	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	A	220;220;159;220;220	ENSP00000066544:S220A;ENSP00000434614:S220A;ENSP00000392802:S159A;ENSP00000437339:S220A;ENSP00000432105:S220A	ENSP00000066544:S220A	S	-	1	0	CDC27	42589462	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.754000	0.91642	2.180000	0.69256	0.455000	0.32223	TCC	.	.		0.323	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
ITGB3	3690	hgsc.bcm.edu	37	17	45363647	45363647	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:45363647C>T	ENST00000559488.1	+	5	652	c.636C>T	c.(634-636)ccC>ccT	p.P212P	ITGB3_ENST00000435993.2_Silent_p.P165P|ITGB3_ENST00000560629.1_Missense_Mutation_p.H201Y|ITGB3_ENST00000571680.1_Silent_p.P212P	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	212	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)	CCTGCTTGCCCATGTTTGGCT	0.522																																					p.P212P		Atlas-SNP	.											.	ITGB3	157	.	0			c.C636T						.						163.0	124.0	137.0					17																	45363647		2203	4300	6503	SO:0001819	synonymous_variant	3690	exon5			CTTGCCCATGTTT		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.636C>T	chr17.hg19:g.45363647C>T		101.0	0.0		86.0	4.0	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Silent	SNP	ENST00000559488.1	hg19	CCDS11511.1																																																																																			.	.		0.522	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
LUC7L3	51747	hgsc.bcm.edu	37	17	48823914	48823914	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:48823914G>A	ENST00000505658.1	+	9	1178	c.989G>A	c.(988-990)cGa>cAa	p.R330Q	LUC7L3_ENST00000240304.1_Missense_Mutation_p.R330Q|LUC7L3_ENST00000544170.1_Missense_Mutation_p.R254Q|LUC7L3_ENST00000393227.2_Missense_Mutation_p.R330Q			O95232	LC7L3_HUMAN	LUC7-like 3 (S. cerevisiae)	330	Arg/Ser-rich.				mRNA splice site selection (GO:0006376)|RNA splicing (GO:0008380)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U1 snRNP (GO:0005685)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	12						AGTAGAGATCGACGAAGAAGC	0.388																																					p.R330Q		Atlas-SNP	.											.	LUC7L3	32	.	0			c.G989A						.						78.0	83.0	81.0					17																	48823914		2203	4300	6503	SO:0001583	missense	51747	exon9			GAGATCGACGAAG		CCDS11573.1	17q21.33	2010-02-17			ENSG00000108848	ENSG00000108848			24309	protein-coding gene	gene with protein product	"""cisplatin resistance associated overexpressed protein"", ""CRE-associated protein"""	609434				10631324, 12565863	Standard	NM_016424		Approved	LUC7A, CROP, OA48-18, CREAP-1, FLJ11063, CRA, hLuc7A	uc002iss.3	O95232	OTTHUMG00000162257	ENST00000505658.1:c.989G>A	chr17.hg19:g.48823914G>A	ENSP00000425092:p.Arg330Gln	322.0	1.0		336.0	179.0	NM_006107	B3KN54|D3DTY1|Q6PHR9|Q9NUY0|Q9P2S7	Missense_Mutation	SNP	ENST00000505658.1	hg19	CCDS11573.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.902268	0.52227	.	.	ENSG00000108848	ENST00000505658;ENST00000393227;ENST00000240304;ENST00000544170	T;T;T;T	0.35048	1.33;1.33;1.33;1.43	5.79	4.83	0.62350	.	0.129696	0.51477	D	0.000097	T	0.37732	0.1014	M	0.63843	1.955	0.58432	D	0.999999	B;B;B	0.21147	0.016;0.052;0.029	B;B;B	0.08055	0.002;0.003;0.002	T	0.19224	-1.0312	10	0.48119	T	0.1	-0.5247	15.1117	0.72362	0.0676:0.0:0.9324:0.0	.	254;330;330	B4DJ96;O95232;A8K3C5	.;LC7L3_HUMAN;.	Q	330;330;330;254	ENSP00000425092:R330Q;ENSP00000376919:R330Q;ENSP00000240304:R330Q;ENSP00000444253:R254Q	ENSP00000240304:R330Q	R	+	2	0	LUC7L3	46178913	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	8.950000	0.93019	1.467000	0.48044	-0.119000	0.15052	CGA	.	.		0.388	LUC7L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368205.2	NM_016424	
NME1	4830	hgsc.bcm.edu	37	17	49237415	49237415	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:49237415C>T	ENST00000393196.3	+	3	332	c.201C>T	c.(199-201)taC>taT	p.Y67Y	NME1_ENST00000336097.3_Silent_p.Y92Y|NME2_ENST00000555572.1_Silent_p.Y92Y|NME1_ENST00000511355.1_Silent_p.Y67Y|NME1-NME2_ENST00000393198.3_Silent_p.Y67Y|NME1_ENST00000480143.1_Silent_p.Y92Y|NME2_ENST00000393193.2_Silent_p.Y67Y|NME2_ENST00000376392.6_Silent_p.Y67Y|NME1-NME2_ENST00000608447.1_Silent_p.Y92Y|NME1_ENST00000013034.3_Silent_p.Y92Y	NM_000269.2	NP_000260.1	P15531	NDKA_HUMAN	NME/NM23 nucleoside diphosphate kinase 1	67					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)	TGGTGAAATACATGCACTCAG	0.498																																					p.Y92Y	GBM(176;1298 2890 6639 30062)	Atlas-SNP	.											.	NME1	12	.	0			c.C276T						.						163.0	133.0	143.0					17																	49237415		2203	4300	6503	SO:0001819	synonymous_variant	4830	exon4			GAAATACATGCAC	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.201C>T	chr17.hg19:g.49237415C>T		77.0	0.0		116.0	5.0	NM_198175	Q6FGK3|Q86XQ2|Q9UDJ6	Silent	SNP	ENST00000393196.3	hg19	CCDS11579.1																																																																																			.	.		0.498	NME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268662.2	NM_000269	
EPX	8288	hgsc.bcm.edu	37	17	56280606	56280606	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:56280606C>T	ENST00000225371.5	+	11	1983	c.1873C>T	c.(1873-1875)Ccg>Tcg	p.P625S		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	625					defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	GCCTCTTTTGCCGGGGGCTCG	0.517																																					p.P625S		Atlas-SNP	.											.	EPX	95	.	0			c.C1873T						.						67.0	71.0	70.0					17																	56280606		2203	4300	6503	SO:0001583	missense	8288	exon11			CTTTTGCCGGGGG	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.1873C>T	chr17.hg19:g.56280606C>T	ENSP00000225371:p.Pro625Ser	120.0	0.0		84.0	5.0	NM_000502	Q4TVP3	Missense_Mutation	SNP	ENST00000225371.5	hg19	CCDS11602.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.193243	0.58017	.	.	ENSG00000121053	ENST00000225371	T	0.69806	-0.43	5.96	5.96	0.96718	.	0.271357	0.42964	D	0.000632	T	0.67183	0.2866	M	0.64997	1.995	0.43698	D	0.996156	B	0.12013	0.005	B	0.17433	0.018	T	0.62407	-0.6861	10	0.52906	T	0.07	-3.8105	17.9158	0.88950	0.0:1.0:0.0:0.0	.	625	P11678	PERE_HUMAN	S	625	ENSP00000225371:P625S	ENSP00000225371:P625S	P	+	1	0	EPX	53635605	0.005000	0.15991	0.983000	0.44433	0.862000	0.49288	1.256000	0.32921	2.832000	0.97577	0.655000	0.94253	CCG	.	.		0.517	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502	
LPO	4025	hgsc.bcm.edu	37	17	56326538	56326538	+	Splice_Site	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:56326538G>T	ENST00000262290.4	+	5	759	c.443G>T	c.(442-444)aGg>aTg	p.R148M	LPO_ENST00000421678.2_Splice_Site_p.R65M|LPO_ENST00000582328.1_Splice_Site_p.R65M|LPO_ENST00000543544.1_Splice_Site_p.R89M	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	148					defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)			breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						TGCAATAACAGGTGGCGGGGC	0.642																																					p.R148M		Atlas-SNP	.											.	LPO	73	.	0			c.G443T						.						49.0	43.0	45.0					17																	56326538		2203	4300	6503	SO:0001630	splice_region_variant	4025	exon5			ATAACAGGTGGCG	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.443+1G>T	chr17.hg19:g.56326538G>T		95.0	0.0		61.0	4.0	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Missense_Mutation	SNP	ENST00000262290.4	hg19	CCDS32689.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.029311	0.54790	.	.	ENSG00000167419	ENST00000262290;ENST00000421678;ENST00000543544	T;T;T	0.69435	-0.4;-0.4;-0.4	5.34	4.37	0.52481	.	0.051265	0.85682	D	0.000000	T	0.79499	0.4456	M	0.77712	2.385	0.51482	D	0.999928	D;D;D;D	0.67145	0.996;0.984;0.992;0.996	D;D;P;D	0.66979	0.934;0.929;0.888;0.948	T	0.79288	-0.1865	10	0.37606	T	0.19	.	13.0866	0.59144	0.0775:0.0:0.9225:0.0	.	65;65;89;148	B4DUH9;E7EMJ3;B4E1M1;P22079	.;.;.;PERL_HUMAN	M	148;65;89	ENSP00000262290:R148M;ENSP00000400245:R65M;ENSP00000445344:R89M	ENSP00000262290:R148M	R	+	2	0	LPO	53681537	1.000000	0.71417	1.000000	0.80357	0.091000	0.18340	4.138000	0.58017	1.245000	0.43885	0.650000	0.86243	AGG	.	.		0.642	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1		Missense_Mutation
BCAS3	54828	hgsc.bcm.edu	37	17	59152380	59152380	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:59152380A>G	ENST00000390652.5	+	21	2205	c.2174A>G	c.(2173-2175)cAg>cGg	p.Q725R	BCAS3_ENST00000588874.1_Splice_Site_p.Q481R|BCAS3_ENST00000588462.1_Splice_Site_p.Q725R|BCAS3_ENST00000585744.1_Splice_Site_p.Q496R|BCAS3_ENST00000589222.1_Splice_Site_p.Q710R|BCAS3_ENST00000408905.3_Splice_Site_p.Q710R|BCAS3_ENST00000407086.3_Splice_Site_p.Q710R	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3											NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			TGGCTTTCCCAGGTAAAACTC	0.398																																					p.Q725R		Atlas-SNP	.											.	BCAS3	90	.	0			c.A2174G						.						82.0	76.0	78.0					17																	59152380		1813	4081	5894	SO:0001630	splice_region_variant	54828	exon21			TTTCCCAGGTAAA	AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"""WD repeat domain containing"""	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.2175+1A>G	chr17.hg19:g.59152380A>G		84.0	0.0		93.0	4.0	NM_001099432		Missense_Mutation	SNP	ENST00000390652.5	hg19	CCDS45749.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.775826	0.90195	.	.	ENSG00000141376	ENST00000390652;ENST00000407086;ENST00000408905	T;T;T	0.39056	1.1;1.14;1.12	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.60274	0.2256	M	0.71206	2.165	0.54753	D	0.999987	D;D;B;D;B	0.60575	0.988;0.988;0.135;0.975;0.135	P;P;B;P;B	0.57911	0.794;0.829;0.059;0.819;0.037	T	0.64368	-0.6424	10	0.72032	D	0.01	.	16.1982	0.82046	1.0:0.0:0.0:0.0	.	710;725;710;725;710	Q9H6U6-3;Q9H6U6-8;Q9H6U6-7;Q9H6U6;Q9H6U6-2	.;.;.;BCAS3_HUMAN;.	R	725;710;710	ENSP00000375067:Q725R;ENSP00000385323:Q710R;ENSP00000386173:Q710R	ENSP00000375067:Q725R	Q	+	2	0	BCAS3	56507162	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	8.962000	0.93254	2.226000	0.72624	0.533000	0.62120	CAG	.	.		0.398	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679	Missense_Mutation
SMARCD2	6603	hgsc.bcm.edu	37	17	61914319	61914319	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:61914319C>T	ENST00000448276.2	-	4	795	c.530G>A	c.(529-531)cGg>cAg	p.R177Q	SMARCD2_ENST00000225742.9_Missense_Mutation_p.R102Q|SMARCD2_ENST00000323347.10_Missense_Mutation_p.R129Q	NM_001098426.1	NP_001091896.1	Q92925	SMRD2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	177					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)	8						GATCTCCATCCGCTTGCGAGC	0.547																																					p.R177Q		Atlas-SNP	.											.	SMARCD2	29	.	0			c.G530A						.						110.0	113.0	112.0					17																	61914319		1998	4165	6163	SO:0001583	missense	6603	exon4			TCCATCCGCTTGC	U66618	CCDS45756.1	17q23.3	2014-07-16			ENSG00000108604	ENSG00000108604			11107	protein-coding gene	gene with protein product	"""mammalian chromatin remodeling complex BRG1-associated factor 60B"", ""Swp73-like protein"", ""chromatin remodeling complex BAF60B subunit"", ""SWI/SNF complex 60 kDa subunit B"""	601736				8804307, 9693044	Standard	NM_001098426		Approved	BAF60B, Rsc6p, CRACD2, PRO2451	uc010deb.1	Q92925	OTTHUMG00000179045	ENST00000448276.2:c.530G>A	chr17.hg19:g.61914319C>T	ENSP00000392617:p.Arg177Gln	103.0	0.0		92.0	4.0	NM_001098426	A5PLL5|A6NNQ7|B4DV56|B4E1R6|Q7L2I6|Q9UHZ1	Missense_Mutation	SNP	ENST00000448276.2	hg19	CCDS45756.1	.	.	.	.	.	.	.	.	.	.	.	22.2	4.261664	0.80358	.	.	ENSG00000108604	ENST00000448276;ENST00000225742;ENST00000450364;ENST00000323347	T;T	0.51817	0.69;0.69	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.71685	0.3369	M	0.83223	2.63	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.79108	0.979;0.992;0.992	T	0.75031	-0.3461	10	0.87932	D	0	-12.8855	16.9239	0.86170	0.0:1.0:0.0:0.0	.	129;140;177	Q92925-3;B9EGA3;Q92925	.;.;SMRD2_HUMAN	Q	177;119;140;129	ENSP00000392617:R177Q;ENSP00000318451:R129Q	ENSP00000225742:R119Q	R	-	2	0	SMARCD2	59268051	1.000000	0.71417	1.000000	0.80357	0.029000	0.11900	7.651000	0.83577	2.865000	0.98341	0.655000	0.94253	CGG	.	.		0.547	SMARCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444544.1	NM_001098426	
CACNG5	27091	hgsc.bcm.edu	37	17	64875093	64875093	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:64875093A>G	ENST00000533854.1	+	3	437	c.200A>G	c.(199-201)gAg>gGg	p.E67G	CACNG5_ENST00000169565.3_Missense_Mutation_p.E67G|CACNG5_ENST00000307139.3_Missense_Mutation_p.E67G			Q9UF02	CCG5_HUMAN	calcium channel, voltage-dependent, gamma subunit 5	67					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ion transmembrane transporter activity (GO:0015075)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	24			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)			TCCACAGGTGAGGAGCGGGGG	0.458																																					p.E67G		Atlas-SNP	.											.	CACNG5	77	.	0			c.A200G						.						105.0	90.0	95.0					17																	64875093		2203	4300	6503	SO:0001583	missense	27091	exon2			CAGGTGAGGAGCG	AF148220	CCDS11665.1	17q24	2004-02-16				ENSG00000075429		"""Calcium channel subunits"""	1409	protein-coding gene	gene with protein product		606405				10613843	Standard	NM_145811		Approved		uc010wqj.2	Q9UF02		ENST00000533854.1:c.200A>G	chr17.hg19:g.64875093A>G	ENSP00000436836:p.Glu67Gly	83.0	0.0		84.0	4.0	NM_145811	A8K2A6|Q547R3|Q8WXS7|Q9UHM3	Missense_Mutation	SNP	ENST00000533854.1	hg19	CCDS11665.1	.	.	.	.	.	.	.	.	.	.	A	17.63	3.438171	0.62955	.	.	ENSG00000075429	ENST00000533854;ENST00000307139;ENST00000169565	D;D;D	0.88896	-2.44;-2.44;-2.44	4.53	4.53	0.55603	.	0.000000	0.85682	D	0.000000	D	0.84915	0.5578	L	0.46157	1.445	0.80722	D	1	B	0.30542	0.284	B	0.34093	0.175	T	0.81504	-0.0903	10	0.24483	T	0.36	-24.6407	12.3224	0.54991	1.0:0.0:0.0:0.0	.	67	Q9UF02	CCG5_HUMAN	G	67	ENSP00000436836:E67G;ENSP00000303092:E67G;ENSP00000169565:E67G	ENSP00000169565:E67G	E	+	2	0	CACNG5	62305555	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.477000	0.66799	1.996000	0.58369	0.533000	0.62120	GAG	.	.		0.458	CACNG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389882.1	NM_014404, NM_145811	
BPTF	2186	hgsc.bcm.edu	37	17	65960451	65960451	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:65960451C>T	ENST00000321892.4	+	27	8824	c.8763C>T	c.(8761-8763)gcC>gcT	p.A2921A	BPTF_ENST00000424123.3_Silent_p.A2639A|BPTF_ENST00000306378.6_Silent_p.A2795A|BPTF_ENST00000335221.5_Silent_p.A2778A			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2921					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)			CAGAGGATGCCATGACAGTGC	0.512																																					p.A2795A		Atlas-SNP	.											.	BPTF	415	.	0			c.C8385T						.						106.0	95.0	99.0					17																	65960451		2203	4300	6503	SO:0001819	synonymous_variant	2186	exon25			GGATGCCATGACA	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.8763C>T	chr17.hg19:g.65960451C>T		179.0	0.0		175.0	7.0	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	hg19																																																																																				.	.		0.512	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
CDC42EP4	23580	hgsc.bcm.edu	37	17	71281766	71281766	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:71281766T>C	ENST00000335793.3	-	2	1268	c.874A>G	c.(874-876)Agc>Ggc	p.S292G	CDC42EP4_ENST00000439510.2_Missense_Mutation_p.S222G|CDC42EP4_ENST00000581014.1_Intron			Q9H3Q1	BORG4_HUMAN	CDC42 effector protein (Rho GTPase binding) 4	292					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	GTP-Rho binding (GO:0017049)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(7)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(166;0.0352)|Lung(188;0.0711)			GAGCCGGGGCTGGGGGCCGCT	0.706																																					p.S292G		Atlas-SNP	.											.	CDC42EP4	19	.	0			c.A874G						.						14.0	18.0	17.0					17																	71281766		2202	4291	6493	SO:0001583	missense	23580	exon2			CGGGGCTGGGGGC	AB042237	CCDS11695.1	17q24-q25	2008-07-18				ENSG00000179604			17147	protein-coding gene	gene with protein product	"""Cdc42 effector protein 4"", ""binder of Rho GTPases 4"""	605468				11035016, 10490598	Standard	NM_012121		Approved	CEP4, KAIA1777, BORG4, MGC3740, MGC17125	uc002jjo.3	Q9H3Q1		ENST00000335793.3:c.874A>G	chr17.hg19:g.71281766T>C	ENSP00000338258:p.Ser292Gly	98.0	0.0		78.0	4.0	NM_012121	B3KUS7|O95828|Q96FT3	Missense_Mutation	SNP	ENST00000335793.3	hg19	CCDS11695.1	.	.	.	.	.	.	.	.	.	.	T	17.17	3.320388	0.60634	.	.	ENSG00000179604	ENST00000335793;ENST00000439510	T;T	0.35236	1.33;1.32	4.91	4.91	0.64330	.	0.225676	0.38492	N	0.001667	T	0.33556	0.0867	M	0.63428	1.95	0.80722	D	1	P;B	0.36599	0.56;0.355	B;B	0.28638	0.092;0.057	T	0.20638	-1.0269	10	0.41790	T	0.15	-20.0915	14.2123	0.65773	0.0:0.0:0.0:1.0	.	222;292	B3KUS7;Q9H3Q1	.;BORG4_HUMAN	G	292;222	ENSP00000338258:S292G;ENSP00000404270:S222G	ENSP00000338258:S292G	S	-	1	0	CDC42EP4	68793361	1.000000	0.71417	0.999000	0.59377	0.600000	0.36913	3.618000	0.54188	1.854000	0.53819	0.397000	0.26171	AGC	.	.		0.706	CDC42EP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441898.1	NM_012121	
SDK2	54549	hgsc.bcm.edu	37	17	71335078	71335078	+	Splice_Site	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:71335078C>T	ENST00000392650.3	-	45	6167	c.6167G>A	c.(6166-6168)gGa>gAa	p.G2056E	SDK2_ENST00000388726.3_Splice_Site_p.G2037E|SDK2_ENST00000410094.1_5'UTR	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	2056					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						GCTGTCACTTCCCTGGGAGGA	0.572																																					p.G2056E		Atlas-SNP	.											.	SDK2	219	.	0			c.G6167A						.						127.0	119.0	122.0					17																	71335078		2203	4300	6503	SO:0001630	splice_region_variant	54549	exon45			TCACTTCCCTGGG	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.6166-1G>A	chr17.hg19:g.71335078C>T		565.0	0.0		537.0	279.0	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	hg19	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227403	0.79576	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893;ENST00000410094	T;T;T	0.60040	0.22;0.24;1.44	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.64571	0.2610	L	0.40543	1.245	0.58432	D	0.999999	D;P	0.52996	0.957;0.948	P;P	0.56612	0.71;0.802	T	0.68387	-0.5422	10	0.62326	D	0.03	.	17.3228	0.87240	0.0:1.0:0.0:0.0	.	2056;2037	Q58EX2;Q58EX2-3	SDK2_HUMAN;.	E	1680;2056;2037;1213;2056;397	ENSP00000376421:G2056E;ENSP00000373378:G2037E;ENSP00000407098:G1213E	ENSP00000324967:G2056E	G	-	2	0	SDK2	68846673	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	3.777000	0.55364	2.172000	0.68678	0.655000	0.94253	GGA	.	.		0.572	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	Missense_Mutation
TMEM104	54868	hgsc.bcm.edu	37	17	72786394	72786394	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:72786394A>G	ENST00000335464.5	+	5	467	c.305A>G	c.(304-306)gAc>gGc	p.D102G	TMEM104_ENST00000582773.1_Missense_Mutation_p.D102G|TMEM104_ENST00000417024.2_Missense_Mutation_p.D115G|TMEM104_ENST00000582330.1_Missense_Mutation_p.D102G	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	102						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					CTCATCCGGGACAACTACGAG	0.612																																					p.D102G		Atlas-SNP	.											.	TMEM104	49	.	0			c.A305G						.						116.0	103.0	108.0					17																	72786394		2203	4300	6503	SO:0001583	missense	54868	exon5			TCCGGGACAACTA	AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.305A>G	chr17.hg19:g.72786394A>G	ENSP00000334849:p.Asp102Gly	61.0	0.0		74.0	4.0	NM_017728	Q8TEU1|Q9NT56|Q9NXH1	Missense_Mutation	SNP	ENST00000335464.5	hg19	CCDS32723.1	.	.	.	.	.	.	.	.	.	.	A	12.20	1.867562	0.32977	.	.	ENSG00000109066	ENST00000335464;ENST00000417024	T;T	0.47177	1.42;0.85	4.97	3.88	0.44766	.	0.395546	0.30329	N	0.009880	T	0.24470	0.0593	N	0.08118	0	0.46701	D	0.999164	B;B;B	0.10296	0.003;0.001;0.0	B;B;B	0.12156	0.007;0.002;0.0	T	0.07558	-1.0766	10	0.21540	T	0.41	-22.2523	9.0102	0.36137	0.9159:0.0:0.0841:0.0	.	115;102;102	B4DKL7;Q8NE00-2;Q8NE00	.;.;TM104_HUMAN	G	102;115	ENSP00000334849:D102G;ENSP00000397676:D115G	ENSP00000334849:D102G	D	+	2	0	TMEM104	70297989	1.000000	0.71417	0.913000	0.36048	0.987000	0.75469	4.636000	0.61339	1.997000	0.58415	0.459000	0.35465	GAC	.	.		0.612	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728	
ITGB4	3691	hgsc.bcm.edu	37	17	73738768	73738768	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:73738768A>G	ENST00000200181.3	+	25	3075	c.2888A>G	c.(2887-2889)gAg>gGg	p.E963G	ITGB4_ENST00000339591.3_Missense_Mutation_p.E963G|ITGB4_ENST00000450894.3_Missense_Mutation_p.E963G|ITGB4_ENST00000579662.1_Missense_Mutation_p.E963G|ITGB4_ENST00000449880.2_Missense_Mutation_p.E963G	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	963					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTGCTGGTGGAGGCCATCGAC	0.652																																					p.E963G		Atlas-SNP	.											.	ITGB4	165	.	0			c.A2888G						.						75.0	57.0	63.0					17																	73738768		2203	4300	6503	SO:0001583	missense	3691	exon25			TGGTGGAGGCCAT		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.2888A>G	chr17.hg19:g.73738768A>G	ENSP00000200181:p.Glu963Gly	117.0	0.0		90.0	5.0	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	hg19	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.231521	0.58777	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	T;T;T	0.76448	-1.02;-0.97;-0.97	5.52	5.52	0.82312	.	0.063637	0.64402	D	0.000008	T	0.81978	0.4937	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.74023	0.982;0.959;0.959	D	0.84469	0.0598	10	0.87932	D	0	.	15.6342	0.76937	1.0:0.0:0.0:0.0	.	963;963;963	P16144-3;A0AVL6;P16144	.;.;ITB4_HUMAN	G	963	ENSP00000200181:E963G;ENSP00000344079:E963G;ENSP00000400217:E963G	ENSP00000200181:E963G	E	+	2	0	ITGB4	71250363	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.440000	0.80464	2.117000	0.64856	0.533000	0.62120	GAG	.	.		0.652	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
UNC13D	201294	hgsc.bcm.edu	37	17	73840396	73840396	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:73840396G>T	ENST00000207549.4	-	1	402	c.23C>A	c.(22-24)cCg>cAg	p.P8Q	UNC13D_ENST00000587504.1_5'Flank|UNC13D_ENST00000412096.2_Missense_Mutation_p.P8Q	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	8					defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCGCTGCTGCGGATGGGAGAG	0.622									Familial Hemophagocytic Lymphohistiocytosis																												p.P8Q		Atlas-SNP	.											.	UNC13D	68	.	0			c.C23A						.						46.0	46.0	46.0					17																	73840396		2200	4300	6500	SO:0001583	missense	201294	exon1	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	TGCTGCGGATGGG	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.23C>A	chr17.hg19:g.73840396G>T	ENSP00000207549:p.Pro8Gln	131.0	0.0		84.0	4.0	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	hg19	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	G	10.50	1.368304	0.24771	.	.	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.70516	-0.43;-0.49	4.04	3.06	0.35304	.	0.728418	0.11948	N	0.513960	T	0.73426	0.3585	L	0.57536	1.79	0.09310	N	1	P	0.41313	0.745	P	0.47786	0.557	T	0.62651	-0.6809	10	0.72032	D	0.01	4.3639	10.5479	0.45070	0.1046:0.0:0.8954:0.0	.	8	Q70J99	UN13D_HUMAN	Q	8	ENSP00000207549:P8Q;ENSP00000388093:P8Q	ENSP00000207549:P8Q	P	-	2	0	UNC13D	71351991	0.001000	0.12720	0.054000	0.19295	0.018000	0.09664	1.055000	0.30467	0.384000	0.24942	-1.134000	0.01955	CCG	.	.		0.622	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
FBF1	85302	hgsc.bcm.edu	37	17	73914288	73914288	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:73914288T>C	ENST00000586717.1	-	20	2432	c.2159A>G	c.(2158-2160)aAg>aGg	p.K720R	FBF1_ENST00000389570.4_Missense_Mutation_p.K720R|FBF1_ENST00000319129.5_Missense_Mutation_p.K719R			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	720					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						CTCTCGGTCCTTCAGCAGCTT	0.677																																					p.K719R		Atlas-SNP	.											.	FBF1	48	.	0			c.A2156G						.						29.0	38.0	35.0					17																	73914288		2119	4228	6347	SO:0001583	missense	85302	exon20			CGGTCCTTCAGCA	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.2159A>G	chr17.hg19:g.73914288T>C	ENSP00000465132:p.Lys720Arg	101.0	0.0		98.0	4.0	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	hg19		.	.	.	.	.	.	.	.	.	.	T	27.9	4.876701	0.91664	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.23754	1.89;1.89	5.19	5.19	0.71726	.	.	.	.	.	T	0.46502	0.1396	L	0.60455	1.87	0.51767	D	0.999933	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.997	T	0.32214	-0.9915	9	0.35671	T	0.21	-38.3299	14.7005	0.69152	0.0:0.0:0.0:1.0	.	734;720;719	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	R	720;720;719;733	ENSP00000374221:K720R;ENSP00000324292:K719R	ENSP00000324292:K719R	K	-	2	0	FBF1	71425883	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.735000	0.68587	1.954000	0.56735	0.460000	0.39030	AAG	.	.		0.677	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
ACOX1	51	hgsc.bcm.edu	37	17	73944528	73944528	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:73944528A>G	ENST00000301608.4	-	13	1799	c.1739T>C	c.(1738-1740)aTg>aCg	p.M580T	ACOX1_ENST00000293217.5_Missense_Mutation_p.M580T|ACOX1_ENST00000537812.1_Missense_Mutation_p.M542T	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	580					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|peroxisome fission (GO:0016559)|positive regulation of cholesterol homeostasis (GO:2000189)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|FAD binding (GO:0071949)|fatty acid binding (GO:0005504)|flavin adenine dinucleotide binding (GO:0050660)|palmitoyl-CoA oxidase activity (GO:0016401)|PDZ domain binding (GO:0030165)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)			large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(1)	14					Flavin adenine dinucleotide(DB03147)	AGGCTCTGTCATGATGCTCCC	0.353																																					p.M580T		Atlas-SNP	.											.	ACOX1	85	.	0			c.T1739C						.						108.0	95.0	100.0					17																	73944528		2203	4300	6503	SO:0001583	missense	51	exon13			TCTGTCATGATGC	U03254	CCDS11734.1, CCDS11735.1	17q25.1	2012-10-04	2010-04-30		ENSG00000161533	ENSG00000161533	1.3.3.6		119	protein-coding gene	gene with protein product		609751	"""acyl-Coenzyme A oxidase 1, palmitoyl"""			8159712	Standard	NM_007292		Approved	PALMCOX	uc002jqe.3	Q15067	OTTHUMG00000180027	ENST00000301608.4:c.1739T>C	chr17.hg19:g.73944528A>G	ENSP00000301608:p.Met580Thr	53.0	0.0		69.0	4.0	NM_007292	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	hg19	CCDS11735.1	.	.	.	.	.	.	.	.	.	.	A	15.93	2.977101	0.53720	.	.	ENSG00000161533	ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781	T;T;T	0.42513	0.97;0.97;0.97	5.25	5.25	0.73442	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.324513	0.38005	N	0.001844	T	0.45836	0.1362	L	0.58583	1.82	0.40381	D	0.979449	B;B;B;B	0.26041	0.127;0.127;0.14;0.014	B;B;B;B	0.32583	0.096;0.096;0.148;0.023	T	0.49513	-0.8932	10	0.66056	D	0.02	-10.2759	15.8659	0.79063	1.0:0.0:0.0:0.0	.	512;542;580;580	F5H0M0;F5GYQ8;Q15067;Q15067-2	.;.;ACOX1_HUMAN;.	T	580;580;542;580;512	ENSP00000301608:M580T;ENSP00000293217:M580T;ENSP00000441257:M542T	ENSP00000293217:M580T	M	-	2	0	ACOX1	71456123	1.000000	0.71417	0.985000	0.45067	0.927000	0.56198	8.460000	0.90369	2.289000	0.77006	0.533000	0.62120	ATG	.	.		0.353	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1		
JMJD6	23210	hgsc.bcm.edu	37	17	74716510	74716510	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:74716510T>C	ENST00000397625.4	-	5	1126	c.1012A>G	c.(1012-1014)Ata>Gta	p.I338V	JMJD6_ENST00000445478.2_Missense_Mutation_p.I338V|JMJD6_ENST00000585429.1_Intron	NM_015167.2	NP_055982.2	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6	338					cell surface receptor signaling pathway (GO:0007166)|erythrocyte development (GO:0048821)|heart development (GO:0007507)|histone H3-R2 demethylation (GO:0070078)|histone H4-R3 demethylation (GO:0070079)|kidney development (GO:0001822)|lung development (GO:0030324)|macrophage activation (GO:0042116)|mRNA processing (GO:0006397)|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine (GO:0018395)|recognition of apoptotic cell (GO:0043654)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|RNA splicing (GO:0008380)|sprouting angiogenesis (GO:0002040)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone demethylase activity (H3-R2 specific) (GO:0033746)|histone demethylase activity (H4-R3 specific) (GO:0033749)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)|peptidyl-lysine 5-dioxygenase activity (GO:0070815)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			endometrium(2)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|skin(2)	16						TCGGAAGCTATCCCTGTGGAC	0.572																																					p.I338V		Atlas-SNP	.											.	JMJD6	57	.	0			c.A1012G						.						80.0	93.0	88.0					17																	74716510		2110	4240	6350	SO:0001583	missense	23210	exon5			AAGCTATCCCTGT	AB011157	CCDS42383.1, CCDS42384.1	17q25	2007-11-20	2007-02-16	2007-02-16	ENSG00000070495	ENSG00000070495			19355	protein-coding gene	gene with protein product		604914	"""phosphatidylserine receptor"""	PTDSR		11877474	Standard	NM_015167		Approved	PTDSR1, KIAA0585	uc002jsn.1	Q6NYC1	OTTHUMG00000169267	ENST00000397625.4:c.1012A>G	chr17.hg19:g.74716510T>C	ENSP00000380750:p.Ile338Val	86.0	0.0		77.0	4.0	NM_001081461	B3KMN8|B4DGX1|Q86VY0|Q8IUM5|Q9Y4E2	Missense_Mutation	SNP	ENST00000397625.4	hg19	CCDS42384.1	.	.	.	.	.	.	.	.	.	.	T	12.60	1.985403	0.35036	.	.	ENSG00000070495	ENST00000445478;ENST00000344991;ENST00000397625	.	.	.	5.61	5.61	0.85477	.	0.045580	0.85682	D	0.000000	T	0.43787	0.1263	N	0.25890	0.77	0.80722	D	1	B;B	0.17268	0.008;0.021	B;B	0.12156	0.006;0.007	T	0.35126	-0.9801	9	0.10902	T	0.67	-17.924	15.8611	0.79021	0.0:0.0:0.0:1.0	.	338;338	Q6NYC1;Q6NYC1-3	JMJD6_HUMAN;.	V	338	.	ENSP00000345857:I338V	I	-	1	0	JMJD6	72228105	1.000000	0.71417	0.855000	0.33649	0.907000	0.53573	5.930000	0.70104	2.145000	0.66743	0.529000	0.55759	ATA	.	.		0.572	JMJD6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403211.1	NM_015167	
RNF213	57674	hgsc.bcm.edu	37	17	78335538	78335538	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:78335538G>A	ENST00000582970.1	+	39	11348	c.11205G>A	c.(11203-11205)ctG>ctA	p.L3735L	CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Silent_p.L1808L|RNF213_ENST00000508628.2_Silent_p.L3784L|CTD-2047H16.4_ENST00000575034.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3735					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CTGCAGGACTGCCCAAGAAGT	0.592																																					p.L3735L		Atlas-SNP	.											.	RNF213	766	.	0			c.G11205A						.						59.0	57.0	58.0					17																	78335538		2203	4300	6503	SO:0001819	synonymous_variant	57674	exon39			AGGACTGCCCAAG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.11205G>A	chr17.hg19:g.78335538G>A		54.0	0.0		70.0	4.0	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	hg19	CCDS58606.1																																																																																			.	.		0.592	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
PDE6G	5148	hgsc.bcm.edu	37	17	79618688	79618688	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:79618688T>C	ENST00000331056.5	-	3	317	c.174A>G	c.(172-174)gaA>gaG	p.E58E	PDE6G_ENST00000573076.1_Silent_p.E108E|PDE6G_ENST00000574777.1_5'UTR|TSPAN10_ENST00000328585.4_RNA|PDE6G_ENST00000571224.1_Silent_p.E58E|PDE6G_ENST00000571004.1_Silent_p.E58E	NM_002602.3	NP_002593.1	P18545	CNRG_HUMAN	phosphodiesterase 6G, cGMP-specific, rod, gamma	58					activation of MAPK activity (GO:0000187)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|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)|cGMP binding (GO:0030553)|enzyme inhibitor activity (GO:0004857)			lung(2)|urinary_tract(1)	3	all_neural(118;0.0878)|all_lung(278;0.175)|Lung NSC(278;0.192)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)		Sildenafil(DB00203)|Vardenafil(DB00862)	TTCCCAGGCCTTCCATTCCAG	0.662																																					p.E58E	GBM(189;38 2147 16440 40945 46567)	Atlas-SNP	.											.	PDE6G	9	.	0			c.A174G						.						77.0	57.0	64.0					17																	79618688		2203	4300	6503	SO:0001819	synonymous_variant	5148	exon3			CAGGCCTTCCATT		CCDS11783.1	17q21.1	2014-01-28				ENSG00000185527	3.1.4.17	"""Phosphodiesterases"""	8789	protein-coding gene	gene with protein product		180073		PDEG		2155175	Standard	NM_002602		Approved	RP57	uc002kay.3	P18545		ENST00000331056.5:c.174A>G	chr17.hg19:g.79618688T>C		102.0	0.0		87.0	4.0	NM_002602	Q3KP63|Q7Z3U8	Silent	SNP	ENST00000331056.5	hg19	CCDS11783.1																																																																																			.	.		0.662	PDE6G-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440314.1		
ZNF750	79755	hgsc.bcm.edu	37	17	80789773	80789773	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:80789773G>A	ENST00000269394.3	-	2	1391	c.558C>T	c.(556-558)aaC>aaT	p.N186N	TBCD_ENST00000397466.2_Intron|TBCD_ENST00000355528.4_Intron|ZNF750_ENST00000572562.1_Intron|TBCD_ENST00000539345.2_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	186					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			TGGCAGTGGGGTTGTGTAAAG	0.607																																					p.N186N		Atlas-SNP	.											.	ZNF750	60	.	0			c.C558T						.						57.0	60.0	59.0					17																	80789773		2203	4300	6503	SO:0001819	synonymous_variant	79755	exon2			AGTGGGGTTGTGT	AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.558C>T	chr17.hg19:g.80789773G>A		96.0	0.0		86.0	4.0	NM_024702	Q9H899	Silent	SNP	ENST00000269394.3	hg19	CCDS11819.1																																																																																			.	.		0.607	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702	
SMCHD1	23347	hgsc.bcm.edu	37	18	2688459	2688459	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:2688459G>T	ENST00000320876.6	+	6	1044	c.706G>T	c.(706-708)Ggt>Tgt	p.G236C	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.G236C	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	236					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TTCCTATTTTGGTGTTGGGGG	0.338																																					p.G236C		Atlas-SNP	.											.	SMCHD1	88	.	0			c.G706T						.						101.0	96.0	97.0					18																	2688459		1866	4099	5965	SO:0001583	missense	23347	exon6			TATTTTGGTGTTG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.706G>T	chr18.hg19:g.2688459G>T	ENSP00000326603:p.Gly236Cys	145.0	0.0		73.0	4.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.714519	0.89112	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	D;D	0.99891	-7.56;-7.56	5.08	5.08	0.68730	ATPase-like, ATP-binding domain (2);	0.060687	0.64402	D	0.000003	D	0.99900	0.9952	M	0.88377	2.95	0.50813	D	0.999893	D	0.89917	1.0	D	0.97110	1.0	D	0.96178	0.9128	10	0.87932	D	0	.	18.8289	0.92130	0.0:0.0:1.0:0.0	.	236	A6NHR9	SMHD1_HUMAN	C	236	ENSP00000326603:G236C;ENSP00000261598:G236C	ENSP00000261598:G236C	G	+	1	0	SMCHD1	2678459	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.927000	0.92846	2.502000	0.84385	0.655000	0.94253	GGT	.	.		0.338	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
SMCHD1	23347	hgsc.bcm.edu	37	18	2694533	2694533	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:2694533T>C	ENST00000320876.6	+	8	1220	c.882T>C	c.(880-882)gaT>gaC	p.D294D	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Silent_p.D294D	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	294					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						AGCCCTCTGATTCTGTTCACA	0.313																																					p.D294D		Atlas-SNP	.											.	SMCHD1	88	.	0			c.T882C						.						49.0	42.0	44.0					18																	2694533		1844	4076	5920	SO:0001819	synonymous_variant	23347	exon8			CTCTGATTCTGTT	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.882T>C	chr18.hg19:g.2694533T>C		133.0	0.0		89.0	4.0	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	hg19	CCDS45822.1																																																																																			.	.		0.313	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
L3MBTL4	91133	hgsc.bcm.edu	37	18	6244510	6244510	+	Silent	SNP	C	C	T	rs200697690		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:6244510C>T	ENST00000284898.6	-	6	497	c.297G>A	c.(295-297)tcG>tcA	p.S99S	L3MBTL4_ENST00000400105.2_Silent_p.S99S|L3MBTL4_ENST00000400104.3_Silent_p.S99S|L3MBTL4_ENST00000317931.7_Silent_p.S99S	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	99					chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				CACAGAATACCGATGGATGTC	0.393																																					p.S99S	Esophageal Squamous(41;748 902 17366 28959 43175)	Atlas-SNP	.											.	L3MBTL4	87	.	0			c.G297A						.						207.0	190.0	196.0					18																	6244510		2203	4300	6503	SO:0001819	synonymous_variant	91133	exon6			GAATACCGATGGA	BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655		"""Sterile alpha motif (SAM) domain containing"""	26677	protein-coding gene	gene with protein product						14702039	Standard	NM_173464		Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.297G>A	chr18.hg19:g.6244510C>T		148.0	0.0		60.0	4.0	NM_173464	A8MTL8|Q8IXS3	Silent	SNP	ENST00000284898.6	hg19	CCDS11839.2																																																																																			.	C|0.999;T|0.001		0.393	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464	
GNAL	2774	hgsc.bcm.edu	37	18	11881066	11881066	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:11881066C>A	ENST00000423027.3	+	12	1399	c.1078C>A	c.(1078-1080)Cgc>Agc	p.R360S	GNAL_ENST00000602628.1_Missense_Mutation_p.R153S|GNAL_ENST00000535121.1_Missense_Mutation_p.R360S|GNAL_ENST00000334049.6_Missense_Mutation_p.R437S|GNAL_ENST00000269162.5_Missense_Mutation_p.R360S			P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type	360					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|response to amphetamine (GO:0001975)|response to caffeine (GO:0031000)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)	12						AGAGAACATCCGCAGGGTGTT	0.612																																					p.R437S		Atlas-SNP	.											.	GNAL	59	.	0			c.C1309A						.						91.0	62.0	72.0					18																	11881066		2203	4300	6503	SO:0001583	missense	2774	exon12			AACATCCGCAGGG	AF493893	CCDS11851.1, CCDS11852.1, CCDS58614.1	18p11.22-p11.21	2003-12-17			ENSG00000141404	ENSG00000141404			4388	protein-coding gene	gene with protein product		139312				1302014	Standard	NM_182978		Approved		uc002kqc.3	P38405	OTTHUMG00000131660	ENST00000423027.3:c.1078C>A	chr18.hg19:g.11881066C>A	ENSP00000408489:p.Arg360Ser	114.0	0.0		62.0	5.0	NM_182978	B7ZA26|Q86XU3	Missense_Mutation	SNP	ENST00000423027.3	hg19	CCDS11852.1	.	.	.	.	.	.	.	.	.	.	C	36	5.705057	0.96812	.	.	ENSG00000141404	ENST00000540217;ENST00000334049;ENST00000535121;ENST00000269162;ENST00000423027;ENST00000535980	D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47	5.55	5.55	0.83447	.	0.046280	0.85682	D	0.000000	D	0.93956	0.8065	M	0.78801	2.425	0.80722	D	1	D;P	0.58620	0.983;0.866	P;P	0.60345	0.873;0.801	D	0.94342	0.7571	10	0.87932	D	0	.	19.4958	0.95072	0.0:1.0:0.0:0.0	.	360;437	P38405;Q86XU3	GNAL_HUMAN;.	S	299;437;360;360;360;153	ENSP00000334051:R437S;ENSP00000439023:R360S;ENSP00000269162:R360S;ENSP00000408489:R360S	ENSP00000269162:R360S	R	+	1	0	GNAL	11871066	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.748000	0.85085	2.591000	0.87537	0.563000	0.77884	CGC	.	.		0.612	GNAL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254561.2	NM_182978, NM_002071	
RBBP8	5932	hgsc.bcm.edu	37	18	20572755	20572755	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:20572755C>A	ENST00000399722.2	+	11	1316	c.965C>A	c.(964-966)cCt>cAt	p.P322H	RBBP8_ENST00000399725.2_Missense_Mutation_p.P322H|RBBP8_ENST00000360790.5_Missense_Mutation_p.P322H|RBBP8_ENST00000327155.5_Missense_Mutation_p.P322H	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	322					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			GAAGAATTACCTACTCGAGTG	0.343								Homologous recombination																													p.P322H		Atlas-SNP	.											.	RBBP8	138	.	0			c.C965A						.						83.0	87.0	86.0					18																	20572755		2194	4299	6493	SO:0001583	missense	5932	exon11			AATTACCTACTCG	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"""CTBP-interacting protein"""	604124	"""retinoblastoma-binding protein 8"", ""Seckel syndrome 2"""	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.965C>A	chr18.hg19:g.20572755C>A	ENSP00000382628:p.Pro322His	130.0	0.0		81.0	4.0	NM_203292	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Missense_Mutation	SNP	ENST00000399722.2	hg19	CCDS11875.1	.	.	.	.	.	.	.	.	.	.	C	5.738	0.320620	0.10845	.	.	ENSG00000101773	ENST00000327155;ENST00000399725;ENST00000399722;ENST00000399721;ENST00000360790	T;T;T;T;T	0.28895	1.6;1.59;1.6;1.6;1.6	5.99	2.83	0.33086	.	0.927132	0.09296	N	0.821685	T	0.15912	0.0383	N	0.14661	0.345	0.18873	N	0.999985	B;B;B	0.13145	0.007;0.001;0.007	B;B;B	0.08055	0.003;0.001;0.003	T	0.16867	-1.0388	10	0.33141	T	0.24	-0.2581	3.2437	0.06789	0.3661:0.425:0.1194:0.0895	.	322;322;322	E7ETY1;A6NKN2;Q99708	.;.;COM1_HUMAN	H	322	ENSP00000323050:P322H;ENSP00000382630:P322H;ENSP00000382628:P322H;ENSP00000382627:P322H;ENSP00000354024:P322H	ENSP00000323050:P322H	P	+	2	0	RBBP8	18826753	0.036000	0.19791	0.016000	0.15963	0.197000	0.23852	1.117000	0.31234	1.500000	0.48636	0.655000	0.94253	CCT	.	.		0.343	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291	
RBBP8	5932	hgsc.bcm.edu	37	18	20573367	20573367	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:20573367A>G	ENST00000399722.2	+	11	1928	c.1577A>G	c.(1576-1578)aAg>aGg	p.K526R	RBBP8_ENST00000399725.2_Missense_Mutation_p.K526R|RBBP8_ENST00000360790.5_Missense_Mutation_p.K526R|RBBP8_ENST00000327155.5_Missense_Mutation_p.K526R	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	526	Damage-recruitment motif.				blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			GAGGCTTTGAAGACCATTCCA	0.468								Homologous recombination																													p.K526R		Atlas-SNP	.											.	RBBP8	138	.	0			c.A1577G						.						43.0	44.0	44.0					18																	20573367		2198	4300	6498	SO:0001583	missense	5932	exon11			CTTTGAAGACCAT	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"""CTBP-interacting protein"""	604124	"""retinoblastoma-binding protein 8"", ""Seckel syndrome 2"""	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.1577A>G	chr18.hg19:g.20573367A>G	ENSP00000382628:p.Lys526Arg	123.0	0.0		61.0	4.0	NM_203292	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Missense_Mutation	SNP	ENST00000399722.2	hg19	CCDS11875.1	.	.	.	.	.	.	.	.	.	.	A	19.47	3.833246	0.71258	.	.	ENSG00000101773	ENST00000327155;ENST00000399725;ENST00000399722;ENST00000399721;ENST00000360790	T;T;T;T;T	0.38401	1.21;1.14;1.21;1.2;1.21	5.97	5.97	0.96955	.	0.503154	0.22734	N	0.056284	T	0.59878	0.2226	M	0.72118	2.19	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.991	D;D;P	0.83275	0.922;0.996;0.79	T	0.62167	-0.6911	10	0.66056	D	0.02	-11.2765	14.2018	0.65710	1.0:0.0:0.0:0.0	.	526;526;526	E7ETY1;A6NKN2;Q99708	.;.;COM1_HUMAN	R	526	ENSP00000323050:K526R;ENSP00000382630:K526R;ENSP00000382628:K526R;ENSP00000382627:K526R;ENSP00000354024:K526R	ENSP00000323050:K526R	K	+	2	0	RBBP8	18827365	0.999000	0.42202	0.997000	0.53966	0.613000	0.37349	4.236000	0.58675	2.288000	0.76882	0.533000	0.62120	AAG	.	.		0.468	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291	
C18orf8	29919	hgsc.bcm.edu	37	18	21109173	21109173	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:21109173C>T	ENST00000269221.3	+	15	1437	c.1327C>T	c.(1327-1329)Ccg>Tcg	p.P443S	C18orf8_ENST00000590868.1_Missense_Mutation_p.P395S	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	443						lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CCGAAGCAGCCCGCTCCTCAA	0.552																																					p.P443S		Atlas-SNP	.											.	C18orf8	58	.	0			c.C1327T						.						69.0	73.0	72.0					18																	21109173		2203	4300	6503	SO:0001583	missense	29919	exon15			AGCAGCCCGCTCC	AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"""colon cancer associated protein Mic1"", ""macrophage inhibitory cytokine 1"""					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.1327C>T	chr18.hg19:g.21109173C>T	ENSP00000269221:p.Pro443Ser	60.0	0.0		35.0	4.0	NM_013326	Q9BU17|Q9Y5M0	Missense_Mutation	SNP	ENST00000269221.3	hg19	CCDS32803.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.505311	0.44558	.	.	ENSG00000141452	ENST00000269221;ENST00000544799;ENST00000540942;ENST00000542734	.	.	.	5.71	5.71	0.89125	.	0.056544	0.64402	D	0.000001	T	0.43055	0.1230	L	0.29908	0.895	0.80722	D	1	B;B	0.16396	0.017;0.001	B;B	0.15484	0.013;0.001	T	0.32348	-0.9910	9	0.06625	T	0.88	-7.9438	15.3516	0.74393	0.0:0.861:0.139:0.0	.	286;443	B7Z2Y1;Q96DM3	.;MIC1_HUMAN	S	443;286;395;286	.	ENSP00000269221:P443S	P	+	1	0	C18orf8	19363171	0.998000	0.40836	0.637000	0.29366	0.803000	0.45373	3.750000	0.55157	2.698000	0.92095	0.561000	0.74099	CCG	.	.		0.552	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326	
ANKRD29	147463	hgsc.bcm.edu	37	18	21214039	21214039	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:21214039T>C	ENST00000592179.1	-	5	559	c.405A>G	c.(403-405)ggA>ggG	p.G135G	ANKRD29_ENST00000322980.9_Silent_p.G135G|ANKRD29_ENST00000284207.7_Silent_p.G135G	NM_173505.2	NP_775776.2	Q8N6D5	ANR29_HUMAN	ankyrin repeat domain 29	135										breast(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)	13	all_cancers(21;5.07e-05)|all_epithelial(16;2.49e-07)|Lung NSC(20;0.00211)|all_lung(20;0.00676)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GGATGTTTGCTCCGTGCTTCA	0.483																																					p.G135G		Atlas-SNP	.											.	ANKRD29	24	.	0			c.A405G						.						116.0	89.0	98.0					18																	21214039		2203	4300	6503	SO:0001819	synonymous_variant	147463	exon5			GTTTGCTCCGTGC	AK057782	CCDS11879.1	18q11.2	2013-01-10			ENSG00000154065	ENSG00000154065		"""Ankyrin repeat domain containing"""	27110	protein-coding gene	gene with protein product							Standard	NM_173505		Approved	FLJ25053	uc002kun.3	Q8N6D5	OTTHUMG00000131875	ENST00000592179.1:c.405A>G	chr18.hg19:g.21214039T>C		169.0	0.0		104.0	5.0	NM_173505	B2R972|Q6ZWE8|Q96LU9	Silent	SNP	ENST00000592179.1	hg19	CCDS11879.1																																																																																			.	.		0.483	ANKRD29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254825.1	NM_173505	
TAF4B	6875	hgsc.bcm.edu	37	18	23847518	23847518	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:23847518A>G	ENST00000269142.5	+	3	1526	c.528A>G	c.(526-528)acA>acG	p.T176T	RP11-25D3.1_ENST00000580975.1_RNA|TAF4B_ENST00000578121.1_Silent_p.T176T|TAF4B_ENST00000400466.2_Silent_p.T176T	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	176					gene expression (GO:0010467)|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)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			TGGCAGTGACACCTGTTAAAA	0.423																																					p.T176T		Atlas-SNP	.											.	TAF4B	71	.	0			c.A528G						.						105.0	101.0	102.0					18																	23847518		1895	4112	6007	SO:0001819	synonymous_variant	6875	exon3			AGTGACACCTGTT	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.528A>G	chr18.hg19:g.23847518A>G		126.0	0.0		89.0	4.0	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	hg19	CCDS42421.1																																																																																			.	.		0.423	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
TRAPPC8	22878	hgsc.bcm.edu	37	18	29437916	29437916	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:29437916A>G	ENST00000283351.4	-	20	3110	c.2775T>C	c.(2773-2775)ctT>ctC	p.L925L	TRAPPC8_ENST00000582539.1_Silent_p.L871L	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	925					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CTCCACAGAGAAGCCCTGTAG	0.333																																					p.L925L		Atlas-SNP	.											.	TRAPPC8	126	.	0			c.T2775C						.						95.0	105.0	102.0					18																	29437916		2203	4300	6503	SO:0001819	synonymous_variant	22878	exon20			ACAGAGAAGCCCT	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"""Trafficking protein particle complex"""	29169	protein-coding gene	gene with protein product	"""general sporulation gene 1 homolog (S. cerevisiae)"""	614136	"""KIAA1012"""	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.2775T>C	chr18.hg19:g.29437916A>G		146.0	0.0		82.0	4.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Silent	SNP	ENST00000283351.4	hg19	CCDS11901.1																																																																																			.	.		0.333	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939	
TRAPPC8	22878	hgsc.bcm.edu	37	18	29497605	29497605	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:29497605G>T	ENST00000283351.4	-	3	713	c.378C>A	c.(376-378)taC>taA	p.Y126*	TRAPPC8_ENST00000582539.1_Nonsense_Mutation_p.Y72*|TRAPPC8_ENST00000582513.1_Nonsense_Mutation_p.Y126*	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	126					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AGGTTTCTCTGTAAGACTCAA	0.328																																					p.Y126X		Atlas-SNP	.											.	TRAPPC8	126	.	0			c.C378A						.						135.0	143.0	141.0					18																	29497605		2203	4300	6503	SO:0001587	stop_gained	22878	exon3			TTCTCTGTAAGAC	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"""Trafficking protein particle complex"""	29169	protein-coding gene	gene with protein product	"""general sporulation gene 1 homolog (S. cerevisiae)"""	614136	"""KIAA1012"""	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.378C>A	chr18.hg19:g.29497605G>T	ENSP00000283351:p.Tyr126*	136.0	0.0		66.0	4.0	NM_014939	A0JP15|B3KME5|Q9H0L2	Nonsense_Mutation	SNP	ENST00000283351.4	hg19	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.625505	0.66901	.	.	ENSG00000153339	ENST00000283351	.	.	.	6.05	-8.27	0.01017	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.9338	0.89006	0.6614:0.0:0.3386:0.0	.	.	.	.	X	126	.	ENSP00000283351:Y126X	Y	-	3	2	TRAPPC8	27751603	0.993000	0.37304	0.238000	0.24106	0.965000	0.64279	0.221000	0.17680	-1.964000	0.01012	-1.000000	0.02509	TAC	.	.		0.328	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939	
MEP1B	4225	hgsc.bcm.edu	37	18	29788190	29788190	+	Missense_Mutation	SNP	C	C	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:29788190C>G	ENST00000269202.6	+	9	922	c.875C>G	c.(874-876)cCc>cGc	p.P292R	MEP1B_ENST00000581447.1_Missense_Mutation_p.P292R	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	292	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TCACAGGTTCCCAGGGGGCCA	0.478																																					p.P292R		Atlas-SNP	.											.	MEP1B	54	.	0			c.C875G						.						97.0	99.0	98.0					18																	29788190		1912	4120	6032	SO:0001583	missense	4225	exon9			AGGTTCCCAGGGG	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.875C>G	chr18.hg19:g.29788190C>G	ENSP00000269202:p.Pro292Arg	154.0	0.0		99.0	27.0	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	hg19	CCDS45846.1	.	.	.	.	.	.	.	.	.	.	C	8.990	0.977567	0.18812	.	.	ENSG00000141434	ENST00000269202	T	0.02050	4.48	5.48	3.67	0.42095	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.773265	0.12702	N	0.446244	T	0.04272	0.0118	L	0.46157	1.445	0.09310	N	1	P	0.34615	0.459	B	0.43103	0.408	T	0.42137	-0.9469	10	0.19147	T	0.46	-0.6288	11.9111	0.52739	0.0:0.8567:0.0:0.1433	.	292	Q16820	MEP1B_HUMAN	R	292	ENSP00000269202:P292R	ENSP00000269202:P292R	P	+	2	0	MEP1B	28042188	0.000000	0.05858	0.001000	0.08648	0.541000	0.35023	1.154000	0.31688	1.308000	0.44962	0.561000	0.74099	CCC	.	.		0.478	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
ZNF396	252884	hgsc.bcm.edu	37	18	32953458	32953458	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:32953458T>C	ENST00000589332.1	-	3	655	c.524A>G	c.(523-525)cAg>cGg	p.Q175R	ZNF396_ENST00000586687.1_Missense_Mutation_p.Q175R|ZNF396_ENST00000306346.1_Missense_Mutation_p.Q175R			Q96N95	ZN396_HUMAN	zinc finger protein 396	175					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)	7						TGATGCTCCCTGGAGCTGCTT	0.527																																					p.Q175R		Atlas-SNP	.											.	ZNF396	28	.	0			c.A524G						.						114.0	101.0	105.0					18																	32953458		2203	4300	6503	SO:0001583	missense	252884	exon3			GCTCCCTGGAGCT	AK055775	CCDS11913.1	18p12	2013-01-09			ENSG00000186496	ENSG00000186496		"""-"", ""Zinc fingers, C2H2-type"""	18824	protein-coding gene	gene with protein product		609600					Standard	NM_145756		Approved	ZSCAN14, FLJ31213	uc010xcf.1	Q96N95	OTTHUMG00000132562	ENST00000589332.1:c.524A>G	chr18.hg19:g.32953458T>C	ENSP00000466500:p.Gln175Arg	275.0	0.0		130.0	6.0	NM_145756	A1L3V0|Q8NF98|Q8TD80	Missense_Mutation	SNP	ENST00000589332.1	hg19		.	.	.	.	.	.	.	.	.	.	T	8.931	0.963336	0.18583	.	.	ENSG00000186496	ENST00000306346;ENST00000399057	T	0.07327	3.2	4.3	-8.6	0.00889	.	.	.	.	.	T	0.03651	0.0104	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.45175	-0.9279	9	0.33141	T	0.24	.	10.9872	0.47528	0.0:0.1576:0.6639:0.1785	.	175	Q96N95-3	.	R	175	ENSP00000302310:Q175R	ENSP00000302310:Q175R	Q	-	2	0	ZNF396	31207456	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.565000	0.05929	-2.202000	0.00745	0.459000	0.35465	CAG	.	.		0.527	ZNF396-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255766.1	NM_145756	
SLC14A2	8170	hgsc.bcm.edu	37	18	43204717	43204717	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:43204717T>C	ENST00000255226.6	+	2	904	c.88T>C	c.(88-90)Tgg>Cgg	p.W30R	SLC14A2_ENST00000586448.1_Missense_Mutation_p.W30R	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	30					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CAGCCCGAGCTGGCCCTCGAC	0.572																																					p.W30R		Atlas-SNP	.											.	SLC14A2	121	.	0			c.T88C						.						80.0	75.0	77.0					18																	43204717		2203	4300	6503	SO:0001583	missense	8170	exon3			CCGAGCTGGCCCT	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"""Solute carriers"""	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.88T>C	chr18.hg19:g.43204717T>C	ENSP00000255226:p.Trp30Arg	91.0	0.0		68.0	5.0	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	hg19	CCDS11924.1	.	.	.	.	.	.	.	.	.	.	T	10.11	1.260877	0.23051	.	.	ENSG00000132874	ENST00000255226;ENST00000323329	T;T	0.65178	0.45;-0.14	5.31	5.31	0.75309	.	0.263214	0.32655	N	0.005810	T	0.65595	0.2706	L	0.57536	1.79	0.30059	N	0.811036	P;D	0.55385	0.91;0.971	B;P	0.50440	0.424;0.641	T	0.68750	-0.5326	10	0.52906	T	0.07	-0.4283	11.6475	0.51269	0.0:0.0:0.0:1.0	.	30;30	Q15849;E7EPU1	UT2_HUMAN;.	R	30	ENSP00000255226:W30R;ENSP00000320689:W30R	ENSP00000255226:W30R	W	+	1	0	SLC14A2	41458715	0.989000	0.36119	0.813000	0.32504	0.148000	0.21650	2.448000	0.44926	2.008000	0.58898	0.334000	0.21626	TGG	.	.		0.572	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		
SLC14A1	6563	hgsc.bcm.edu	37	18	43329905	43329905	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:43329905A>G	ENST00000321925.4	+	10	1391	c.1159A>G	c.(1159-1161)Agc>Ggc	p.S387G	SLC14A1_ENST00000402943.2_Missense_Mutation_p.S282G|SLC14A1_ENST00000591541.1_Missense_Mutation_p.S91G|SLC14A1_ENST00000589700.1_3'UTR|SLC14A1_ENST00000586142.1_Missense_Mutation_p.S387G|RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000436407.3_Missense_Mutation_p.S443G|SLC14A1_ENST00000415427.3_Missense_Mutation_p.S443G|SLC14A1_ENST00000502059.2_Missense_Mutation_p.S279G|SLC14A1_ENST00000535474.1_Missense_Mutation_p.S255G	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	387					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						AATGGTGGAAAGCCCTTTGTG	0.453																																					p.S443G		Atlas-SNP	.											.	SLC14A1	84	.	0			c.A1327G						.						118.0	116.0	117.0					18																	43329905		2203	4300	6503	SO:0001583	missense	6563	exon9			GTGGAAAGCCCTT	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"""Blood group antigens"", ""Solute carriers"""	10918	protein-coding gene	gene with protein product		613868	"""Kidd blood group"", ""solute carrier family 14 (urea transporter), member 1"""	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.1159A>G	chr18.hg19:g.43329905A>G	ENSP00000318546:p.Ser387Gly	143.0	0.0		93.0	4.0	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Missense_Mutation	SNP	ENST00000321925.4	hg19	CCDS11925.1	.	.	.	.	.	.	.	.	.	.	A	13.18	2.159723	0.38119	.	.	ENSG00000141469	ENST00000321925;ENST00000415427;ENST00000502059;ENST00000402943;ENST00000535474;ENST00000436407	T;T;T;T;T;T	0.53423	0.8;0.66;0.8;0.82;0.62;0.66	5.64	3.28	0.37604	.	0.420374	0.25842	N	0.027948	T	0.36690	0.0976	L	0.42245	1.32	0.28739	N	0.902051	B;B;B	0.14438	0.01;0.002;0.003	B;B;B	0.13407	0.009;0.005;0.005	T	0.29701	-1.0003	10	0.49607	T	0.09	-8.3904	7.1926	0.25834	0.7501:0.0:0.2499:0.0	.	443;279;387	Q13336-2;B3KXJ3;Q13336	.;.;UT1_HUMAN	G	387;443;279;282;255;443	ENSP00000318546:S387G;ENSP00000412309:S443G;ENSP00000442180:S279G;ENSP00000385320:S282G;ENSP00000441998:S255G;ENSP00000390637:S443G	ENSP00000318546:S387G	S	+	1	0	SLC14A1	41583903	0.997000	0.39634	0.124000	0.21820	0.022000	0.10575	2.633000	0.46519	0.510000	0.28216	0.482000	0.46254	AGC	.	.		0.453	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865	
MYO5B	4645	hgsc.bcm.edu	37	18	47421462	47421462	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:47421462T>C	ENST00000285039.7	-	22	3193	c.2894A>G	c.(2893-2895)gAg>gGg	p.E965G	MYO5B_ENST00000324581.6_Missense_Mutation_p.E106G	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	965					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		GTGCACCAGCTCCTTCTTCAG	0.577																																					p.E965G		Atlas-SNP	.											.	MYO5B	178	.	0			c.A2894G						.						70.0	70.0	70.0					18																	47421462		2033	4187	6220	SO:0001583	missense	4645	exon22			ACCAGCTCCTTCT	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.2894A>G	chr18.hg19:g.47421462T>C	ENSP00000285039:p.Glu965Gly	145.0	0.0		78.0	4.0	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	hg19	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	T	15.99	2.995585	0.54147	.	.	ENSG00000167306	ENST00000285039;ENST00000324581	T;T	0.21361	2.01;2.01	5.68	5.68	0.88126	.	0.123004	0.53938	D	0.000047	T	0.26882	0.0658	M	0.61703	1.905	0.51482	D	0.999926	B;P	0.36753	0.3;0.568	B;B	0.37387	0.078;0.248	T	0.02533	-1.1145	10	0.46703	T	0.11	.	15.6047	0.76658	0.0:0.0:0.0:1.0	.	965;106	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	G	965;106	ENSP00000285039:E965G;ENSP00000315531:E106G	ENSP00000285039:E965G	E	-	2	0	MYO5B	45675460	1.000000	0.71417	1.000000	0.80357	0.630000	0.37929	4.313000	0.59160	2.163000	0.67991	0.402000	0.26972	GAG	.	.		0.577	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
TCF4	6925	hgsc.bcm.edu	37	18	52937094	52937094	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:52937094G>A	ENST00000356073.4	-	11	1501	c.890C>T	c.(889-891)aCg>aTg	p.T297M	TCF4_ENST00000563760.1_5'UTR|TCF4_ENST00000561831.3_Missense_Mutation_p.T137M|TCF4_ENST00000398339.1_Missense_Mutation_p.T399M|TCF4_ENST00000537578.1_Missense_Mutation_p.T273M|TCF4_ENST00000457482.3_Missense_Mutation_p.T137M|TCF4_ENST00000566286.1_Missense_Mutation_p.T295M|TCF4_ENST00000543082.1_Missense_Mutation_p.T255M|TCF4_ENST00000564228.1_Missense_Mutation_p.T226M|TCF4_ENST00000565018.2_Missense_Mutation_p.T297M|TCF4_ENST00000537856.3_Missense_Mutation_p.T167M|TCF4_ENST00000570287.2_Missense_Mutation_p.T137M|TCF4_ENST00000564403.2_Missense_Mutation_p.T303M|TCF4_ENST00000540999.1_Missense_Mutation_p.T273M|TCF4_ENST00000566279.1_Missense_Mutation_p.T237M|TCF4_ENST00000570177.2_Missense_Mutation_p.T167M|TCF4_ENST00000567880.1_Missense_Mutation_p.T237M|TCF4_ENST00000561992.1_Missense_Mutation_p.T167M|TCF4_ENST00000564999.1_Missense_Mutation_p.T297M|TCF4_ENST00000544241.2_Missense_Mutation_p.T226M|TCF4_ENST00000354452.3_Missense_Mutation_p.T297M|TCF4_ENST00000568673.1_Missense_Mutation_p.T273M|TCF4_ENST00000568740.1_Missense_Mutation_p.T272M	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	297					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)		GGCAGGAGGCGTACAGGAAGA	0.463																																					p.T399M		Atlas-SNP	.											.	TCF4	178	.	0			c.C1196T						.						167.0	136.0	146.0					18																	52937094		2203	4300	6503	SO:0001583	missense	6925	exon12			GGAGGCGTACAGG	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.890C>T	chr18.hg19:g.52937094G>A	ENSP00000348374:p.Thr297Met	175.0	0.0		96.0	4.0	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	Missense_Mutation	SNP	ENST00000356073.4	hg19	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.952152	0.92660	.	.	ENSG00000196628	ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339	T;T;T;T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.76385	0.3980	M	0.83603	2.65	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.91635	0.953;0.987;0.97;0.987;0.999;0.911;0.953;0.953;0.949;0.942	T	0.78974	-0.1992	10	0.87932	D	0	-11.1751	18.8159	0.92076	0.0:0.0:1.0:0.0	.	273;297;273;137;399;297;255;226;137;295	B7Z5M6;G0LNT9;B7Z6Y1;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5	.;.;.;.;.;ITF2_HUMAN;.;.;.;.	M	297;137;297;255;273;273;226;167;399	ENSP00000346440:T297M;ENSP00000409447:T137M;ENSP00000348374:T297M;ENSP00000439656:T255M;ENSP00000445202:T273M;ENSP00000440731:T273M;ENSP00000441562:T226M;ENSP00000439827:T167M;ENSP00000381382:T399M	ENSP00000346440:T297M	T	-	2	0	TCF4	51088092	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	8.998000	0.93550	2.734000	0.93682	0.460000	0.39030	ACG	.	.		0.463	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199	
ST8SIA3	51046	hgsc.bcm.edu	37	18	55027274	55027274	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:55027274T>C	ENST00000324000.3	+	4	2943	c.909T>C	c.(907-909)atT>atC	p.I303I		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	303					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)		GCACAGGTATTCTTATGTACA	0.418																																					p.I303I		Atlas-SNP	.											.	ST8SIA3	73	.	0			c.T909C						.						112.0	104.0	107.0					18																	55027274		2203	4300	6503	SO:0001819	synonymous_variant	51046	exon4			AGGTATTCTTATG	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.909T>C	chr18.hg19:g.55027274T>C		172.0	0.0		79.0	4.0	NM_015879	A8K0F2|Q6B085|Q9NS41	Silent	SNP	ENST00000324000.3	hg19	CCDS32834.1																																																																																			.	.		0.418	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879	
CDH20	28316	hgsc.bcm.edu	37	18	59221741	59221741	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:59221741C>A	ENST00000262717.4	+	12	2617	c.2219C>A	c.(2218-2220)cCg>cAg	p.P740Q	CDH20_ENST00000538374.1_Missense_Mutation_p.P740Q|CDH20_ENST00000536675.2_Missense_Mutation_p.P740Q			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	740					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				CTGTGGGCACCGCCCTTCGAC	0.647																																					p.P740Q		Atlas-SNP	.											CDH20,NS,carcinoma,0,1	CDH20	117	.	0			c.C2219A						.						37.0	30.0	33.0					18																	59221741		2203	4300	6503	SO:0001583	missense	28316	exon11			GGGCACCGCCCTT	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"""Cadherins / Major cadherins"""	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.2219C>A	chr18.hg19:g.59221741C>A	ENSP00000262717:p.Pro740Gln	95.0	0.0		45.0	2.0	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	hg19	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.637951	0.87760	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.80033	-1.33;-1.33;-1.33	5.78	5.78	0.91487	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.92925	0.7749	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93752	0.7059	10	0.87932	D	0	.	20.3668	0.98882	0.0:1.0:0.0:0.0	.	740	Q9HBT6	CAD20_HUMAN	Q	740	ENSP00000444767:P740Q;ENSP00000442226:P740Q;ENSP00000262717:P740Q	ENSP00000262717:P740Q	P	+	2	0	CDH20	57372721	1.000000	0.71417	0.994000	0.49952	0.905000	0.53344	7.756000	0.85195	2.894000	0.99253	0.655000	0.94253	CCG	.	.		0.647	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891	
SERPINB2	5055	hgsc.bcm.edu	37	18	61569075	61569075	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:61569075G>T	ENST00000299502.4	+	6	717	c.637G>T	c.(637-639)Gag>Tag	p.E213*	SERPINB2_ENST00000482254.1_3'UTR|SERPINB2_ENST00000457692.1_Nonsense_Mutation_p.E213*	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	213					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	AACTCCATTTGAGAAGAAACT	0.388																																					p.E213X		Atlas-SNP	.											.	SERPINB2	63	.	0			c.G637T						.						107.0	110.0	109.0					18																	61569075		2203	4300	6503	SO:0001587	stop_gained	5055	exon6			CCATTTGAGAAGA	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"""Serine (or cysteine) peptidase inhibitors"""	8584	protein-coding gene	gene with protein product		173390	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"""	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.637G>T	chr18.hg19:g.61569075G>T	ENSP00000299502:p.Glu213*	101.0	0.0		91.0	4.0	NM_002575	Q96E96	Nonsense_Mutation	SNP	ENST00000299502.4	hg19	CCDS11989.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	6.690516|6.690516	0.97764|0.97764	.|.	.|.	ENSG00000197632|ENSG00000242550	ENST00000299502;ENST00000457692|ENST00000397996;ENST00000418725	.|.	.|.	.|.	5.79|5.79	0.804|0.804	0.18697|0.18697	.|.	0.424440|.	0.27886|.	N|.	0.017456|.	.|.	.|.	.|.	.|.	.|.	.|.	0.53688|0.53688	D|D	0.999974|0.999974	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.07644|.	T|.	0.81|.	.|.	12.5443|12.5443	0.56190|0.56190	0.1523:0.3234:0.5244:0.0|0.1523:0.3234:0.5244:0.0	.|.	.|.	.|.	.|.	X|L	213|89	.|.	ENSP00000299502:E213X|.	E|X	+|+	1|2	0|2	SERPINB2|SERPINB10	59720055|59720055	0.000000|0.000000	0.05858|0.05858	0.982000|0.982000	0.44146|0.44146	0.992000|0.992000	0.81027|0.81027	-1.608000|-1.608000	0.02068|0.02068	-0.149000|-0.149000	0.11215|0.11215	0.650000|0.650000	0.86243|0.86243	GAG|TGA	.	.		0.388	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
DSEL	92126	hgsc.bcm.edu	37	18	65178261	65178261	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:65178261T>C	ENST00000310045.7	-	2	5088	c.3615A>G	c.(3613-3615)gaA>gaG	p.E1205E	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	1195					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				AGCAGATGTTTTCAATTAGTT	0.373																																					p.E1205E		Atlas-SNP	.											.	DSEL	196	.	0			c.A3615G						.						104.0	101.0	102.0					18																	65178261		2203	4300	6503	SO:0001819	synonymous_variant	92126	exon2			GATGTTTTCAATT	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.3615A>G	chr18.hg19:g.65178261T>C		242.0	0.0		120.0	6.0	NM_032160	Q17RH1|Q6P5Z3	Silent	SNP	ENST00000310045.7	hg19	CCDS11995.1																																																																																			.	.		0.373	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
ZNF407	55628	hgsc.bcm.edu	37	18	72516010	72516010	+	Intron	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr18:72516010T>C	ENST00000299687.5	+	3	4877				ZNF407_ENST00000309902.6_Silent_p.C1656C|ZNF407_ENST00000582337.1_Silent_p.C1656C|ZNF407_ENST00000577538.1_Intron	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		AAAGTCTTTGTGAGCACTTTT	0.433																																					p.C1656C		Atlas-SNP	.											.	ZNF407	231	.	0			c.T4968C						.						119.0	112.0	114.0					18																	72516010		692	1591	2283	SO:0001627	intron_variant	55628	exon4			TCTTTGTGAGCAC	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.4877+22552T>C	chr18.hg19:g.72516010T>C		121.0	0.0		96.0	4.0	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	hg19	CCDS45885.1																																																																																			.	.		0.433	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
MIER2	54531	hgsc.bcm.edu	37	19	327889	327889	+	Missense_Mutation	SNP	T	T	C	rs376851727		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:327889T>C	ENST00000264819.4	-	4	354	c.344A>G	c.(343-345)aAc>aGc	p.N115S	MIER2_ENST00000592722.1_5'UTR	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	115					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(4)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		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)		GTCTGGGAGGTTCGGGGCCAC	0.617																																					p.N115S		Atlas-SNP	.											.	MIER2	51	.	0			c.A344G						.	T	SER/ASN	0,4406		0,0,2203	105.0	87.0	93.0		344	-4.8	0.0	19		93	1,8599		0,1,4299	no	missense	MIER2	NM_017550.1	46	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	115/546	327889	1,13005	2203	4300	6503	SO:0001583	missense	54531	exon4			GGGAGGTTCGGGG	AB033019	CCDS32855.1	19p13.3	2008-02-05	2006-04-20	2006-04-20		ENSG00000105556			29210	protein-coding gene	gene with protein product			"""KIAA1193"""	KIAA1193		10574462	Standard	NM_017550		Approved		uc002lok.1	Q8N344		ENST00000264819.4:c.344A>G	chr19.hg19:g.327889T>C	ENSP00000264819:p.Asn115Ser	146.0	0.0		113.0	5.0	NM_017550	Q9ULM7	Missense_Mutation	SNP	ENST00000264819.4	hg19	CCDS32855.1	.	.	.	.	.	.	.	.	.	.	.	4.151	0.026419	0.08054	0.0	1.16E-4	ENSG00000105556	ENST00000264819	T	0.21361	2.01	5.01	-4.82	0.03171	.	1.871750	0.03258	N	0.182788	T	0.17066	0.0410	L	0.41236	1.265	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.23976	-1.0173	10	0.24483	T	0.36	0.0017	9.8058	0.40792	0.0:0.1465:0.6075:0.246	.	115	Q8N344	MIER2_HUMAN	S	115	ENSP00000264819:N115S	ENSP00000264819:N115S	N	-	2	0	MIER2	278889	0.004000	0.15560	0.001000	0.08648	0.125000	0.20455	0.204000	0.17335	-1.165000	0.02786	-0.376000	0.06991	AAC	.	.		0.617	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843	
BSG	682	hgsc.bcm.edu	37	19	582316	582316	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:582316C>A	ENST00000333511.3	+	7	1150	c.1080C>A	c.(1078-1080)gcC>gcA	p.A360A	BSG_ENST00000545507.2_Silent_p.A151A|BSG_ENST00000346916.4_Silent_p.A180A|BSG_ENST00000353555.4_Silent_p.A244A	NM_001728.3	NP_001719.2	P35613	BASI_HUMAN	basigin (Ok blood group)	360					blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular metabolic process (GO:0044237)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis of dentin-containing tooth (GO:0042475)|protein targeting to plasma membrane (GO:0072661)|pyruvate metabolic process (GO:0006090)|response to cAMP (GO:0051591)|response to mercury ion (GO:0046689)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|lung(1)	5		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-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)		ATGACGACGCCGGCTCTGCAC	0.642																																					p.A360A		Atlas-SNP	.											.	BSG	48	.	0			c.C1080A						.						27.0	32.0	31.0					19																	582316		2196	4294	6490	SO:0001819	synonymous_variant	682	exon7			CGACGCCGGCTCT	L10240	CCDS12032.1, CCDS12033.1, CCDS12034.1, CCDS58635.1	19p13.3	2014-07-19	2014-01-02		ENSG00000172270	ENSG00000172270		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1116	protein-coding gene	gene with protein product	"""Ok blood group"""	109480	"""basigin"""	OK		8404035, 7812975	Standard	NM_198591		Approved	EMMPRIN, CD147	uc002loz.4	P35613		ENST00000333511.3:c.1080C>A	chr19.hg19:g.582316C>A		118.0	0.0		74.0	4.0	NM_001728	A6NJW1|D3YLG5|Q7Z796|Q8IZL7	Silent	SNP	ENST00000333511.3	hg19	CCDS12033.1																																																																																			.	.		0.642	BSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438630.2	NM_001728	
KISS1R	84634	hgsc.bcm.edu	37	19	917723	917723	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:917723G>A	ENST00000234371.5	+	1	374	c.221G>A	c.(220-222)cGg>cAg	p.R74Q	KISS1R_ENST00000606939.1_Missense_Mutation_p.R74Q	NM_032551.4	NP_115940.2	Q969F8	KISSR_HUMAN	KISS1 receptor	74					activation of MAPKK activity (GO:0000186)|arachidonic acid secretion (GO:0050482)|calcium-mediated signaling (GO:0019722)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|positive regulation of hormone secretion (GO:0046887)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of synaptic transmission (GO:0050806)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide binding (GO:0042923)|neuropeptide receptor activity (GO:0008188)			cervix(1)|kidney(1)|ovary(1)|pancreas(1)|skin(1)	5		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|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)		AAGCCGATGCGGACCGTGACC	0.706																																					p.R74Q		Atlas-SNP	.											.	KISS1R	10	.	0			c.G221A						.						25.0	21.0	22.0					19																	917723		2198	4296	6494	SO:0001583	missense	84634	exon1			CGATGCGGACCGT	AB051065	CCDS12049.1	19p13.3	2012-08-10	2006-02-15	2006-02-15	ENSG00000116014	ENSG00000116014		"""GPCR / Class A : RF amide peptide receptors"""	4510	protein-coding gene	gene with protein product		604161	"""G protein-coupled receptor 54"""	GPR54		10100623	Standard	NM_032551		Approved	HOT7T175, AXOR12	uc002lqk.4	Q969F8		ENST00000234371.5:c.221G>A	chr19.hg19:g.917723G>A	ENSP00000234371:p.Arg74Gln	123.0	0.0		94.0	4.0	NM_032551	A5D8U2|B2RTV1|Q96QG0	Missense_Mutation	SNP	ENST00000234371.5	hg19	CCDS12049.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.722913	0.68959	.	.	ENSG00000116014	ENST00000234371	T	0.42131	0.98	3.94	1.72	0.24424	GPCR, rhodopsin-like superfamily (1);	0.203848	0.38326	N	0.001727	T	0.37919	0.1021	M	0.66439	2.03	0.40293	D	0.978526	B	0.33637	0.42	B	0.35413	0.202	T	0.12528	-1.0544	10	0.30854	T	0.27	.	8.494	0.33117	0.2055:0.0:0.7945:0.0	.	74	Q969F8	KISSR_HUMAN	Q	74	ENSP00000234371:R74Q	ENSP00000234371:R74Q	R	+	2	0	KISS1R	868723	1.000000	0.71417	0.919000	0.36401	0.960000	0.62799	2.844000	0.48246	0.242000	0.21303	0.400000	0.26472	CGG	.	.		0.706	KISS1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458217.3	NM_032551	
IZUMO4	113177	hgsc.bcm.edu	37	19	2096945	2096945	+	Start_Codon_SNP	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:2096945A>G	ENST00000395301.3	+	1	65	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	IZUMO4_ENST00000395296.1_Start_Codon_SNP_p.M1V|IZUMO4_ENST00000395307.2_Start_Codon_SNP_p.M1V|MOB3A_ENST00000357066.3_5'Flank	NM_001039846.1	NP_001034935.1	Q1ZYL8	IZUM4_HUMAN	IZUMO family member 4	1						extracellular region (GO:0005576)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	6						CGGGACGGGCATGGCCCTGCT	0.697											OREG0025135	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M1V		Atlas-SNP	.											.	IZUMO4	25	.	0			c.A1G						.						33.0	38.0	36.0					19																	2096945		2200	4294	6494	SO:0001582	initiator_codon_variant	113177	exon1			ACGGGCATGGCCC	BC014609	CCDS35499.1, CCDS42458.1	19p13.3	2014-02-17	2010-07-29	2010-07-29	ENSG00000099840	ENSG00000099840		"""-"""	26950	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 36"""	C19orf36		12975309, 19658160, 22957301	Standard	XM_005259480		Approved		uc002luw.1	Q1ZYL8	OTTHUMG00000141290	ENST00000395301.3:c.1A>G	chr19.hg19:g.2096945A>G	ENSP00000378712:p.Met1Val	39.0	0.0	9	32.0	5.0	NM_001039846	A7RA93|A7RA94|Q6UXA2|Q96FT6|Q96L02	Missense_Mutation	SNP	ENST00000395301.3	hg19	CCDS42458.1	.	.	.	.	.	.	.	.	.	.	A	12.08	1.831968	0.32421	.	.	ENSG00000099840	ENST00000395307;ENST00000300960;ENST00000395296;ENST00000395301	T;T;T;T	0.34275	1.77;1.82;1.37;1.81	4.19	4.19	0.49359	.	.	.	.	.	T	0.39886	0.1095	.	.	.	0.80722	D	1	P;P	0.51933	0.949;0.949	P;P	0.47251	0.542;0.542	T	0.39482	-0.9612	8	0.87932	D	0	-34.1497	10.1825	0.42977	1.0:0.0:0.0:0.0	.	1;1	A7RA93;Q1ZYL8	.;IZUM4_HUMAN	V	48;1;1;1	ENSP00000378718:M48V;ENSP00000300960:M1V;ENSP00000378709:M1V;ENSP00000378712:M1V	ENSP00000300960:M1V	M	+	1	0	IZUMO4	2047945	0.997000	0.39634	1.000000	0.80357	0.280000	0.26924	1.498000	0.35660	1.835000	0.53391	0.379000	0.24179	ATG	.	.		0.697	IZUMO4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280536.3	NM_052878	Missense_Mutation
GIPC3	126326	hgsc.bcm.edu	37	19	3586866	3586866	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:3586866A>G	ENST00000322315.5	+	3	511	c.466A>G	c.(466-468)Agc>Ggc	p.S156G		NM_133261.2	NP_573568.1	Q8TF64	GIPC3_HUMAN	GIPC PDZ domain containing family, member 3	156	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.									breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0025)|STAD - Stomach adenocarcinoma(1328;0.18)		CGTGGGTGACAGCATCGAAGC	0.632											OREG0025154	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S156G		Atlas-SNP	.											.	GIPC3	27	.	0			c.A466G						.						54.0	50.0	51.0					19																	3586866		2202	4300	6502	SO:0001583	missense	126326	exon3			GGTGACAGCATCG	AB073738	CCDS32871.1	19p13.3	2011-11-29				ENSG00000179855			18183	protein-coding gene	gene with protein product		608792	"""chromosome 19 open reading frame 64"", ""deafness, autosomal recessive 72"", ""deafness, autosomal recessive 15"""	C19orf64, DFNB72, DFNB15		11836571, 21326233	Standard	NM_133261		Approved	DFNB95	uc002lyd.4	Q8TF64		ENST00000322315.5:c.466A>G	chr19.hg19:g.3586866A>G	ENSP00000319254:p.Ser156Gly	172.0	0.0	612	113.0	5.0	NM_133261	O75227	Missense_Mutation	SNP	ENST00000322315.5	hg19	CCDS32871.1	.	.	.	.	.	.	.	.	.	.	A	16.72	3.200602	0.58126	.	.	ENSG00000179855	ENST00000322315	T	0.27402	1.67	4.45	4.45	0.53987	PDZ/DHR/GLGF (4);	0.147777	0.64402	D	0.000010	T	0.23410	0.0566	L	0.27053	0.805	0.32532	N	0.534849	P	0.36753	0.568	B	0.36959	0.237	T	0.35076	-0.9803	10	0.52906	T	0.07	-40.31	12.565	0.56304	1.0:0.0:0.0:0.0	.	156	Q8TF64	GIPC3_HUMAN	G	156	ENSP00000319254:S156G	ENSP00000319254:S156G	S	+	1	0	GIPC3	3537866	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	5.989000	0.70587	1.641000	0.50575	0.459000	0.35465	AGC	.	.		0.632	GIPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394577.1	NM_133261	
APBA3	9546	hgsc.bcm.edu	37	19	3754233	3754233	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:3754233G>A	ENST00000316757.3	-	4	922	c.722C>T	c.(721-723)aCg>aTg	p.T241M	AC005954.3_ENST00000591962.1_RNA|AC005954.4_ENST00000586503.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	241	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCCATGCGCGTGCTGGTGGG	0.716																																					p.T241M		Atlas-SNP	.											.	APBA3	28	.	0			c.C722T						.																																			SO:0001583	missense	9546	exon4			ATGCGCGTGCTGG	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"""X11-like 2"""	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.722C>T	chr19.hg19:g.3754233G>A	ENSP00000315136:p.Thr241Met	76.0	0.0		69.0	4.0	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	hg19	CCDS12110.1	.	.	.	.	.	.	.	.	.	.	G	9.472	1.095827	0.20552	.	.	ENSG00000011132	ENST00000316757	T	0.23147	1.92	4.63	3.59	0.41128	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.304109	0.29987	N	0.010684	T	0.21062	0.0507	L	0.55743	1.74	0.34727	D	0.729309	P	0.36110	0.537	B	0.30251	0.113	T	0.30822	-0.9965	10	0.59425	D	0.04	.	8.4739	0.33001	0.204:0.0:0.796:0.0	.	241	O96018	APBA3_HUMAN	M	241	ENSP00000315136:T241M	ENSP00000315136:T241M	T	-	2	0	APBA3	3705233	0.015000	0.18098	0.633000	0.29310	0.212000	0.24457	1.436000	0.34980	0.927000	0.37143	0.462000	0.41574	ACG	.	.		0.716	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
PLIN5	440503	hgsc.bcm.edu	37	19	4531823	4531823	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:4531823C>T	ENST00000381848.3	-	3	152	c.72G>A	c.(70-72)caG>caA	p.Q24Q	CTB-50L17.14_ENST00000586020.1_Missense_Mutation_p.S42N	NM_001013706.2	NP_001013728.2	Q00G26	PLIN5_HUMAN	perilipin 5	24	Essential for lipid droplet targeting. {ECO:0000250}.|Interaction with LIPE. {ECO:0000250}.				lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|mitochondrion localization (GO:0051646)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of lipase activity (GO:0060192)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of triglyceride catabolic process (GO:0010897)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of lipase activity (GO:0060193)|positive regulation of lipid storage (GO:0010884)|positive regulation of sequestering of triglyceride (GO:0010890)|positive regulation of triglyceride biosynthetic process (GO:0010867)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)				endometrium(4)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10						CCACCACACGCTGCACCACGT	0.677																																					p.Q24Q		Atlas-SNP	.											.	PLIN5	27	.	0			c.G72A						.						8.0	11.0	10.0					19																	4531823		2038	4140	6178	SO:0001819	synonymous_variant	440503	exon3			CACACGCTGCACC	DQ839131	CCDS42473.1	19p13.3	2009-08-12			ENSG00000214456	ENSG00000214456		"""Perilipins"""	33196	protein-coding gene	gene with protein product	"""lipid storage droplet protein 5"""	613248				17234449, 19638644	Standard	NM_001013706		Approved	LSDP5, LSDA5, OXPAT, MLDP	uc002mas.3	Q00G26		ENST00000381848.3:c.72G>A	chr19.hg19:g.4531823C>T		88.0	0.0		80.0	5.0	NM_001013706	A2RRC1|Q6ZS68	Silent	SNP	ENST00000381848.3	hg19	CCDS42473.1																																																																																			.	.		0.677	PLIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458647.1	NM_001013706	
DPP9	91039	hgsc.bcm.edu	37	19	4694679	4694679	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:4694679C>A	ENST00000598800.1	-	14	1928	c.1423G>T	c.(1423-1425)Ggg>Tgg	p.G475W	DPP9_ENST00000594671.1_Missense_Mutation_p.G475W|DPP9_ENST00000597849.1_Missense_Mutation_p.G504W|DPP9_ENST00000262960.9_Missense_Mutation_p.G504W			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	475						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)	p.G583W(1)		cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		TCACCTTCCCCGGGGCTGAAG	0.552																																					p.G504W		Atlas-SNP	.											DPP9,NS,carcinoma,0,1	DPP9	59	.	1	Substitution - Missense(1)	lung(1)	c.G1510T						.						26.0	29.0	28.0					19																	4694679		2027	4171	6198	SO:0001583	missense	91039	exon13			CTTCCCCGGGGCT	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"""dipeptidylpeptidase 9"""				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.1423G>T	chr19.hg19:g.4694679C>A	ENSP00000469603:p.Gly475Trp	73.0	0.0		74.0	3.0	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Missense_Mutation	SNP	ENST00000598800.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.72	1.723574	0.30593	.	.	ENSG00000142002	ENST00000357909;ENST00000381797;ENST00000262960	T	0.34072	1.38	3.76	-1.36	0.09085	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	1.401490	0.04391	N	0.362400	T	0.45196	0.1330	L	0.43152	1.355	0.09310	N	1	D;D	0.71674	0.986;0.998	P;D	0.65573	0.906;0.936	T	0.29912	-0.9996	10	0.72032	D	0.01	-8.9261	2.0833	0.03640	0.1261:0.3911:0.1243:0.3585	.	475;504	Q86TI2;Q1ZZB8	DPP9_HUMAN;.	W	583;445;504	ENSP00000262960:G504W	ENSP00000262960:G504W	G	-	1	0	DPP9	4645679	0.000000	0.05858	0.210000	0.23637	0.595000	0.36748	-0.178000	0.09782	-0.704000	0.05042	-1.134000	0.01955	GGG	.	.		0.552	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2		
FEM1A	55527	hgsc.bcm.edu	37	19	4792908	4792908	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:4792908T>C	ENST00000269856.3	+	1	1181	c.1042T>C	c.(1042-1044)Tat>Cat	p.Y348H	AC005523.2_ENST00000601192.1_RNA|AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000596170.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	348					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		GGTCCTGGCCTATGACTATTC	0.642																																					p.Y348H		Atlas-SNP	.											.	FEM1A	41	.	0			c.T1042C						.						36.0	41.0	39.0					19																	4792908		2203	4297	6500	SO:0001583	missense	55527	exon1			CTGGCCTATGACT	BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"""Ankyrin repeat domain containing"""	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.1042T>C	chr19.hg19:g.4792908T>C	ENSP00000269856:p.Tyr348His	81.0	0.0		72.0	5.0	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Missense_Mutation	SNP	ENST00000269856.3	hg19	CCDS12135.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.943645	0.73672	.	.	ENSG00000141965	ENST00000269856	T	0.74947	-0.89	4.73	4.73	0.59995	.	0.000000	0.64402	U	0.000004	D	0.88362	0.6416	M	0.92923	3.36	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	D	0.89148	0.3521	10	0.33940	T	0.23	-6.4772	14.231	0.65892	0.0:0.0:0.0:1.0	.	348	Q9BSK4	FEM1A_HUMAN	H	348	ENSP00000269856:Y348H	ENSP00000269856:Y348H	Y	+	1	0	FEM1A	4743908	1.000000	0.71417	0.988000	0.46212	0.991000	0.79684	7.856000	0.86956	1.768000	0.52137	0.402000	0.26972	TAT	.	.		0.642	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1		
DENND1C	79958	hgsc.bcm.edu	37	19	6470311	6470311	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:6470311G>T	ENST00000381480.2	-	18	1469	c.1357C>A	c.(1357-1359)Cgc>Agc	p.R453S	DENND1C_ENST00000543576.1_Missense_Mutation_p.R409S	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	453					positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						CTCACCGAGCGGTACATGTTC	0.592																																					p.R453S		Atlas-SNP	.											.	DENND1C	93	.	0			c.C1357A						.						43.0	48.0	47.0					19																	6470311		2058	4190	6248	SO:0001583	missense	79958	exon18			CCGAGCGGTACAT	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"""DENN/MADD domain containing"""	26225	protein-coding gene	gene with protein product		613634	"""family with sequence similarity 31, member C"""	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.1357C>A	chr19.hg19:g.6470311G>T	ENSP00000370889:p.Arg453Ser	143.0	0.0		123.0	5.0	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	hg19	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.738879	0.49045	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.11277	2.97;2.79	4.99	4.99	0.66335	.	0.192145	0.32703	N	0.005751	T	0.13114	0.0318	L	0.42245	1.32	0.35958	D	0.834372	B	0.33919	0.432	B	0.39379	0.298	T	0.10428	-1.0630	10	0.87932	D	0	-26.9138	10.9417	0.47276	0.0:0.0:0.8125:0.1875	.	453	Q8IV53	DEN1C_HUMAN	S	453;409	ENSP00000370889:R453S;ENSP00000437805:R409S	ENSP00000370889:R453S	R	-	1	0	DENND1C	6421311	1.000000	0.71417	1.000000	0.80357	0.489000	0.33432	2.284000	0.43478	2.313000	0.78055	0.455000	0.32223	CGC	.	.		0.592	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898	
FBN3	84467	hgsc.bcm.edu	37	19	8161405	8161405	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:8161405C>T	ENST00000600128.1	-	44	5876	c.5462G>A	c.(5461-5463)tGc>tAc	p.C1821Y	FBN3_ENST00000270509.2_Missense_Mutation_p.C1821Y|FBN3_ENST00000601739.1_Missense_Mutation_p.C1821Y			Q75N90	FBN3_HUMAN	fibrillin 3	1821	EGF-like 28. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TGTGTCCATGCAGTCACCATG	0.577																																					p.C1821Y		Atlas-SNP	.											.	FBN3	300	.	0			c.G5462A						.						133.0	91.0	106.0					19																	8161405		2203	4300	6503	SO:0001583	missense	84467	exon43			TCCATGCAGTCAC		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.5462G>A	chr19.hg19:g.8161405C>T	ENSP00000470498:p.Cys1821Tyr	77.0	0.0		88.0	4.0	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	hg19	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.115218	0.77210	.	.	ENSG00000142449	ENST00000270509	D	0.99445	-5.91	3.63	3.63	0.41609	Epidermal growth factor-like (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.99722	0.9892	H	0.97783	4.075	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.96980	0.9714	10	0.87932	D	0	.	15.6411	0.77001	0.0:1.0:0.0:0.0	.	1821	Q75N90	FBN3_HUMAN	Y	1821	ENSP00000270509:C1821Y	ENSP00000270509:C1821Y	C	-	2	0	FBN3	8067405	1.000000	0.71417	0.998000	0.56505	0.892000	0.51952	5.339000	0.65953	1.695000	0.51148	0.655000	0.94253	TGC	.	.		0.577	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
OR1M1	125963	hgsc.bcm.edu	37	19	9204494	9204494	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:9204494A>G	ENST00000429566.3	+	1	640	c.574A>G	c.(574-576)Acc>Gcc	p.T192A		NM_001004456.1	NP_001004456.1	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M, member 1	192						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(4)|large_intestine(3)|lung(17)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						GTGCACGGACACCTCTGTGAA	0.562																																					p.T192A		Atlas-SNP	.											.	OR1M1	52	.	0			c.A574G						.						147.0	119.0	129.0					19																	9204494		2203	4300	6503	SO:0001583	missense	125963	exon1			ACGGACACCTCTG		CCDS32896.1	19p13.2	2013-09-20			ENSG00000170929	ENSG00000170929		"""GPCR / Class A : Olfactory receptors"""	8220	protein-coding gene	gene with protein product							Standard	NM_001004456		Approved	OR19-6	uc010xkj.2	Q8NGA1	OTTHUMG00000179930	ENST00000429566.3:c.574A>G	chr19.hg19:g.9204494A>G	ENSP00000401966:p.Thr192Ala	65.0	0.0		61.0	5.0	NM_001004456	B9EHA6|Q6IFJ3|Q96R91	Missense_Mutation	SNP	ENST00000429566.3	hg19	CCDS32896.1	.	.	.	.	.	.	.	.	.	.	g	9.467	1.094709	0.20471	.	.	ENSG00000170929	ENST00000305465;ENST00000429566	T	0.00235	8.48	3.8	1.66	0.24008	GPCR, rhodopsin-like superfamily (1);	0.103104	0.43110	N	0.000603	T	0.00241	0.0007	M	0.87097	2.86	0.09310	N	1	B	0.09022	0.002	B	0.14023	0.01	T	0.49437	-0.8940	10	0.87932	D	0	.	4.2253	0.10577	0.6002:0.0:0.0924:0.3074	.	192	Q8NGA1	OR1M1_HUMAN	A	195;192	ENSP00000401966:T192A	ENSP00000303195:T195A	T	+	1	0	OR1M1	9065494	0.001000	0.12720	0.014000	0.15608	0.002000	0.02628	1.365000	0.34182	0.157000	0.19338	-0.289000	0.09944	ACC	.	.		0.562	OR1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448993.1		
ZNF317	57693	hgsc.bcm.edu	37	19	9271853	9271853	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:9271853T>C	ENST00000247956.6	+	7	1837	c.1532T>C	c.(1531-1533)tTc>tCc	p.F511S	ZNF317_ENST00000360385.3_Missense_Mutation_p.F479S	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	511					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						GGCAAGGCCTTCAGGAACCAG	0.552																																					p.F511S		Atlas-SNP	.											.	ZNF317	61	.	0			c.T1532C						.						81.0	68.0	72.0					19																	9271853		2203	4300	6503	SO:0001583	missense	57693	exon7			AGGCCTTCAGGAA	AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"""Zinc fingers, C2H2-type"", ""-"""	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.1532T>C	chr19.hg19:g.9271853T>C	ENSP00000247956:p.Phe511Ser	65.0	0.0		70.0	5.0	NM_020933	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	Missense_Mutation	SNP	ENST00000247956.6	hg19	CCDS12210.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.444134	0.63067	.	.	ENSG00000130803	ENST00000247956;ENST00000360385	T;T	0.44482	0.92;0.92	2.72	2.72	0.32119	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44285	D	0.000478	T	0.63510	0.2517	M	0.87971	2.92	0.37440	D	0.91439	D;D	0.89917	1.0;1.0	D;D	0.87578	0.986;0.998	T	0.70439	-0.4871	10	0.87932	D	0	-25.5393	7.2844	0.26330	0.0:0.0:0.0:1.0	.	479;511	Q96PQ6-2;Q96PQ6	.;ZN317_HUMAN	S	511;479	ENSP00000247956:F511S;ENSP00000353554:F479S	ENSP00000247956:F511S	F	+	2	0	ZNF317	9132853	0.825000	0.29262	0.386000	0.26170	0.754000	0.42855	2.301000	0.43628	1.502000	0.48669	0.482000	0.46254	TTC	.	.		0.552	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933	
OLFM2	93145	hgsc.bcm.edu	37	19	9968053	9968053	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:9968053G>T	ENST00000264833.4	-	4	651	c.466C>A	c.(466-468)Ctc>Atc	p.L156I	OLFM2_ENST00000590841.1_Missense_Mutation_p.L78I	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	156					protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)				breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						CTGCCGGAGAGATTCCTCACC	0.632																																					p.L156I		Atlas-SNP	.											.	OLFM2	42	.	0			c.C466A						.						104.0	82.0	90.0					19																	9968053		2203	4300	6503	SO:0001583	missense	93145	exon4			CGGAGAGATTCCT	AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"""noelin 2"""						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.466C>A	chr19.hg19:g.9968053G>T	ENSP00000264833:p.Leu156Ile	89.0	0.0		62.0	4.0	NM_058164	Q6IMJ3|Q96FC2	Missense_Mutation	SNP	ENST00000264833.4	hg19	CCDS12221.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.039488	0.55003	.	.	ENSG00000105088	ENST00000264833	D	0.90504	-2.68	3.84	3.84	0.44239	.	0.000000	0.64402	D	0.000002	D	0.89192	0.6645	L	0.47016	1.485	0.54753	D	0.999987	P	0.45044	0.849	P	0.47941	0.562	D	0.88086	0.2810	9	.	.	.	.	13.3045	0.60345	0.0:0.0:1.0:0.0	.	156	O95897	NOE2_HUMAN	I	156	ENSP00000264833:L156I	.	L	-	1	0	OLFM2	9829053	1.000000	0.71417	0.979000	0.43373	0.145000	0.21501	6.403000	0.73264	1.988000	0.58038	0.462000	0.41574	CTC	.	.		0.632	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1		
KEAP1	9817	hgsc.bcm.edu	37	19	10610159	10610159	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:10610159G>T	ENST00000171111.5	-	2	1098	c.551C>A	c.(550-552)gCc>gAc	p.A184D	KEAP1_ENST00000393623.2_Missense_Mutation_p.A184D|KEAP1_ENST00000588024.1_5'UTR	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	184	BACK.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GATGCCGATGGCATTGCTGGG	0.582																																					p.A184D		Atlas-SNP	.											.	KEAP1	182	.	0			c.C551A						.						116.0	93.0	101.0					19																	10610159		2203	4300	6503	SO:0001583	missense	9817	exon2			CCGATGGCATTGC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.551C>A	chr19.hg19:g.10610159G>T	ENSP00000171111:p.Ala184Asp	93.0	0.0		88.0	5.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.586878	0.86851	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.72282	-0.64;-0.64	4.81	4.81	0.61882	BTB/Kelch-associated (1);	0.052992	0.85682	D	0.000000	D	0.82618	0.5076	M	0.71036	2.16	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.85078	0.0944	10	0.87932	D	0	.	15.3825	0.74669	0.0:0.0:1.0:0.0	.	184	Q14145	KEAP1_HUMAN	D	184	ENSP00000171111:A184D;ENSP00000377245:A184D	ENSP00000171111:A184D	A	-	2	0	KEAP1	10471159	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.017000	0.57167	2.232000	0.73038	0.561000	0.74099	GCC	.	.		0.582	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289	
ZNF653	115950	hgsc.bcm.edu	37	19	11606896	11606896	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:11606896A>G	ENST00000293771.5	-	3	564	c.428T>C	c.(427-429)cTg>cCg	p.L143P	ZNF653_ENST00000593191.1_5'UTR|CTC-398G3.6_ENST00000585656.1_Missense_Mutation_p.W114R	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	143					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						TAGCTCCGCCAGGTGCGGCTC	0.642																																					p.L143P	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											.	ZNF653	48	.	0			c.T428C						.						110.0	77.0	88.0					19																	11606896		2203	4300	6503	SO:0001583	missense	115950	exon3			TCCGCCAGGTGCG	AY072704	CCDS12261.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"""	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.428T>C	chr19.hg19:g.11606896A>G	ENSP00000293771:p.Leu143Pro	80.0	0.0		74.0	4.0	NM_138783	Q96AS7	Missense_Mutation	SNP	ENST00000293771.5	hg19	CCDS12261.1	.	.	.	.	.	.	.	.	.	.	A	16.46	3.128368	0.56721	.	.	ENSG00000161914	ENST00000293771	T	0.22336	1.96	4.52	4.52	0.55395	.	0.163743	0.41396	D	0.000889	T	0.27134	0.0665	L	0.29908	0.895	0.80722	D	1	D	0.57899	0.981	P	0.55161	0.77	T	0.03148	-1.1067	10	0.87932	D	0	-19.5122	12.9624	0.58466	1.0:0.0:0.0:0.0	.	143	Q96CK0	ZN653_HUMAN	P	143	ENSP00000293771:L143P	ENSP00000293771:L143P	L	-	2	0	ZNF653	11467896	1.000000	0.71417	0.899000	0.35326	0.133000	0.20885	7.612000	0.82975	1.912000	0.55364	0.459000	0.35465	CTG	.	.		0.642	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
BEST2	54831	hgsc.bcm.edu	37	19	12866497	12866497	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:12866497T>C	ENST00000549706.1	+	7	1107	c.783T>C	c.(781-783)gcT>gcC	p.A261A	BEST2_ENST00000042931.1_Silent_p.A261A|BEST2_ENST00000553030.1_Silent_p.A261A			Q8NFU1	BEST2_HUMAN	bestrophin 2	261					chloride transmembrane transport (GO:1902476)|membrane depolarization (GO:0051899)|sensory perception of smell (GO:0007608)	chloride channel complex (GO:0034707)|cilium (GO:0005929)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	12						TGGACCCGGCTCAGGGTTACA	0.607																																					p.A261A		Atlas-SNP	.											.	BEST2	35	.	0			c.T783C						.						93.0	98.0	96.0					19																	12866497		2048	4227	6275	SO:0001819	synonymous_variant	54831	exon6			CCCGGCTCAGGGT	AF440756	CCDS42506.1	19p13.13	2014-08-12	2006-10-18	2006-10-18	ENSG00000039987	ENSG00000039987		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17107	protein-coding gene	gene with protein product		607335	"""vitelliform macular dystrophy 2-like 1"""	VMD2L1		12032738, 16912113	Standard	NM_017682		Approved	FLJ20132	uc002mux.3	Q8NFU1	OTTHUMG00000169293	ENST00000549706.1:c.783T>C	chr19.hg19:g.12866497T>C		168.0	0.0		150.0	7.0	NM_017682	Q53YQ8|Q9NXP0	Silent	SNP	ENST00000549706.1	hg19	CCDS42506.1																																																																																			.	.		0.607	BEST2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403343.1	NM_017682	
CC2D1A	54862	hgsc.bcm.edu	37	19	14024289	14024289	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:14024289G>A	ENST00000318003.7	+	6	827	c.586G>A	c.(586-588)Gcc>Acc	p.A196T	CC2D1A_ENST00000589606.1_Missense_Mutation_p.A196T	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	196	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)			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)			GCCGCCAGTGGCCATAGGAAA	0.617																																					p.A196T		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G586A						.						35.0	44.0	41.0					19																	14024289		2009	4157	6166	SO:0001583	missense	54862	exon6			CCAGTGGCCATAG	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.586G>A	chr19.hg19:g.14024289G>A	ENSP00000313601:p.Ala196Thr	139.0	0.0		120.0	6.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	hg19	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.085832	0.55861	.	.	ENSG00000132024	ENST00000318003;ENST00000254346;ENST00000389233	T	0.26660	1.72	5.2	5.2	0.72013	.	0.058980	0.64402	D	0.000003	T	0.35595	0.0937	M	0.79011	2.435	0.80722	D	1	B;B	0.27351	0.117;0.176	B;B	0.27380	0.043;0.079	T	0.30119	-0.9989	10	0.72032	D	0.01	-15.0001	17.4931	0.87710	0.0:0.0:1.0:0.0	.	196;196	Q6P1N0-2;Q6P1N0	.;C2D1A_HUMAN	T	196;34;171	ENSP00000313601:A196T	ENSP00000254346:A34T	A	+	1	0	CC2D1A	13885289	1.000000	0.71417	0.965000	0.40720	0.096000	0.18686	6.122000	0.71608	2.425000	0.82216	0.462000	0.41574	GCC	.	.		0.617	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
LPHN1	22859	hgsc.bcm.edu	37	19	14274128	14274128	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:14274128G>T	ENST00000340736.6	-	6	797	c.500C>A	c.(499-501)cCg>cAg	p.P167Q	LPHN1_ENST00000591528.1_5'UTR|LPHN1_ENST00000361434.3_Missense_Mutation_p.P162Q|CTB-55O6.12_ENST00000592086.1_RNA|CTB-55O6.12_ENST00000588387.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	167	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CGCCTGCAGCGGGTCCTTGCA	0.652																																					p.P167Q		Atlas-SNP	.											.	LPHN1	107	.	0			c.C500A						.						41.0	34.0	36.0					19																	14274128		2202	4300	6502	SO:0001583	missense	22859	exon6			TGCAGCGGGTCCT	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"""-"", ""GPCR / Class B : Orphans"""	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.500C>A	chr19.hg19:g.14274128G>T	ENSP00000340688:p.Pro167Gln	135.0	0.0		77.0	4.0	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	hg19	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.549032	0.86127	.	.	ENSG00000072071	ENST00000340736;ENST00000361434	D;D	0.89810	-2.57;-2.57	5.06	5.06	0.68205	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.95698	0.8601	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.96704	0.9520	10	0.87932	D	0	.	15.9461	0.79796	0.0:0.0:1.0:0.0	.	162;167	O94910-2;O94910	.;LPHN1_HUMAN	Q	167;162	ENSP00000340688:P167Q;ENSP00000355328:P162Q	ENSP00000340688:P167Q	P	-	2	0	LPHN1	14135128	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	9.783000	0.99037	2.347000	0.79759	0.655000	0.94253	CCG	.	.		0.652	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921	
NOTCH3	4854	hgsc.bcm.edu	37	19	15297800	15297800	+	Splice_Site	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:15297800C>A	ENST00000263388.2	-	12	1916		c.e12-1			NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3						forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CAGTTCACACCTAGGGGCCAG	0.587																																					.		Atlas-SNP	.											.	NOTCH3	340	.	0			c.1841-1G>T						.						77.0	55.0	63.0					19																	15297800		2203	4300	6503	SO:0001630	splice_region_variant	4854	exon13			TCACACCTAGGGG	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.1841-1G>T	chr19.hg19:g.15297800C>A		51.0	0.0		49.0	4.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Splice_Site	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.072292	0.55646	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	.	.	.	4.52	4.52	0.55395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3814	0.83462	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NOTCH3	15158800	1.000000	0.71417	0.997000	0.53966	0.545000	0.35147	7.670000	0.83925	2.219000	0.72066	0.655000	0.94253	.	.	.		0.587	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	Intron
SIN3B	23309	hgsc.bcm.edu	37	19	16977294	16977294	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:16977294A>G	ENST00000248054.5	+	12	1754	c.1733A>G	c.(1732-1734)aAc>aGc	p.N578S	SIN3B_ENST00000379803.1_Missense_Mutation_p.N610S|SIN3B_ENST00000595541.1_Missense_Mutation_p.N168S					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						CAGGCTGTGAACTTCAAGCAG	0.592																																					p.N610S		Atlas-SNP	.											.	SIN3B	90	.	0			c.A1829G						.						156.0	111.0	126.0					19																	16977294		2203	4300	6503	SO:0001583	missense	23309	exon13			CTGTGAACTTCAA	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"""SIN3 homolog B, transcription regulator (yeast)"", ""SIN3 transcription regulator homolog B (yeast)"""			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.1733A>G	chr19.hg19:g.16977294A>G	ENSP00000248054:p.Asn578Ser	74.0	0.0		92.0	4.0	NM_015260		Missense_Mutation	SNP	ENST00000248054.5	hg19		.	.	.	.	.	.	.	.	.	.	A	23.5	4.426872	0.83667	.	.	ENSG00000127511	ENST00000379803;ENST00000248054	T;T	0.43294	0.95;0.95	4.96	4.96	0.65561	.	0.098476	0.64402	D	0.000001	T	0.56499	0.1989	M	0.63169	1.94	0.80722	D	1	D;P;P	0.76494	0.999;0.832;0.938	P;P;P	0.62740	0.906;0.525;0.54	T	0.53063	-0.8491	10	0.20046	T	0.44	-13.1387	14.6166	0.68552	1.0:0.0:0.0:0.0	.	168;578;610	B7Z392;O75182-2;O75182	.;.;SIN3B_HUMAN	S	610;578	ENSP00000369131:N610S;ENSP00000248054:N578S	ENSP00000248054:N578S	N	+	2	0	SIN3B	16838294	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.097000	0.94193	1.850000	0.53721	0.402000	0.26972	AAC	.	.		0.592	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260	
BABAM1	29086	hgsc.bcm.edu	37	19	17384927	17384927	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:17384927G>A	ENST00000359435.4	+	5	670	c.477G>A	c.(475-477)ctG>ctA	p.L159L	CTD-2278I10.6_ENST00000596542.1_Silent_p.L81L|BABAM1_ENST00000598188.1_Silent_p.L159L|BABAM1_ENST00000595632.1_Intron|BABAM1_ENST00000601043.1_Silent_p.L159L|BABAM1_ENST00000447614.2_Silent_p.L159L|BABAM1_ENST00000448635.2_Intron	NM_001033549.1	NP_001028721.1	Q9NWV8	BABA1_HUMAN	BRISC and BRCA1 A complex member 1	159	VWFA-like.				chromatin modification (GO:0016568)|double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5						TGTCTGGCCTGACCTCCGACC	0.667																																					p.L159L		Atlas-SNP	.											.	BABAM1	14	.	0			c.G477A						.						59.0	68.0	65.0					19																	17384927		2064	4203	6267	SO:0001819	synonymous_variant	29086	exon5			TGGCCTGACCTCC	AK000578	CCDS46012.1, CCDS74310.1	19p13.11	2011-02-21	2011-02-21	2011-01-31	ENSG00000105393	ENSG00000105393			25008	protein-coding gene	gene with protein product	"""Mediator of Rap80 Interactions and Targeting 40 kD"", ""new component of the BRCA1 A complex"""	612766	"""chromosome 19 open reading frame 62"""	C19orf62		11042152	Standard	NM_001288756		Approved	FLJ20571, HSPC142, NBA1, MERIT40	uc002nfv.3	Q9NWV8		ENST00000359435.4:c.477G>A	chr19.hg19:g.17384927G>A		90.0	0.0		82.0	4.0	NM_014173	A8MQT0|B4DRY9|B4DVR1|Q6FIA0|Q9P018	Silent	SNP	ENST00000359435.4	hg19	CCDS46012.1																																																																																			.	.		0.667	BABAM1-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463471.1	NM_014173	
MAP1S	55201	hgsc.bcm.edu	37	19	17837556	17837556	+	Nonsense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:17837556C>T	ENST00000324096.4	+	5	1514	c.1363C>T	c.(1363-1365)Cga>Tga	p.R455*	MAP1S_ENST00000544059.2_Nonsense_Mutation_p.R429*|CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000597681.1_Intron	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	455	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						GAGGTTCCTGCGAGAGCCCGT	0.721																																					p.R455X		Atlas-SNP	.											.	MAP1S	74	.	0			c.C1363T						.						4.0	5.0	4.0					19																	17837556		2014	4009	6023	SO:0001587	stop_gained	55201	exon5			TTCCTGCGAGAGC	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"""chromosome 19 open reading frame 5"", ""VCY2 interacting protein 1"", ""BPY2 interacting protein 1"""	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.1363C>T	chr19.hg19:g.17837556C>T	ENSP00000325313:p.Arg455*	49.0	0.0		46.0	10.0	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Nonsense_Mutation	SNP	ENST00000324096.4	hg19	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.929511	0.92389	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	.	.	.	3.88	3.88	0.44766	.	0.000000	0.44097	D	0.000494	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.2846	8.9029	0.35505	0.2231:0.7769:0.0:0.0	.	.	.	.	X	455;429	.	ENSP00000325313:R455X	R	+	1	2	MAP1S	17698556	0.890000	0.30428	0.071000	0.20095	0.110000	0.19582	1.758000	0.38410	1.700000	0.51204	0.491000	0.48974	CGA	.	.		0.721	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174	
SLC5A5	6528	hgsc.bcm.edu	37	19	17988801	17988801	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:17988801T>C	ENST00000222248.3	+	7	1215	c.868T>C	c.(868-870)Ttc>Ctc	p.F290L		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	290					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)			NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						GGTCGGCCTGTTCCTGATCGT	0.622																																					p.F290L	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											.	SLC5A5	67	.	0			c.T868C						.						110.0	78.0	89.0					19																	17988801		2203	4300	6503	SO:0001583	missense	6528	exon7			GGCCTGTTCCTGA		CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"""Solute carriers"""	11040	protein-coding gene	gene with protein product		601843	"""solute carrier family 5 (sodium iodide symporter), member 5"""			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.868T>C	chr19.hg19:g.17988801T>C	ENSP00000222248:p.Phe290Leu	82.0	0.0		75.0	4.0	NM_000453	O43702|Q2M335|Q9NYB6	Missense_Mutation	SNP	ENST00000222248.3	hg19	CCDS12368.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.869649	0.51588	.	.	ENSG00000105641	ENST00000222248	D	0.86497	-2.13	4.87	-1.41	0.08941	.	0.401940	0.29218	N	0.012800	T	0.62085	0.2399	N	0.04373	-0.215	0.27072	N	0.963304	B	0.18166	0.026	B	0.21708	0.036	T	0.53301	-0.8458	10	0.09843	T	0.71	.	1.687	0.02844	0.2579:0.0774:0.2656:0.3991	.	290	Q92911	SC5A5_HUMAN	L	290	ENSP00000222248:F290L	ENSP00000222248:F290L	F	+	1	0	SLC5A5	17849801	0.988000	0.35896	0.963000	0.40424	0.928000	0.56348	0.889000	0.28282	-0.595000	0.05828	0.454000	0.30748	TTC	.	.		0.622	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1		
COMP	1311	hgsc.bcm.edu	37	19	18896349	18896349	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:18896349T>C	ENST00000222271.2	-	15	1720	c.1676A>G	c.(1675-1677)gAg>gGg	p.E559G	COMP_ENST00000542601.2_Missense_Mutation_p.E526G|COMP_ENST00000425807.1_Missense_Mutation_p.E506G	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	559	Mediates cell survival and induction of the IAP family of survival proteins.|TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CTGCACGATCTCCCTTCCCTG	0.642																																					p.E559G		Atlas-SNP	.											.	COMP	62	.	0			c.A1676G						.						82.0	84.0	83.0					19																	18896349		2203	4300	6503	SO:0001583	missense	1311	exon15			ACGATCTCCCTTC	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"""thrombospondin-5"""	600310	"""cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"""	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.1676A>G	chr19.hg19:g.18896349T>C	ENSP00000222271:p.Glu559Gly	136.0	0.0		156.0	7.0	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Missense_Mutation	SNP	ENST00000222271.2	hg19	CCDS12385.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.984908	0.93044	.	.	ENSG00000105664	ENST00000542601;ENST00000222271;ENST00000425807;ENST00000454701	D;D;D	0.97161	-4.27;-4.27;-4.27	4.6	4.6	0.57074	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.85682	U	0.000000	D	0.98585	0.9527	M	0.91717	3.235	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99552	1.0966	10	0.87932	D	0	-47.6512	12.7731	0.57432	0.0:0.0:0.0:1.0	.	506;559	B4DKJ3;P49747	.;COMP_HUMAN	G	526;559;506;546	ENSP00000439156:E526G;ENSP00000222271:E559G;ENSP00000403792:E506G	ENSP00000222271:E559G	E	-	2	0	COMP	18757349	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.552000	0.82192	1.705000	0.51264	0.397000	0.26171	GAG	.	.		0.642	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095	
DDX49	54555	hgsc.bcm.edu	37	19	19035101	19035101	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:19035101A>G	ENST00000247003.4	+	7	903	c.836A>G	c.(835-837)cAc>cGc	p.H279R	DDX49_ENST00000599156.1_3'UTR|AC002985.3_ENST00000596918.1_Intron|DDX49_ENST00000438170.2_Missense_Mutation_p.H172R	NM_019070.4	NP_061943.2	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	279	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	18			Epithelial(12;0.0289)			GTGGCTCTGCACTCCATGATG	0.627																																					p.H279R		Atlas-SNP	.											.	DDX49	37	.	0			c.A836G						.						95.0	56.0	69.0					19																	19035101		2203	4300	6503	SO:0001583	missense	54555	exon7			CTCTGCACTCCAT		CCDS12390.1	19p12	2008-02-05				ENSG00000105671		"""DEAD-boxes"""	18684	protein-coding gene	gene with protein product							Standard	NM_019070		Approved	FLJ10432	uc002nkq.2	Q9Y6V7		ENST00000247003.4:c.836A>G	chr19.hg19:g.19035101A>G	ENSP00000247003:p.His279Arg	188.0	0.0		145.0	6.0	NM_019070	E7ENA0|Q53FJ1|Q9BVQ8	Missense_Mutation	SNP	ENST00000247003.4	hg19	CCDS12390.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.302383	0.81136	.	.	ENSG00000105671	ENST00000247003;ENST00000438170	T;T	0.08102	3.13;3.13	5.03	5.03	0.67393	Helicase, C-terminal (3);	0.049846	0.85682	D	0.000000	T	0.38746	0.1052	M	0.93978	3.48	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.53041	-0.8494	10	0.87932	D	0	-22.6557	13.9201	0.63926	1.0:0.0:0.0:0.0	.	279;279	A8K7A1;Q9Y6V7	.;DDX49_HUMAN	R	279;172	ENSP00000247003:H279R;ENSP00000395377:H172R	ENSP00000247003:H279R	H	+	2	0	DDX49	18896101	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	8.927000	0.92846	1.899000	0.54978	0.402000	0.26972	CAC	.	.		0.627	DDX49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464593.1	NM_019070	
ZNF682	91120	hgsc.bcm.edu	37	19	20117129	20117129	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:20117129C>A	ENST00000397165.2	-	4	1342	c.1182G>T	c.(1180-1182)gaG>gaT	p.E394D	ZNF682_ENST00000595736.1_Missense_Mutation_p.E318D|ZNF682_ENST00000596019.1_Intron|ZNF682_ENST00000358523.5_Missense_Mutation_p.E362D|ZNF682_ENST00000397162.1_Missense_Mutation_p.E362D|ZNF682_ENST00000597972.1_Missense_Mutation_p.E400D	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	394					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						TGTAGGGTTTCTCTCCAGTGT	0.378																																					p.E394D		Atlas-SNP	.											ZNF682,NS,carcinoma,0,1	ZNF682	51	.	0			c.G1182T						.						62.0	67.0	65.0					19																	20117129		2127	4261	6388	SO:0001583	missense	91120	exon4			GGGTTTCTCTCCA	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"""Zinc fingers, C2H2-type"", ""-"""	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.1182G>T	chr19.hg19:g.20117129C>A	ENSP00000380351:p.Glu394Asp	33.0	0.0		45.0	2.0	NM_033196	B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	hg19	CCDS42533.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.383808	0.25031	.	.	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000341262;ENST00000358523	T;T;T	0.26810	1.71;1.71;1.71	1.09	-0.0727	0.13738	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18759	0.0450	L	0.33485	1.01	0.27686	N	0.946271	B	0.21520	0.057	B	0.30179	0.112	T	0.34304	-0.9834	9	0.72032	D	0.01	.	4.8624	0.13590	0.0:0.7293:0.0:0.2707	.	394	O95780	ZN682_HUMAN	D	394;362;63;362	ENSP00000380351:E394D;ENSP00000380348:E362D;ENSP00000351324:E362D	ENSP00000340236:E63D	E	-	3	2	ZNF682	19978129	0.998000	0.40836	0.897000	0.35233	0.885000	0.51271	0.420000	0.21263	0.488000	0.27723	0.491000	0.48974	GAG	.	.		0.378	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196	
ZNF486	90649	hgsc.bcm.edu	37	19	20308359	20308359	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:20308359C>A	ENST00000335117.8	+	4	897	c.840C>A	c.(838-840)acC>acA	p.T280T	CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	280					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						ACCCCTATACCCTTACTACAC	0.363																																					p.T280T		Atlas-SNP	.											.	ZNF486	74	.	0			c.C840A						.						48.0	52.0	51.0					19																	20308359		2150	4277	6427	SO:0001819	synonymous_variant	90649	exon4			CTATACCCTTACT	BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"""Zinc fingers, C2H2-type"", ""-"""	20807	protein-coding gene	gene with protein product			"""KRAB domain only 2"""	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.840C>A	chr19.hg19:g.20308359C>A		74.0	0.0		76.0	5.0	NM_052852	Q0VG00	Silent	SNP	ENST00000335117.8	hg19	CCDS46029.1																																																																																			.	.		0.363	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852	
ZNF208	7757	hgsc.bcm.edu	37	19	22156027	22156027	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:22156027A>G	ENST00000397126.4	-	4	1957	c.1809T>C	c.(1807-1809)caT>caC	p.H603H	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	603					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)				TCTCACCAGTATGAATTCTCT	0.363																																					p.H603H		Atlas-SNP	.											.	ZNF208	817	.	0			c.T1809C						.						51.0	54.0	53.0					19																	22156027		2088	4235	6323	SO:0001819	synonymous_variant	7757	exon4			ACCAGTATGAATT	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.1809T>C	chr19.hg19:g.22156027A>G		63.0	0.0		62.0	31.0	NM_007153		Silent	SNP	ENST00000397126.4	hg19	CCDS54240.1																																																																																			.	.		0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
ZNF91	7644	hgsc.bcm.edu	37	19	23542731	23542731	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:23542731G>T	ENST00000300619.7	-	4	3255	c.3050C>A	c.(3049-3051)aCt>aAt	p.T1017N	ZNF91_ENST00000397082.2_Missense_Mutation_p.T985N|ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	1017					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TTTCTCTCCAGTGTGCATCCT	0.383																																					p.T1017N		Atlas-SNP	.											.	ZNF91	349	.	0			c.C3050A						.						95.0	97.0	97.0					19																	23542731		2192	4296	6488	SO:0001583	missense	7644	exon4			TCTCCAGTGTGCA	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.3050C>A	chr19.hg19:g.23542731G>T	ENSP00000300619:p.Thr1017Asn	72.0	0.0		88.0	4.0	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	G	8.568	0.879416	0.17467	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.26067	1.76;1.76	1.47	-0.478	0.12093	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36524	0.0970	L	0.39147	1.195	0.27898	N	0.939069	D;D	0.76494	0.958;0.999	B;D	0.81914	0.368;0.995	T	0.25328	-1.0135	9	0.87932	D	0	.	8.2531	0.31739	0.0:0.3106:0.6894:0.0	.	985;1017	Q05481-2;Q05481	.;ZNF91_HUMAN	N	1017;985	ENSP00000300619:T1017N;ENSP00000380272:T985N	ENSP00000300619:T1017N	T	-	2	0	ZNF91	23334571	0.107000	0.21998	0.050000	0.19076	0.089000	0.18198	0.222000	0.17699	-0.184000	0.10567	0.175000	0.17021	ACT	.	.		0.383	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
ZNF675	171392	hgsc.bcm.edu	37	19	23836866	23836866	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:23836866C>T	ENST00000359788.4	-	4	1037	c.869G>A	c.(868-870)gGc>gAc	p.G290D	ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron|ZNF675_ENST00000600313.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	290					bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				AAAGGCTTTGCCACATTCTTC	0.378																																					p.G290D		Atlas-SNP	.											.,1	ZNF675	88	.	0			c.G869A						.						52.0	56.0	55.0					19																	23836866		2202	4297	6499	SO:0001583	missense	171392	exon4			GCTTTGCCACATT		CCDS32981.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	30768	protein-coding gene	gene with protein product	"""TRAF6 inhibitory zinc finger"""					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.869G>A	chr19.hg19:g.23836866C>T	ENSP00000352836:p.Gly290Asp	44.0	1.0		64.0	4.0	NM_138330	Q8N211	Missense_Mutation	SNP	ENST00000359788.4	hg19	CCDS32981.1	.	.	.	.	.	.	.	.	.	.	.	8.427	0.847732	0.17034	.	.	ENSG00000197372	ENST00000359788	T	0.07444	3.19	0.916	0.916	0.19373	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12178	0.0296	L	0.43646	1.37	0.31650	N	0.646979	D	0.54772	0.968	P	0.52159	0.691	T	0.15752	-1.0426	9	0.52906	T	0.07	.	8.5828	0.33640	0.0:1.0:0.0:0.0	.	290	Q8TD23	ZN675_HUMAN	D	290	ENSP00000352836:G290D	ENSP00000352836:G290D	G	-	2	0	ZNF675	23628706	0.024000	0.19004	0.307000	0.25127	0.307000	0.27823	-0.013000	0.12678	0.300000	0.22699	0.305000	0.20034	GGC	.	.		0.378	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330	
CEP89	84902	hgsc.bcm.edu	37	19	33370210	33370210	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:33370210T>C	ENST00000305768.5	-	19	2298	c.2210A>G	c.(2209-2211)cAg>cGg	p.Q737R	CTD-2085J24.4_ENST00000586628.2_lincRNA	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	737					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						GAGTGTGTCCTGGAGAAGTTC	0.517																																					p.Q737R		Atlas-SNP	.											.	CEP89	82	.	0			c.A2210G						.						170.0	166.0	167.0					19																	33370210		2203	4300	6503	SO:0001583	missense	84902	exon19			GTGTCCTGGAGAA	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.2210A>G	chr19.hg19:g.33370210T>C	ENSP00000306105:p.Gln737Arg	126.0	0.0		149.0	6.0	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	hg19	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	T	9.127	1.010514	0.19277	.	.	ENSG00000121289	ENST00000305768	T	0.29655	1.56	5.12	1.84	0.25277	.	0.275893	0.30118	N	0.010374	T	0.25005	0.0607	L	0.54323	1.7	0.21473	N	0.999676	B	0.09022	0.002	B	0.11329	0.006	T	0.22487	-1.0215	10	0.20519	T	0.43	-7.482	9.1166	0.36762	0.0:0.2351:0.0:0.7649	.	737	Q96ST8	CEP89_HUMAN	R	737	ENSP00000306105:Q737R	ENSP00000306105:Q737R	Q	-	2	0	CEP89	38062050	0.287000	0.24315	0.492000	0.27490	0.031000	0.12232	0.756000	0.26419	0.369000	0.24510	-0.379000	0.06801	CAG	.	.		0.517	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
WDR88	126248	hgsc.bcm.edu	37	19	33647326	33647326	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:33647326C>A	ENST00000355868.3	+	7	951	c.875C>A	c.(874-876)tCc>tAc	p.S292Y	WDR88_ENST00000361680.2_Missense_Mutation_p.S292Y	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	292										breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					TGTACAAGCTCCTGGGATAAA	0.478																																					p.S292Y		Atlas-SNP	.											.	WDR88	50	.	0			c.C875A						.						124.0	116.0	119.0					19																	33647326		2203	4300	6503	SO:0001583	missense	126248	exon7			CAAGCTCCTGGGA	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"""WD repeat domain containing"""	26999	protein-coding gene	gene with protein product			"""PQQ repeat and WD repeat domain containing"""	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.875C>A	chr19.hg19:g.33647326C>A	ENSP00000348129:p.Ser292Tyr	85.0	0.0		91.0	4.0	NM_173479	Q8NEF8	Missense_Mutation	SNP	ENST00000355868.3	hg19	CCDS12429.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.295518	0.81025	.	.	ENSG00000166359	ENST00000355868;ENST00000361680	T;T	0.74421	-0.84;-0.84	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.636153	0.16440	N	0.214330	D	0.90635	0.7063	H	0.94503	3.545	0.33014	D	0.52796	D	0.89917	1.0	D	0.97110	1.0	D	0.93738	0.7047	10	0.87932	D	0	.	18.2199	0.89898	0.0:1.0:0.0:0.0	.	292	Q6ZMY6	WDR88_HUMAN	Y	292	ENSP00000348129:S292Y;ENSP00000355148:S292Y	ENSP00000348129:S292Y	S	+	2	0	WDR88	38339166	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	5.550000	0.67268	2.639000	0.89480	0.555000	0.69702	TCC	.	.		0.478	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479	
ZNF302	55900	hgsc.bcm.edu	37	19	35173713	35173713	+	Missense_Mutation	SNP	C	C	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:35173713C>G	ENST00000446502.2	+	4	381	c.173C>G	c.(172-174)tCt>tGt	p.S58C	ZNF302_ENST00000507959.1_Missense_Mutation_p.S14C|ZNF302_ENST00000423823.2_Missense_Mutation_p.S14C|ZNF302_ENST00000505365.2_Missense_Mutation_p.S14C|ZNF302_ENST00000509528.1_Intron|ZNF302_ENST00000505242.1_Missense_Mutation_p.S14C|ZNF302_ENST00000457781.2_Missense_Mutation_p.S14C			Q9NR11	ZN302_HUMAN	zinc finger protein 302	14	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			ATAGACTTCTCTCATGAAGAG	0.438																																					p.S14C		Atlas-SNP	.											.	ZNF302	27	.	0			c.C41G						.						76.0	63.0	67.0					19																	35173713		1840	4053	5893	SO:0001583	missense	55900	exon3			ACTTCTCTCATGA	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"""Zinc fingers, C2H2-type"", ""-"""	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.173C>G	chr19.hg19:g.35173713C>G	ENSP00000396379:p.Ser58Cys	296.0	0.0		281.0	89.0	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	hg19		.	.	.	.	.	.	.	.	.	.	C	12.70	2.015761	0.35606	.	.	ENSG00000089335	ENST00000502743;ENST00000506901;ENST00000457781;ENST00000505242;ENST00000505163;ENST00000423823;ENST00000507959;ENST00000446502;ENST00000505365	T;T;T;T;T;T;T;T;T	0.02944	4.1;4.1;4.1;4.1;4.1;4.1;4.1;4.1;4.1	1.39	1.39	0.22231	.	.	.	.	.	T	0.16471	0.0396	M	0.92122	3.275	0.22112	N	0.999352	D;P;P	0.89917	1.0;0.833;0.895	D;P;P	0.79108	0.992;0.638;0.658	T	0.03175	-1.1064	9	0.87932	D	0	.	6.0849	0.19962	0.0:1.0:0.0:0.0	.	14;58;14	B4DMN2;E7EVR1;Q9NR11-2	.;.;.	C	14;14;14;14;14;14;14;58;14	ENSP00000423460:S14C;ENSP00000424292:S14C;ENSP00000391067:S14C;ENSP00000421028:S14C;ENSP00000421696:S14C;ENSP00000405219:S14C;ENSP00000421201:S14C;ENSP00000396379:S58C;ENSP00000423235:S14C	ENSP00000405219:S14C	S	+	2	0	ZNF302	39865553	0.034000	0.19679	0.998000	0.56505	0.921000	0.55340	0.870000	0.28010	0.737000	0.32582	0.313000	0.20887	TCT	.	.		0.438	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1		
CD22	933	hgsc.bcm.edu	37	19	35835730	35835730	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:35835730A>G	ENST00000085219.5	+	10	2101		c.e10-1		CD22_ENST00000544992.2_Splice_Site|CD22_ENST00000270311.6_Splice_Site|CD22_ENST00000341773.6_Splice_Site|MIR5196_ENST00000578146.1_RNA|CD22_ENST00000419549.2_Splice_Site|CD22_ENST00000594250.1_Splice_Site|CD22_ENST00000536635.2_Splice_Site	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule						cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			TTCTCCACCCAGATAGCCCGG	0.612																																					.	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.2036-2A>G						.						114.0	119.0	117.0					19																	35835730		2203	4300	6503	SO:0001630	splice_region_variant	933	exon10			CCACCCAGATAGC	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1643	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 2"""	107266	"""CD22 antigen"""			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.2036-1A>G	chr19.hg19:g.35835730A>G		82.0	0.0		78.0	4.0	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Splice_Site	SNP	ENST00000085219.5	hg19	CCDS12457.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.133854	0.37630	.	.	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992;ENST00000270311;ENST00000419549	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5374	0.50645	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CD22	40527570	0.996000	0.38824	0.932000	0.37286	0.434000	0.31775	4.138000	0.58017	1.995000	0.58328	0.383000	0.25322	.	.	.		0.612	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771	Intron
ZBTB32	27033	hgsc.bcm.edu	37	19	36206306	36206306	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:36206306C>A	ENST00000392197.2	+	3	1096	c.778C>A	c.(778-780)Cct>Act	p.P260T	KMT2B_ENST00000222270.7_5'Flank|KMT2B_ENST00000420124.1_5'Flank|KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000341701.1_5'Flank|ZBTB32_ENST00000262630.3_Missense_Mutation_p.P260T			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	260					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGGGGGCCAGCCTGCCCTGTG	0.672																																					p.P260T		Atlas-SNP	.											.	ZBTB32	33	.	0			c.C778A						.						41.0	44.0	43.0					19																	36206306		2201	4297	6498	SO:0001583	missense	27033	exon2			GGCCAGCCTGCCC	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16763	protein-coding gene	gene with protein product	"""repressor of GATA"""	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.778C>A	chr19.hg19:g.36206306C>A	ENSP00000376035:p.Pro260Thr	80.0	0.0		34.0	8.0	NM_014383	Q8WVP2	Missense_Mutation	SNP	ENST00000392197.2	hg19	CCDS12471.1	.	.	.	.	.	.	.	.	.	.	C	15.25	2.779130	0.49891	.	.	ENSG00000011590	ENST00000262630;ENST00000392197	T;T	0.09723	2.95;2.95	5.33	-0.725	0.11174	.	0.314536	0.23405	N	0.048535	T	0.06280	0.0162	L	0.27053	0.805	0.26342	N	0.977351	B	0.34103	0.437	B	0.34590	0.186	T	0.25882	-1.0119	10	0.48119	T	0.1	-0.6659	4.803	0.13307	0.0:0.5096:0.1541:0.3363	.	260	Q9Y2Y4	ZBT32_HUMAN	T	260	ENSP00000262630:P260T;ENSP00000376035:P260T	ENSP00000262630:P260T	P	+	1	0	ZBTB32	40898146	0.001000	0.12720	1.000000	0.80357	0.995000	0.86356	-0.165000	0.09968	0.203000	0.20529	0.655000	0.94253	CCT	.	.		0.672	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383	
ZNF461	92283	hgsc.bcm.edu	37	19	37134755	37134755	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:37134755T>C	ENST00000588268.1	-	5	469	c.242A>G	c.(241-243)aAa>aGa	p.K81R	ZNF461_ENST00000360357.4_Intron|ZNF461_ENST00000540605.2_5'Flank	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	81					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)			tccccaagttttccatgtacc	0.254																																					p.K81R		Atlas-SNP	.											.	ZNF461	73	.	0			c.A242G						.						96.0	83.0	87.0					19																	37134755		915	2073	2988	SO:0001583	missense	92283	exon5			CAAGTTTTCCATG	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.242A>G	chr19.hg19:g.37134755T>C	ENSP00000467931:p.Lys81Arg	96.0	0.0		92.0	4.0	NM_153257	A8K9W9|Q6VSF7|Q9ULZ8	Missense_Mutation	SNP	ENST00000588268.1	hg19	CCDS54257.1	.	.	.	.	.	.	.	.	.	.	T	7.933	0.740996	0.15642	.	.	ENSG00000197808	ENST00000396893;ENST00000396892	.	.	.	0.625	0.625	0.17665	.	.	.	.	.	T	0.22003	0.0530	N	0.12961	0.28	0.25117	N	0.990676	P	0.34587	0.458	B	0.39152	0.292	T	0.23655	-1.0182	7	0.33940	T	0.23	.	.	.	.	.	81	Q8TAF7	ZN461_HUMAN	R	81;16	.	ENSP00000380101:K16R	K	-	2	0	ZNF461	41826595	0.568000	0.26635	0.281000	0.24762	0.595000	0.36748	0.533000	0.23082	0.488000	0.27723	0.164000	0.16699	AAA	.	.		0.254	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257	
ZNF850	342892	hgsc.bcm.edu	37	19	37239944	37239944	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:37239944A>G	ENST00000591344.1	-	5	2156	c.1998T>C	c.(1996-1998)atT>atC	p.I666I	ZNF850_ENST00000589390.1_Intron	NM_001193552.1|NM_001267779.1	NP_001180481.1|NP_001254708.1	A8MQ14	ZN850_HUMAN	zinc finger protein 850	666					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										CACCAGTGTGAATTCTGTGAT	0.443																																					p.I666I		Atlas-SNP	.											.	ZNF850	14	.	0			c.T1998C						.																																			SO:0001819	synonymous_variant	342892	exon5			AGTGTGAATTCTG	BC052603	CCDS59379.1, CCDS74350.1	19q13.12	2013-01-08	2010-08-02	2010-08-02		ENSG00000267041		"""Zinc fingers, C2H2-type"", ""-"""	27994	protein-coding gene	gene with protein product			"""zinc finger protein 850 pseudogene"", ""zinc finger protein 850 (pseudogene)"""	ZNF850P		12477932	Standard	NM_001193552		Approved		uc010efc.3	A8MQ14		ENST00000591344.1:c.1998T>C	chr19.hg19:g.37239944A>G		23.0	0.0		18.0	4.0	NM_001193552		Silent	SNP	ENST00000591344.1	hg19	CCDS59379.1																																																																																			.	.		0.443	ZNF850-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453557.1	XM_001720258	
RYR1	6261	hgsc.bcm.edu	37	19	39016021	39016021	+	Missense_Mutation	SNP	G	G	T	rs369422480		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:39016021G>T	ENST00000359596.3	+	71	10505	c.10505G>T	c.(10504-10506)cGg>cTg	p.R3502L	RYR1_ENST00000355481.4_Missense_Mutation_p.R3497L|AC067969.1_ENST00000597015.1_RNA|RYR1_ENST00000360985.3_Missense_Mutation_p.R3502L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3502					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CGGGGGGACCGGTACTCTGTG	0.622																																					p.R3502L		Atlas-SNP	.											.	RYR1	708	.	0			c.G10505T						.						111.0	115.0	113.0					19																	39016021		2203	4300	6503	SO:0001583	missense	6261	exon71			GGGACCGGTACTC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.10505G>T	chr19.hg19:g.39016021G>T	ENSP00000352608:p.Arg3502Leu	102.0	0.0		98.0	4.0	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.355030	0.24512	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985;ENST00000538206	D;D;D	0.96967	-4.18;-4.19;-4.18	4.3	4.3	0.51218	.	0.000000	0.64402	U	0.000003	D	0.91415	0.7291	N	0.26042	0.785	0.46749	D	0.999187	B;B;B	0.25809	0.135;0.135;0.083	B;B;B	0.22753	0.041;0.041;0.018	D	0.88302	0.2950	10	0.18710	T	0.47	.	13.1415	0.59438	0.0:0.0:0.8396:0.1604	.	3502;3497;3502	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	L	3502;3497;3502;422	ENSP00000352608:R3502L;ENSP00000347667:R3497L;ENSP00000354254:R3502L	ENSP00000347667:R3497L	R	+	2	0	RYR1	43707861	1.000000	0.71417	1.000000	0.80357	0.324000	0.28378	7.503000	0.81632	2.379000	0.81126	0.655000	0.94253	CGG	.	.		0.622	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
IFNL1	282618	hgsc.bcm.edu	37	19	39788656	39788656	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:39788656T>C	ENST00000333625.2	+	3	399	c.302T>C	c.(301-303)gTc>gCc	p.V101A		NM_172140.1	NP_742152.1	Q8IU54	IFNL1_HUMAN	interferon, lambda 1	101					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of cell proliferation (GO:0008285)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of memory T cell differentiation (GO:0043381)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of immune response (GO:0050778)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-28 receptor complex (GO:0032002)	interleukin-28 receptor binding (GO:0032003)|receptor binding (GO:0005102)										ACGCTGAAGGTCCTGGAGGCC	0.642																																					p.V101A		Atlas-SNP	.											.	.	.	.	0			c.T302C						.						51.0	53.0	53.0					19																	39788656		2203	4300	6503	SO:0001583	missense	282618	exon3			TGAAGGTCCTGGA	AY129150	CCDS12531.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000182393	ENSG00000182393		"""Interferons"""	18363	protein-coding gene	gene with protein product		607403	"""interleukin 29"", ""interleukin 29 (interferon, lambda 1)"""	IL29			Standard	NM_172140		Approved	IL-29	uc002okv.3	Q8IU54		ENST00000333625.2:c.302T>C	chr19.hg19:g.39788656T>C	ENSP00000329991:p.Val101Ala	114.0	0.0		117.0	5.0	NM_172140	A0AV25|Q17R34	Missense_Mutation	SNP	ENST00000333625.2	hg19	CCDS12531.1	.	.	.	.	.	.	.	.	.	.	T	11.92	1.782812	0.31502	.	.	ENSG00000182393	ENST00000333625	T	0.48836	0.8	4.56	4.56	0.56223	.	0.000000	0.56097	D	0.000031	T	0.65739	0.2720	M	0.84326	2.69	0.09310	N	1	D	0.71674	0.998	D	0.66847	0.947	T	0.60439	-0.7263	10	0.87932	D	0	-17.9068	7.8105	0.29228	0.1857:0.0:0.0:0.8143	.	101	Q8IU54	IL29_HUMAN	A	101	ENSP00000329991:V101A	ENSP00000329991:V101A	V	+	2	0	IL29	44480496	0.988000	0.35896	0.219000	0.23793	0.069000	0.16628	1.541000	0.36126	1.843000	0.53566	0.260000	0.18958	GTC	.	.		0.642	IFNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463834.1	NM_172140	
FCGBP	8857	hgsc.bcm.edu	37	19	40433822	40433822	+	Silent	SNP	G	G	A	rs375117067		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:40433822G>A	ENST00000221347.6	-	2	454	c.447C>T	c.(445-447)ccC>ccT	p.P149P		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	149	IgGFc-binding.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CTGAGGTGCCGGGGGGTGTGA	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		19391	0.0		0.0	False		,,,				2504	0.001				p.P149P		Atlas-SNP	.											.	FCGBP	416	.	0			c.C447T						.	G		0,4406		0,0,2203	50.0	49.0	49.0		447	-8.3	0.0	19		49	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	FCGBP	NM_003890.2		0,3,6500	AA,AG,GG		0.0349,0.0,0.0231		149/5406	40433822	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	8857	exon2			GGTGCCGGGGGGT	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.447C>T	chr19.hg19:g.40433822G>A		82.0	0.0		60.0	4.0	NM_003890	O95784	Silent	SNP	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.		0.607	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PSMC4	5704	hgsc.bcm.edu	37	19	40480515	40480515	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:40480515T>C	ENST00000157812.2	+	5	752	c.554T>C	c.(553-555)cTc>cCc	p.L185P	PSMC4_ENST00000455878.2_Missense_Mutation_p.L154P	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	185				L -> V (in Ref. 4; AAC32612). {ECO:0000305}.	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)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|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)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					GAGCTCCCGCTCACGCATTTC	0.627																																					p.L185P	Colon(105;1478 1543 4034 6132 38638)	Atlas-SNP	.											.	PSMC4	48	.	0			c.T554C						.						55.0	59.0	58.0					19																	40480515		2203	4300	6503	SO:0001583	missense	5704	exon5			TCCCGCTCACGCA	U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9551	protein-coding gene	gene with protein product	"""protease 26S subunit 6"", ""Tat-binding protein 7"", ""MB67 interacting protein"""	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.554T>C	chr19.hg19:g.40480515T>C	ENSP00000157812:p.Leu185Pro	94.0	0.0		62.0	4.0	NM_006503	Q96FV5|Q9UBM3|Q9UEX3	Missense_Mutation	SNP	ENST00000157812.2	hg19	CCDS12547.1	.	.	.	.	.	.	.	.	.	.	t	15.52	2.856524	0.51376	.	.	ENSG00000013275	ENST00000157812;ENST00000455878	D;D	0.95622	-3.76;-3.76	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.98163	0.9393	M	0.93720	3.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99184	1.0868	10	0.87932	D	0	-5.5019	13.1587	0.59533	0.0:0.0:0.0:1.0	.	154;185	P43686-2;P43686	.;PRS6B_HUMAN	P	185;154	ENSP00000157812:L185P;ENSP00000413869:L154P	ENSP00000157812:L185P	L	+	2	0	PSMC4	45172355	1.000000	0.71417	0.042000	0.18584	0.068000	0.16541	6.066000	0.71185	1.986000	0.57962	0.459000	0.35465	CTC	.	.		0.627	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503	
CNTD2	79935	hgsc.bcm.edu	37	19	40732473	40732473	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:40732473A>G	ENST00000430325.2	-	1	124	c.76T>C	c.(76-78)Tct>Cct	p.S26P	CNTD2_ENST00000433940.1_Missense_Mutation_p.S26P|CNTD2_ENST00000513948.1_5'Flank	NM_024877.3	NP_079153.2	Q9H8S5	CNTD2_HUMAN	cyclin N-terminal domain containing 2	26					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					lung(1)|prostate(1)	2						TGCAAAGGAGAGGGCCTGGGG	0.706																																					p.S26P		Atlas-SNP	.											.	CNTD2	22	.	0			c.T76C						.						8.0	11.0	10.0					19																	40732473		2172	4249	6421	SO:0001583	missense	79935	exon1			AAGGAGAGGGCCT	AK023327	CCDS12551.1, CCDS12551.2	19q13.2	2014-07-03				ENSG00000105219			25805	protein-coding gene	gene with protein product	"""cyclin P"""					11237006	Standard	NM_024877		Approved	FLJ13265, CCNP	uc010xvi.2	Q9H8S5		ENST00000430325.2:c.76T>C	chr19.hg19:g.40732473A>G	ENSP00000396755:p.Ser26Pro	121.0	0.0		112.0	7.0	NM_024877	B4DX65	Missense_Mutation	SNP	ENST00000430325.2	hg19	CCDS12551.2	.	.	.	.	.	.	.	.	.	.	A	13.84	2.358236	0.41801	.	.	ENSG00000105219	ENST00000430325;ENST00000433940	T	0.35236	1.32	4.31	3.21	0.36854	.	0.988702	0.08230	N	0.977802	T	0.33731	0.0873	.	.	.	0.09310	N	1	P	0.50943	0.94	P	0.44860	0.462	T	0.21759	-1.0236	9	0.62326	D	0.03	-25.408	6.5989	0.22689	0.7871:0.0:0.0:0.2129	.	26	B4DX65	.	P	26	ENSP00000396755:S26P	ENSP00000221818:S26P	S	-	1	0	CNTD2	45424313	0.000000	0.05858	0.008000	0.14137	0.093000	0.18481	-0.211000	0.09332	1.938000	0.56188	0.459000	0.35465	TCT	.	.		0.706	CNTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360785.1	NM_024877	
AKT2	208	hgsc.bcm.edu	37	19	40761108	40761108	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:40761108T>C	ENST00000392038.2	-	4	542	c.244A>G	c.(244-246)Aca>Gca	p.T82A	AKT2_ENST00000424901.1_Missense_Mutation_p.T82A|AKT2_ENST00000311278.6_Missense_Mutation_p.T82A|AKT2_ENST00000579047.1_Missense_Mutation_p.T20A	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2	82	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			TCGATGACTGTGGTCCACTGC	0.602			A		"""ovarian, pancreatic """																																p.T82A		Atlas-SNP	.		Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	.	AKT2	53	.	0			c.A244G						.						135.0	130.0	131.0					19																	40761108		2203	4300	6503	SO:0001583	missense	208	exon4			TGACTGTGGTCCA	M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	392	protein-coding gene	gene with protein product		164731				1409633	Standard	NM_001626		Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.244A>G	chr19.hg19:g.40761108T>C	ENSP00000375892:p.Thr82Ala	138.0	0.0		121.0	6.0	NM_001626	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Missense_Mutation	SNP	ENST00000392038.2	hg19	CCDS12552.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.284485	0.40394	.	.	ENSG00000105221	ENST00000392038;ENST00000358335;ENST00000424901;ENST00000311278;ENST00000537834;ENST00000452077;ENST00000392037;ENST00000416362;ENST00000423127;ENST00000456441;ENST00000416994	T;T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	4.71	4.71	0.59529	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.107611	0.64402	D	0.000009	T	0.62332	0.2419	M	0.90542	3.125	0.80722	D	1	B;B;P;B	0.39480	0.217;0.403;0.675;0.201	P;B;B;B	0.44772	0.46;0.2;0.345;0.261	T	0.70706	-0.4798	10	0.66056	D	0.02	.	13.152	0.59494	0.0:0.0:0.0:1.0	.	82;20;82;82	B7Z8Z9;B4DG79;Q0VAN0;P31751	.;.;.;AKT2_HUMAN	A	82;81;82;82;82;82;82;82;82;82;82	ENSP00000375892:T82A;ENSP00000399532:T82A;ENSP00000309428:T82A;ENSP00000404083:T82A;ENSP00000375891:T82A;ENSP00000407999:T82A;ENSP00000403842:T82A;ENSP00000396532:T82A;ENSP00000392458:T82A	ENSP00000309428:T82A	T	-	1	0	AKT2	45452948	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	3.106000	0.50322	1.770000	0.52166	0.482000	0.46254	ACA	.	.		0.602	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626	
C19orf47	126526	hgsc.bcm.edu	37	19	40832372	40832372	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:40832372T>C	ENST00000582783.1	-	7	584	c.572A>G	c.(571-573)gAg>gGg	p.E191G	C19orf47_ENST00000392035.2_Missense_Mutation_p.E124G	NM_001256440.1	NP_001243369.1	Q8N9M1	CS047_HUMAN	chromosome 19 open reading frame 47	191						nucleus (GO:0005634)				endometrium(5)|kidney(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20			Lung(22;0.000636)			CAGGCTCTCCTCCTCCCGGCG	0.632																																					p.E191G		Atlas-SNP	.											.	C19orf47	61	.	0			c.A572G						.						53.0	43.0	46.0					19																	40832372		2203	4300	6503	SO:0001583	missense	126526	exon7			CTCTCCTCCTCCC	AL834131	CCDS58662.1	19q13.2	2012-07-20			ENSG00000160392	ENSG00000160392			26723	protein-coding gene	gene with protein product						12477932	Standard	NM_001256440		Approved	FLJ36888	uc002oni.5	Q8N9M1	OTTHUMG00000179028	ENST00000582783.1:c.572A>G	chr19.hg19:g.40832372T>C	ENSP00000463159:p.Glu191Gly	93.0	0.0		76.0	4.0	NM_001256440	Q8IZ33|Q8N0V9	Missense_Mutation	SNP	ENST00000582783.1	hg19	CCDS58662.1	.	.	.	.	.	.	.	.	.	.	T	19.23	3.787564	0.70337	.	.	ENSG00000160392	ENST00000357884;ENST00000392035	D	0.99523	-6.08	5.54	5.54	0.83059	.	0.202588	0.51477	D	0.000097	D	0.98927	0.9636	M	0.67953	2.075	0.49798	D	0.999826	P	0.47545	0.897	P	0.51615	0.675	D	0.98427	1.0580	10	0.34782	T	0.22	-19.27	11.1937	0.48700	0.0:0.0:0.1537:0.8463	.	191	Q8N9M1	CS047_HUMAN	G	191;124	ENSP00000375889:E124G	ENSP00000350556:E191G	E	-	2	0	C19orf47	45524212	0.999000	0.42202	1.000000	0.80357	0.662000	0.39071	1.360000	0.34125	2.115000	0.64714	0.379000	0.24179	GAG	.	.		0.632	C19orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444488.1	NM_178830	
SHKBP1	92799	hgsc.bcm.edu	37	19	41094616	41094616	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:41094616G>T	ENST00000291842.5	+	14	1472	c.1423G>T	c.(1423-1425)Gct>Tct	p.A475S	SHKBP1_ENST00000600733.1_Missense_Mutation_p.A450S|SHKBP1_ENST00000597649.1_3'UTR	NM_138392.3	NP_612401.2	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	475					protein homooligomerization (GO:0051260)					breast(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(3)|urinary_tract(1)	29			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CACCCCACTCGCTTCCTTTAA	0.617																																					p.A475S		Atlas-SNP	.											.	SHKBP1	68	.	0			c.G1423T						.						96.0	92.0	93.0					19																	41094616		2203	4300	6503	SO:0001583	missense	92799	exon14			CCACTCGCTTCCT	AF258553	CCDS12560.1	19q13.2	2013-01-10				ENSG00000160410		"""WD repeat domain containing"""	19214	protein-coding gene	gene with protein product						11152963	Standard	NM_138392		Approved	PP203, Sb1	uc002oob.3	Q8TBC3		ENST00000291842.5:c.1423G>T	chr19.hg19:g.41094616G>T	ENSP00000291842:p.Ala475Ser	123.0	0.0		88.0	5.0	NM_138392	Q8N2I6|Q8WY93|Q96IB8	Missense_Mutation	SNP	ENST00000291842.5	hg19	CCDS12560.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.511755	0.44660	.	.	ENSG00000160410	ENST00000291842;ENST00000446701	T	0.45668	0.89	4.21	3.17	0.36434	WD40 repeat-like-containing domain (1);	0.126948	0.52532	D	0.000071	T	0.51041	0.1651	L	0.60845	1.875	0.44136	D	0.996924	D;P;B;B;B;B	0.59767	0.986;0.812;0.084;0.207;0.195;0.086	P;P;B;B;B;B	0.55871	0.786;0.48;0.028;0.05;0.022;0.028	T	0.52779	-0.8530	10	0.56958	D	0.05	-15.8193	11.1437	0.48417	0.0927:0.0:0.9073:0.0	.	353;255;398;312;475;475	B4DLI0;B4DUW2;B4DUV2;B3KVX8;B2R6W9;Q8TBC3	.;.;.;.;.;SHKB1_HUMAN	S	475;255	ENSP00000291842:A475S	ENSP00000291842:A475S	A	+	1	0	SHKBP1	45786456	0.995000	0.38212	0.311000	0.25182	0.870000	0.49936	2.654000	0.46699	0.989000	0.38761	0.462000	0.41574	GCT	.	.		0.617	SHKBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462613.2	NM_138392	
ETHE1	23474	hgsc.bcm.edu	37	19	44012185	44012185	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:44012185T>C	ENST00000292147.2	-	6	689	c.623A>G	c.(622-624)gAg>gGg	p.E208G	ETHE1_ENST00000600651.1_Missense_Mutation_p.E208G	NM_014297.3	NP_055112.2	O95571	ETHE1_HUMAN	ethylmalonic encephalopathy 1	208					cellular nitrogen compound metabolic process (GO:0034641)|glutathione metabolic process (GO:0006749)|hydrogen sulfide metabolic process (GO:0070813)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|sulfur dioxygenase activity (GO:0050313)			central_nervous_system(1)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	5		Prostate(69;0.0153)				CAGAGTCCTCTCCTCCTCCAC	0.557																																					p.E208G		Atlas-SNP	.											.	ETHE1	7	.	0			c.A623G						.						74.0	59.0	64.0					19																	44012185		2203	4300	6503	SO:0001583	missense	23474	exon6			GTCCTCTCCTCCT		CCDS12622.1	19q13.32	2014-06-20				ENSG00000105755	1.13.11.18		23287	protein-coding gene	gene with protein product		608451				19136963	Standard	NM_014297		Approved	YF13H12, HSCO	uc002owp.3	O95571		ENST00000292147.2:c.623A>G	chr19.hg19:g.44012185T>C	ENSP00000292147:p.Glu208Gly	85.0	0.0		79.0	4.0	NM_014297	Q96HR0|Q9H001	Missense_Mutation	SNP	ENST00000292147.2	hg19	CCDS12622.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.608626	0.87258	.	.	ENSG00000105755	ENST00000292147	D	0.97066	-4.23	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.98820	0.9602	H	0.95365	3.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.993;0.997	D	0.99490	1.0950	10	0.87932	D	0	-8.9073	13.0221	0.58794	0.0:0.0:0.0:1.0	.	181;208	B2RCZ7;O95571	.;ETHE1_HUMAN	G	208	ENSP00000292147:E208G	ENSP00000292147:E208G	E	-	2	0	ETHE1	48704025	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.780000	0.68956	2.232000	0.73038	0.524000	0.50904	GAG	.	.		0.557	ETHE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463184.1	NM_014297	
IRGC	56269	hgsc.bcm.edu	37	19	44223753	44223753	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:44223753C>T	ENST00000244314.5	+	2	1242	c.1043C>T	c.(1042-1044)tCc>tTc	p.S348F		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	348						membrane (GO:0016020)	GTP binding (GO:0005525)|hydrolase activity, acting on acid anhydrides (GO:0016817)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(2)	25		Prostate(69;0.0435)				CGGCTCTATTCCCAGTCGTCC	0.672																																					p.S348F	Colon(189;350 2037 11447 13433 38914)	Atlas-SNP	.											.	IRGC	67	.	0			c.C1043T						.						40.0	42.0	42.0					19																	44223753		2203	4300	6503	SO:0001583	missense	56269	exon2			TCTATTCCCAGTC	BC066939	CCDS12629.1	19q13.32	2008-02-05	2005-10-31	2005-10-31	ENSG00000124449	ENSG00000124449			28835	protein-coding gene	gene with protein product			"""immunity-related GTPase family, cinema 1"""	IRGC1		12477932	Standard	NM_019612		Approved	Iigp5, CINEMA	uc002oxh.3	Q6NXR0	OTTHUMG00000154587	ENST00000244314.5:c.1043C>T	chr19.hg19:g.44223753C>T	ENSP00000244314:p.Ser348Phe	93.0	0.0		63.0	4.0	NM_019612	Q05BR8	Missense_Mutation	SNP	ENST00000244314.5	hg19	CCDS12629.1	.	.	.	.	.	.	.	.	.	.	C	7.932	0.740907	0.15642	.	.	ENSG00000124449	ENST00000244314	T	0.25912	1.77	4.67	4.67	0.58626	.	0.713966	0.12326	N	0.478873	T	0.20210	0.0486	L	0.31578	0.945	0.09310	N	1	P	0.44195	0.828	B	0.39935	0.314	T	0.08889	-1.0700	10	0.56958	D	0.05	.	10.3517	0.43939	0.1963:0.8037:0.0:0.0	.	348	Q6NXR0	IIGP5_HUMAN	F	348	ENSP00000244314:S348F	ENSP00000244314:S348F	S	+	2	0	IRGC	48915593	0.001000	0.12720	0.812000	0.32479	0.032000	0.12392	1.187000	0.32090	2.151000	0.67156	0.655000	0.94253	TCC	.	.		0.672	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612	
ZNF284	342909	hgsc.bcm.edu	37	19	44590982	44590982	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:44590982G>A	ENST00000421176.3	+	5	1567	c.1351G>A	c.(1351-1353)Gga>Aga	p.G451R	RNU6-902P_ENST00000517212.1_RNA|ZNF223_ENST00000591793.1_3'UTR	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	451					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)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				GGTCCACACGGGAGAGAGACC	0.423																																					p.G451R		Atlas-SNP	.											.	ZNF284	38	.	0			c.G1351A						.						80.0	86.0	84.0					19																	44590982		2199	4299	6498	SO:0001583	missense	342909	exon5			CACACGGGAGAGA	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"""Zinc fingers, C2H2-type"", ""-"""	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.1351G>A	chr19.hg19:g.44590982G>A	ENSP00000411032:p.Gly451Arg	168.0	0.0		154.0	52.0	NM_001037813	Q86WM1	Missense_Mutation	SNP	ENST00000421176.3	hg19	CCDS46099.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.299969	0.81136	.	.	ENSG00000186026	ENST00000421176	T	0.26223	1.75	2.37	1.3	0.21679	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.45657	0.1353	M	0.70787	2.145	0.25856	N	0.983884	D	0.89917	1.0	D	0.91635	0.999	T	0.20605	-1.0270	9	0.72032	D	0.01	.	7.9186	0.29833	0.1366:0.0:0.8634:0.0	.	451	Q2VY69	ZN284_HUMAN	R	451	ENSP00000411032:G451R	ENSP00000411032:G451R	G	+	1	0	ZNF284	49282822	0.279000	0.24239	0.005000	0.12908	0.984000	0.73092	3.147000	0.50639	0.319000	0.23209	0.462000	0.41574	GGA	.	.		0.423	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813	
ZNF227	7770	hgsc.bcm.edu	37	19	44740282	44740282	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:44740282C>A	ENST00000313040.7	+	6	1904	c.1699C>A	c.(1699-1701)Caa>Aaa	p.Q567K	ZNF235_ENST00000589799.1_3'UTR|ZNF227_ENST00000391961.2_Missense_Mutation_p.Q516K|ZNF227_ENST00000589005.1_Missense_Mutation_p.Q516K	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	567					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)				TAAACTACACCAAGTAATTCA	0.403																																					p.Q567K		Atlas-SNP	.											.	ZNF227	62	.	0			c.C1699A						.						67.0	72.0	71.0					19																	44740282		2203	4300	6503	SO:0001583	missense	7770	exon6			CTACACCAAGTAA	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.1699C>A	chr19.hg19:g.44740282C>A	ENSP00000321049:p.Gln567Lys	113.0	0.0		142.0	6.0	NM_182490	B3KRU7|B7Z5P9	Missense_Mutation	SNP	ENST00000313040.7	hg19	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.318756	0.60524	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980	T;T	0.07216	3.21;3.21	4.36	3.23	0.37069	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07954	0.0199	N	0.24115	0.695	0.80722	D	1	B;B;P;B	0.45126	0.123;0.123;0.851;0.123	B;B;P;B	0.45071	0.074;0.117;0.468;0.117	T	0.38972	-0.9636	9	0.36615	T	0.2	.	12.1839	0.54227	0.1714:0.8286:0.0:0.0	.	488;546;519;567	B7Z6M2;Q658S5;Q9NS43;Q86WZ6	.;.;.;ZN227_HUMAN	K	567;524;516;546	ENSP00000321049:Q567K;ENSP00000375823:Q516K	ENSP00000321049:Q567K	Q	+	1	0	ZNF227	49432122	0.001000	0.12720	0.581000	0.28614	0.818000	0.46254	1.002000	0.29796	2.125000	0.65367	0.563000	0.77884	CAA	.	.		0.403	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490	
ZNF229	7772	hgsc.bcm.edu	37	19	44933201	44933201	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:44933201T>C	ENST00000588931.1	-	6	2188	c.1755A>G	c.(1753-1755)tcA>tcG	p.S585S	ZNF229_ENST00000291187.4_Silent_p.S579S|CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000591289.1_Intron	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	585					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(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				TGTGAAGGTCTGAATTCCGCC	0.572																																					p.S585S		Atlas-SNP	.											.	ZNF229	123	.	0			c.A1755G						.						52.0	56.0	55.0					19																	44933201		2186	4295	6481	SO:0001819	synonymous_variant	7772	exon6			AAGGTCTGAATTC	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"""Zinc fingers, C2H2-type"", ""-"""	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.1755A>G	chr19.hg19:g.44933201T>C		95.0	0.0		85.0	4.0	NM_014518	B2RWN3|Q59FV2|Q86WL9	Silent	SNP	ENST00000588931.1	hg19	CCDS42574.1																																																																																			.	.		0.572	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
ZNF180	7733	hgsc.bcm.edu	37	19	44982061	44982061	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:44982061T>C	ENST00000221327.4	-	5	918	c.637A>G	c.(637-639)Ata>Gta	p.I213V	ZNF180_ENST00000391956.4_Missense_Mutation_p.I188V|ZNF180_ENST00000592529.1_Missense_Mutation_p.I186V|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000586637.1_3'UTR	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	213					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(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				TGGTTTCTTATGGGTATAACT	0.363																																					p.I213V	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.A637G						.						88.0	87.0	87.0					19																	44982061		2203	4300	6503	SO:0001583	missense	7733	exon5			TTCTTATGGGTAT	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.637A>G	chr19.hg19:g.44982061T>C	ENSP00000221327:p.Ile213Val	96.0	0.0		95.0	4.0	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	hg19	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-1.984302	0.00443	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.07021	3.23;3.26	4.89	-3.24	0.05094	.	0.306273	0.23541	N	0.047079	T	0.03178	0.0093	N	0.19112	0.55	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.39482	-0.9612	10	0.15066	T	0.55	-7.4476	1.8481	0.03163	0.1245:0.3207:0.2698:0.2849	.	188;212;213	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	V	213;188	ENSP00000221327:I213V;ENSP00000375818:I188V	ENSP00000221327:I213V	I	-	1	0	ZNF180	49673901	0.001000	0.12720	0.003000	0.11579	0.029000	0.11900	-0.054000	0.11826	-0.537000	0.06290	0.533000	0.62120	ATA	.	.		0.363	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
VASP	7408	hgsc.bcm.edu	37	19	46032507	46032507	+	IGR	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:46032507A>G	ENST00000245932.6	+	0	2305				OPA3_ENST00000323060.3_Missense_Mutation_p.V117A	NM_003370.3	NP_003361.1	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein						actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|neural tube closure (GO:0001843)|positive regulation of actin filament polymerization (GO:0030838)|protein homotetramerization (GO:0051289)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	profilin binding (GO:0005522)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)	18		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)		CTCCCTGGCAACACGTCGCTC	0.677																																					p.V117A		Atlas-SNP	.											.	OPA3	19	.	0			c.T350C						.						31.0	31.0	31.0					19																	46032507		2200	4299	6499	SO:0001628	intergenic_variant	80207	exon2			CTGGCAACACGTC		CCDS33051.1	19q13.32	2012-02-22			ENSG00000125753	ENSG00000125753			12652	protein-coding gene	gene with protein product		601703				8812448	Standard	XM_005259199		Approved		uc002pcg.3	P50552			chr19.hg19:g.46032507A>G		82.0	0.0		100.0	4.0	NM_001017989	B2RBT9|Q6PIZ1|Q93035	Missense_Mutation	SNP	ENST00000245932.6	hg19	CCDS33051.1	.	.	.	.	.	.	.	.	.	.	A	1.983	-0.433637	0.04669	.	.	ENSG00000125741	ENST00000323060	D	0.81499	-1.5	3.67	-1.71	0.08133	.	1.518070	0.03623	N	0.236680	T	0.54775	0.1879	.	.	.	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.48281	-0.9049	9	0.07644	T	0.81	-0.1509	0.4545	0.00507	0.2179:0.1594:0.336:0.2867	.	117	Q9H6K4-2	.	A	117	ENSP00000319817:V117A	ENSP00000319817:V117A	V	-	2	0	OPA3	50724347	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.071000	0.14594	0.001000	0.14605	-0.441000	0.05720	GTT	.	.		0.677	VASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459589.1		
DMPK	1760	hgsc.bcm.edu	37	19	46280628	46280628	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:46280628T>C	ENST00000291270.4	-	8	1228	c.1103A>G	c.(1102-1104)gAc>gGc	p.D368G	DMPK_ENST00000458663.2_Missense_Mutation_p.D368G|DMPK_ENST00000595361.1_5'Flank|DMPK_ENST00000600757.1_Missense_Mutation_p.D378G|DMPK_ENST00000343373.4_Missense_Mutation_p.D378G|DMPK_ENST00000354227.5_Missense_Mutation_p.D368G|DMPK_ENST00000447742.2_Missense_Mutation_p.D368G	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase	368	AGC-kinase C-terminal.				cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)			endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		CTCCACCAAGTCGAAGTTGCA	0.622																																					p.D378G	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-SNP	.											.	DMPK	74	.	0			c.A1133G						.						45.0	38.0	40.0					19																	46280628		2202	4300	6502	SO:0001583	missense	1760	exon7			ACCAAGTCGAAGT	L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"""dystrophia myotonica 1"", ""DM protein kinase"", ""myotonin protein kinase A"", ""myotonic dystrophy associated protein kinase"", ""thymopoietin homolog"""	605377	"""dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"""	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.1103A>G	chr19.hg19:g.46280628T>C	ENSP00000291270:p.Asp368Gly	101.0	0.0		87.0	4.0	NM_001081563	E5KR08|Q16205|Q6P5Z6	Missense_Mutation	SNP	ENST00000291270.4	hg19	CCDS12674.1	.	.	.	.	.	.	.	.	.	.	t	23.6	4.437347	0.83885	.	.	ENSG00000104936	ENST00000458663;ENST00000342805;ENST00000291270;ENST00000447742;ENST00000377750;ENST00000343373;ENST00000348168;ENST00000354227	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.63	4.63	0.57726	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.139434	0.32624	N	0.005845	T	0.63873	0.2548	M	0.78456	2.415	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.87578	0.996;0.996;0.997;0.998;0.997;0.992;0.998;0.995	T	0.68708	-0.5337	10	0.87932	D	0	.	12.289	0.54807	0.0:0.0:0.0:1.0	.	368;368;394;368;368;368;415;378	Q09013-12;Q09013-16;G5E982;E5KR07;E5KR05;Q09013;Q59FU6;E5KR08	.;.;.;.;.;DMPK_HUMAN;.;.	G	368;394;368;368;368;378;378;368	ENSP00000401753:D368G;ENSP00000291270:D368G;ENSP00000413417:D368G;ENSP00000345997:D378G;ENSP00000346168:D368G	ENSP00000291270:D368G	D	-	2	0	DMPK	50972468	1.000000	0.71417	0.992000	0.48379	0.719000	0.41307	7.703000	0.84585	2.065000	0.61736	0.459000	0.35465	GAC	.	.		0.622	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409	
ARHGAP35	2909	hgsc.bcm.edu	37	19	47423542	47423542	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:47423542A>G	ENST00000404338.3	+	1	1610	c.1610A>G	c.(1609-1611)cAa>cGa	p.Q537R		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	537	FF 4.				axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										CAAAAGCTCCAAGCAGAGCGT	0.473																																					p.Q537R		Atlas-SNP	.											.	.	.	.	0			c.A1610G						.						162.0	158.0	159.0					19																	47423542		1994	4173	6167	SO:0001583	missense	2909	exon1			AGCTCCAAGCAGA	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"""Rho GTPase activating proteins"""	4591	protein-coding gene	gene with protein product		605277	"""glucocorticoid receptor DNA binding factor 1"""	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.1610A>G	chr19.hg19:g.47423542A>G	ENSP00000385720:p.Gln537Arg	68.0	0.0		92.0	5.0	NM_004491	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	hg19	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	A	13.32	2.201121	0.38905	.	.	ENSG00000160007	ENST00000317082;ENST00000501576;ENST00000404338	T	0.29655	1.56	5.82	5.82	0.92795	.	0.102535	0.64402	D	0.000002	T	0.27027	0.0662	N	0.22421	0.69	0.80722	D	1	B	0.32101	0.356	B	0.36922	0.236	T	0.08371	-1.0725	10	0.54805	T	0.06	-26.4002	15.1603	0.72778	1.0:0.0:0.0:0.0	.	537	Q9NRY4-2	.	R	537	ENSP00000385720:Q537R	ENSP00000324820:Q537R	Q	+	2	0	ARHGAP35	52115382	0.999000	0.42202	0.964000	0.40570	0.951000	0.60555	4.477000	0.60223	2.225000	0.72522	0.459000	0.35465	CAA	.	.		0.473	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491	
TULP2	7288	hgsc.bcm.edu	37	19	49384335	49384335	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:49384335G>A	ENST00000221399.3	-	13	1640	c.1496C>T	c.(1495-1497)aCc>aTc	p.T499I		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	499					visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		GAAGTCCATGGTGAATGTGTC	0.488																																					p.T499I		Atlas-SNP	.											.	TULP2	60	.	0			c.C1496T						.						117.0	116.0	117.0					19																	49384335		2203	4300	6503	SO:0001583	missense	7288	exon13			TCCATGGTGAATG	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"""cancer/testis antigen 65"""	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.1496C>T	chr19.hg19:g.49384335G>A	ENSP00000221399:p.Thr499Ile	72.0	0.0		82.0	4.0	NM_003323	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	hg19	CCDS12739.1	.	.	.	.	.	.	.	.	.	.	G	16.46	3.129716	0.56721	.	.	ENSG00000104804	ENST00000221399;ENST00000522341	D;D	0.97941	-4.62;-4.62	4.81	3.78	0.43462	Tubby, C-terminal (4);	0.061993	0.64402	D	0.000004	D	0.98213	0.9409	M	0.73430	2.235	0.53005	D	0.999969	D	0.76494	0.999	D	0.73708	0.981	D	0.98550	1.0636	10	0.87932	D	0	-17.476	11.1381	0.48386	0.0912:0.0:0.9088:0.0	.	499	O00295	TULP2_HUMAN	I	499;59	ENSP00000221399:T499I;ENSP00000429131:T59I	ENSP00000221399:T499I	T	-	2	0	TULP2	54076147	1.000000	0.71417	1.000000	0.80357	0.320000	0.28249	7.205000	0.77881	1.179000	0.42884	-0.136000	0.14681	ACC	.	.		0.488	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323	
PRMT1	3276	hgsc.bcm.edu	37	19	50185170	50185170	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:50185170A>G	ENST00000391851.4	+	3	271	c.142A>G	c.(142-144)Atg>Gtg	p.M48V	MIR5088_ENST00000581740.1_RNA|PRMT1_ENST00000532489.1_Missense_Mutation_p.M20V|PRMT1_ENST00000454376.2_Missense_Mutation_p.M66V	NM_198318.4	NP_938074.2	Q99873	ANM1_HUMAN	protein arginine methyltransferase 1	56	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell surface receptor signaling pathway (GO:0007166)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of megakaryocyte differentiation (GO:0045653)|neuron projection development (GO:0031175)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|protein methylation (GO:0006479)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|identical protein binding (GO:0042802)|methyltransferase activity (GO:0008168)|N-methyltransferase activity (GO:0008170)|poly(A) RNA binding (GO:0044822)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(2)	12		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)		GCCCTAGGAGATGCTGAAGGA	0.617																																					p.M66V		Atlas-SNP	.											.	PRMT1	31	.	0			c.A196G						.						61.0	48.0	52.0					19																	50185170		2203	4300	6503	SO:0001583	missense	3276	exon4			TAGGAGATGCTGA	D66904	CCDS42592.1, CCDS46145.1, CCDS74425.1	19q13	2014-06-12	2006-02-16	2006-02-16	ENSG00000126457	ENSG00000126457	2.1.1.125	"""Protein arginine methyltransferases"""	5187	protein-coding gene	gene with protein product		602950	"""HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 2"", ""HMT1 hnRNP methyltransferase-like 2 (S. cerevisiae)"""	HRMT1L2		9545638	Standard	NM_001207042		Approved	HCP1, ANM1	uc010enf.2	Q99873	OTTHUMG00000167568	ENST00000391851.4:c.142A>G	chr19.hg19:g.50185170A>G	ENSP00000375724:p.Met48Val	94.0	0.0		85.0	4.0	NM_001536	B4E3C3|G5E9B6|Q15529|Q2VP93|Q6LEU5|Q8WUW5|Q99872|Q99874|Q9NZ04|Q9NZ05|Q9NZ06	Missense_Mutation	SNP	ENST00000391851.4	hg19	CCDS42592.1	.	.	.	.	.	.	.	.	.	.	A	11.47	1.649565	0.29336	.	.	ENSG00000126457	ENST00000529284;ENST00000532489;ENST00000527382;ENST00000528623;ENST00000534465;ENST00000391851;ENST00000449059;ENST00000454376;ENST00000529836;ENST00000526224;ENST00000527412	T;T;T;T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.40067	0.1102	M	0.77712	2.385	0.80722	D	1	D;P;D;P	0.56968	0.962;0.855;0.978;0.91	B;B;P;P	0.49637	0.315;0.288;0.617;0.617	T	0.44847	-0.9301	10	0.87932	D	0	-12.5087	12.7696	0.57412	1.0:0.0:0.0:0.0	.	56;20;48;42	Q99873;E9PKG1;G5E9B6;Q99873-2	ANM1_HUMAN;.;.;.	V	20;20;20;42;20;48;42;66;42;20;45	ENSP00000432349:M20V;ENSP00000433556:M20V;ENSP00000432538:M20V;ENSP00000431957:M20V;ENSP00000375724:M48V;ENSP00000406162:M66V;ENSP00000437273:M42V;ENSP00000432788:M20V;ENSP00000436732:M45V	ENSP00000375724:M48V	M	+	1	0	PRMT1	54876982	1.000000	0.71417	1.000000	0.80357	0.012000	0.07955	8.816000	0.91979	2.124000	0.65301	0.523000	0.50628	ATG	.	.		0.617	PRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395065.1	NM_001536	
SIGLEC7	27036	hgsc.bcm.edu	37	19	51648215	51648215	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:51648215A>G	ENST00000317643.6	+	3	828	c.759A>G	c.(757-759)acA>acG	p.T253T	SIGLEC7_ENST00000600577.1_Intron|SIGLEC7_ENST00000305628.7_Splice_Site_p.T160T	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	253	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		GAGAAGGCACAGGTAGGATGG	0.612																																					p.T253T		Atlas-SNP	.											.	SIGLEC7	74	.	0			c.A759G						.						109.0	102.0	104.0					19																	51648215		2203	4300	6503	SO:0001630	splice_region_variant	27036	exon3			AGGCACAGGTAGG	AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10876	protein-coding gene	gene with protein product		604410	"""sialic acid binding Ig-like lectin 19, pseudogene"", ""sialic acid binding Ig-like lectin, pseudogene 2"""	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.760+1A>G	chr19.hg19:g.51648215A>G		73.0	0.0		88.0	4.0	NM_014385	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Silent	SNP	ENST00000317643.6	hg19	CCDS12826.1																																																																																			.	.		0.612	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543	Silent
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919307	51919307	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:51919307A>G	ENST00000339313.5	-	5	985	c.869T>C	c.(868-870)cTg>cCg	p.L290P	SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.L207P|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.L290P|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.L232P|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.L290P|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.L232P|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.L242P			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	290	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		TCTGTTCTGCAGGACCCAGCT	0.652																																					p.L290P		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.T869C						.						18.0	23.0	21.0					19																	51919307		2201	4299	6500	SO:0001583	missense	89790	exon5			TTCTGCAGGACCC	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.869T>C	chr19.hg19:g.51919307A>G	ENSP00000345243:p.Leu290Pro	82.0	0.0		82.0	4.0	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	hg19	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	8.476	0.858590	0.17178	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000441969;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;T;T;T;T;T;T;T	0.45668	1.46;1.46;1.46;1.46;1.46;1.46;1.46;0.89	4.37	2.1	0.27182	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.498950	0.15393	N	0.264731	T	0.61862	0.2381	M	0.86864	2.845	0.37215	D	0.904993	D;D;D;D;P;D	0.89917	1.0;1.0;1.0;1.0;0.494;0.999	D;D;D;D;B;D	0.91635	0.999;0.999;0.998;0.997;0.221;0.985	T	0.63202	-0.6690	10	0.46703	T	0.11	.	4.2091	0.10503	0.5813:0.1982:0.0:0.2206	.	242;290;290;232;232;290	C9JM10;B7ZL04;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;SIG10_HUMAN	P	290;207;290;232;232;242;290;104	ENSP00000342389:L290P;ENSP00000396742:L207P;ENSP00000348646:L290P;ENSP00000408387:L232P;ENSP00000389132:L232P;ENSP00000414324:L242P;ENSP00000345243:L290P;ENSP00000435281:L104P	ENSP00000345243:L290P	L	-	2	0	SIGLEC10	56611119	0.436000	0.25586	0.716000	0.30569	0.129000	0.20672	0.708000	0.25719	0.710000	0.31997	0.260000	0.18958	CTG	.	.		0.652	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
ZNF470	388566	hgsc.bcm.edu	37	19	57089654	57089654	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:57089654A>G	ENST00000330619.8	+	6	2543	c.1857A>G	c.(1855-1857)aaA>aaG	p.K619K	ZNF470_ENST00000391709.3_Silent_p.K619K|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	619					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(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		CTGGTGAGAAACCTTATGAAT	0.428																																					p.K619K		Atlas-SNP	.											.	ZNF470	103	.	0			c.A1857G						.						81.0	79.0	80.0					19																	57089654		2203	4300	6503	SO:0001819	synonymous_variant	388566	exon6			TGAGAAACCTTAT	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"""Zinc fingers, C2H2-type"", ""-"""	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.1857A>G	chr19.hg19:g.57089654A>G		52.0	0.0		90.0	5.0	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Silent	SNP	ENST00000330619.8	hg19	CCDS33122.1																																																																																			.	.		0.428	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668	
ZNF304	57343	hgsc.bcm.edu	37	19	57867978	57867978	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:57867978G>T	ENST00000282286.5	+	3	914	c.741G>T	c.(739-741)gaG>gaT	p.E247D	ZNF304_ENST00000391705.3_Missense_Mutation_p.E247D|ZNF304_ENST00000598744.1_Missense_Mutation_p.E205D|ZNF304_ENST00000443917.2_Missense_Mutation_p.E294D			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	247					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(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)	26		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		CTCATGCTGAGGTGAGACCCT	0.438																																					p.E247D		Atlas-SNP	.											.	ZNF304	74	.	0			c.G741T						.						89.0	85.0	86.0					19																	57867978		2203	4300	6503	SO:0001583	missense	57343	exon3			TGCTGAGGTGAGA	AJ276316	CCDS12950.1, CCDS74462.1	19q13.4	2013-01-08				ENSG00000131845		"""Zinc fingers, C2H2-type"", ""-"""	13505	protein-coding gene	gene with protein product		613840					Standard	XM_005259090		Approved		uc010ygw.2	Q9HCX3		ENST00000282286.5:c.741G>T	chr19.hg19:g.57867978G>T	ENSP00000282286:p.Glu247Asp	92.0	0.0		94.0	4.0	NM_020657		Missense_Mutation	SNP	ENST00000282286.5	hg19	CCDS12950.1	.	.	.	.	.	.	.	.	.	.	g	11.55	1.671545	0.29693	.	.	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.15256	2.44;2.44;2.44	3.82	-3.28	0.05033	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10937	0.0267	L	0.41079	1.255	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.001;0.002	T	0.36720	-0.9736	9	0.66056	D	0.02	.	2.0199	0.03506	0.3923:0.13:0.3494:0.1284	.	247;294	Q9HCX3;E7EQD3	ZN304_HUMAN;.	D	247;247;294	ENSP00000282286:E247D;ENSP00000375586:E247D;ENSP00000401642:E294D	ENSP00000282286:E247D	E	+	3	2	ZNF304	62559790	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.586000	0.23894	-0.595000	0.05828	0.454000	0.30748	GAG	.	.		0.438	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1		
ZNF211	10520	hgsc.bcm.edu	37	19	58153448	58153448	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:58153448A>G	ENST00000347302.3	+	3	1773	c.1594A>G	c.(1594-1596)Acg>Gcg	p.T532A	ZNF211_ENST00000240731.4_Missense_Mutation_p.T545A|ZNF211_ENST00000299871.5_Missense_Mutation_p.T597A|ZNF211_ENST00000544273.1_Missense_Mutation_p.T544A|ZNF211_ENST00000541801.1_Missense_Mutation_p.T523A|ZNF211_ENST00000254182.7_Missense_Mutation_p.T523A|ZNF211_ENST00000420680.1_Missense_Mutation_p.T536A|ZNF211_ENST00000391703.3_Missense_Mutation_p.T471A	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	532					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CAGAGTTCACACGGGAAAAAG	0.458																																					p.T597A		Atlas-SNP	.											.	ZNF211	78	.	0			c.A1789G						.						104.0	101.0	102.0					19																	58153448		2203	4300	6503	SO:0001583	missense	10520	exon5			GTTCACACGGGAA	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.1594A>G	chr19.hg19:g.58153448A>G	ENSP00000339562:p.Thr532Ala	107.0	0.0		95.0	4.0	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Missense_Mutation	SNP	ENST00000347302.3	hg19	CCDS12957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	21.0|21.0	4.076156|4.076156	0.76415|0.76415	.|.	.|.	ENSG00000121417|ENSG00000121417	ENST00000407202|ENST00000420680;ENST00000347302;ENST00000254182;ENST00000391703;ENST00000541801;ENST00000299871;ENST00000544273;ENST00000240731	T|T;T;T;T;T;T;T;T	0.67523|0.26518	-0.27|1.73;1.73;1.73;1.73;1.73;1.73;1.73;1.73	3.23|3.23	3.23|3.23	0.37069|0.37069	.|Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	T|T	0.25827|0.25827	0.0629|0.0629	L|L	0.52759|0.52759	1.655|1.655	0.28604|0.28604	N|N	0.908997|0.908997	.|B;B;B;P;B;B	.|0.45768	.|0.384;0.384;0.323;0.866;0.438;0.438	.|B;B;B;B;B;B	.|0.41466	.|0.22;0.22;0.147;0.358;0.328;0.328	T|T	0.13308|0.13308	-1.0514|-1.0514	7|9	0.87932|0.87932	D|D	0|0	.|.	10.8985|10.8985	0.47036|0.47036	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|536;544;597;523;532;545	.|Q13398-4;Q13398-3;F8WDV2;Q13398-2;Q13398;B9ZVW1	.|.;.;.;.;ZN211_HUMAN;.	R|A	535|536;532;523;471;523;597;544;545	ENSP00000384436:H535R|ENSP00000399193:T536A;ENSP00000339562:T532A;ENSP00000254182:T523A;ENSP00000375584:T471A;ENSP00000442601:T523A;ENSP00000299871:T597A;ENSP00000441386:T544A;ENSP00000240731:T545A	ENSP00000384436:H535R|ENSP00000240731:T545A	H|T	+|+	2|1	0|0	ZNF211|ZNF211	62845260|62845260	0.522000|0.522000	0.26266|0.26266	0.223000|0.223000	0.23860|0.23860	0.963000|0.963000	0.63663|0.63663	2.143000|2.143000	0.42187|0.42187	1.467000|1.467000	0.48044|0.48044	0.477000|0.477000	0.44152|0.44152	CAC|ACG	.	.		0.458	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
ZSCAN1	284312	hgsc.bcm.edu	37	19	58564802	58564802	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:58564802C>A	ENST00000282326.1	+	6	857	c.610C>A	c.(610-612)Cgg>Agg	p.R204R		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	204					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		CACAGGGTCCCGGGCCCGCTT	0.652																																					p.R204R		Atlas-SNP	.											.	ZSCAN1	102	.	0			c.C610A						.						45.0	48.0	47.0					19																	58564802		2203	4296	6499	SO:0001819	synonymous_variant	284312	exon6			GGGTCCCGGGCCC	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"""-"", ""Zinc fingers, C2H2-type"""	23712	protein-coding gene	gene with protein product			"""zinc finger with SCAN domain 1"""			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.610C>A	chr19.hg19:g.58564802C>A		61.0	0.0		65.0	4.0	NM_182572	Q3B798|Q6WLH8|Q86WS8	Silent	SNP	ENST00000282326.1	hg19	CCDS12969.1																																																																																			.	.		0.652	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572	
ZNF324	25799	hgsc.bcm.edu	37	19	58982592	58982592	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:58982592G>T	ENST00000536459.2	+	4	1442	c.733G>T	c.(733-735)Gag>Tag	p.E245*	ZNF324_ENST00000535298.1_Nonsense_Mutation_p.E22*|ZNF446_ENST00000596341.1_5'Flank|ZNF324_ENST00000196482.3_Nonsense_Mutation_p.E245*			O75467	Z324A_HUMAN	zinc finger protein 324	245					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E245K(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(2)|prostate(2)|urinary_tract(2)	16		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		GACCTGGGACGAGCTGGGCGA	0.637																																					p.E245X		Atlas-SNP	.											ZNF324,colon,carcinoma,0,1	ZNF324	46	.	1	Substitution - Missense(1)	large_intestine(1)	c.G733T						.						25.0	28.0	27.0					19																	58982592		2197	4292	6489	SO:0001587	stop_gained	25799	exon4			TGGGACGAGCTGG	AF060503	CCDS12981.1	19q13.43	2013-01-08				ENSG00000083812		"""Zinc fingers, C2H2-type"", ""-"""	14096	protein-coding gene	gene with protein product							Standard	NM_014347		Approved	ZF5128, ZNF324A	uc002qsw.2	O75467		ENST00000536459.2:c.733G>T	chr19.hg19:g.58982592G>T	ENSP00000444812:p.Glu245*	170.0	0.0		180.0	52.0	NM_014347	B3KRX1	Nonsense_Mutation	SNP	ENST00000536459.2	hg19	CCDS12981.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.463256	0.84425	.	.	ENSG00000083812	ENST00000378044;ENST00000196482;ENST00000536459;ENST00000539101;ENST00000535298	.	.	.	3.72	1.2	0.21068	.	0.360135	0.20437	N	0.092359	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	3.8068	0.08780	0.1844:0.259:0.5566:0.0	.	.	.	.	X	245;245;245;235;22	.	ENSP00000196482:E245X	E	+	1	0	ZNF324	63674404	0.677000	0.27577	0.021000	0.16686	0.046000	0.14306	0.923000	0.28757	0.356000	0.24157	0.455000	0.32223	GAG	.	.		0.637	ZNF324-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467044.1	NM_014347	
SLC27A5	10998	hgsc.bcm.edu	37	19	59011753	59011753	+	Missense_Mutation	SNP	G	G	A	rs371196997		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:59011753G>A	ENST00000263093.2	-	6	1530	c.1421C>T	c.(1420-1422)gCg>gTg	p.A474V	SLC27A5_ENST00000601355.1_Missense_Mutation_p.A390V|SLC27A5_ENST00000594786.1_5'Flank|SLC27A5_ENST00000599700.1_5'Flank	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	474					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)		CACAGGCTCCGCCGCCTCCAT	0.622																																					p.A474V		Atlas-SNP	.											.	SLC27A5	58	.	0			c.C1421T						.	G	VAL/ALA	0,4406		0,0,2203	105.0	96.0	99.0		1421	-5.4	0.0	19		99	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLC27A5	NM_012254.2	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	474/691	59011753	1,13005	2203	4300	6503	SO:0001583	missense	10998	exon6			GGCTCCGCCGCCT	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.1421C>T	chr19.hg19:g.59011753G>A	ENSP00000263093:p.Ala474Val	83.0	0.0		72.0	4.0	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	hg19	CCDS12983.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.872513	0.33069	0.0	1.16E-4	ENSG00000083807	ENST00000263093	T	0.48522	0.81	5.33	-5.45	0.02616	AMP-dependent synthetase/ligase (1);	0.493199	0.22705	N	0.056644	T	0.29389	0.0732	L	0.27053	0.805	0.09310	N	1	B	0.15930	0.015	B	0.17098	0.017	T	0.05386	-1.0888	10	0.35671	T	0.21	-3.5408	13.4242	0.61015	0.1033:0.0:0.7245:0.1722	.	474	Q9Y2P5	S27A5_HUMAN	V	474	ENSP00000263093:A474V	ENSP00000263093:A474V	A	-	2	0	SLC27A5	63703565	0.189000	0.23263	0.001000	0.08648	0.394000	0.30568	0.697000	0.25556	-1.301000	0.02338	-0.363000	0.07495	GCG	.	.		0.622	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
MZF1	7593	hgsc.bcm.edu	37	19	59082638	59082638	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr19:59082638G>T	ENST00000215057.2	-	2	679	c.119C>A	c.(118-120)cCt>cAt	p.P40H	MZF1_ENST00000594234.1_Missense_Mutation_p.P40H|MZF1_ENST00000599369.1_Missense_Mutation_p.P40H|AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA|AC016629.8_ENST00000600534.1_RNA|MZF1_ENST00000594108.1_Missense_Mutation_p.P40H	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	40					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in 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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		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;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		TGCAGCTTCAGGGCCTGGGTC	0.657																																					p.P40H		Atlas-SNP	.											.	MZF1	37	.	0			c.C119A						.						26.0	29.0	28.0					19																	59082638		2203	4300	6503	SO:0001583	missense	7593	exon2			GCTTCAGGGCCTG	M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"""-"", ""Zinc fingers, C2H2-type"""	13108	protein-coding gene	gene with protein product		194550	"""zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"""	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.119C>A	chr19.hg19:g.59082638G>T	ENSP00000215057:p.Pro40His	76.0	0.0		90.0	4.0	NM_198055	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	hg19	CCDS12988.1	.	.	.	.	.	.	.	.	.	.	.	11.28	1.592594	0.28357	.	.	ENSG00000099326	ENST00000215057	T	0.06849	3.25	4.35	2.13	0.27403	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (2);	0.390912	0.18930	N	0.127254	T	0.24314	0.0589	M	0.85462	2.755	0.28327	N	0.921974	D;B	0.67145	0.996;0.173	P;B	0.61397	0.888;0.187	T	0.04320	-1.0960	9	.	.	.	-2.5914	7.2443	0.26114	0.2091:0.0:0.7909:0.0	.	40;40	Q7Z729;P28698	.;MZF1_HUMAN	H	40	ENSP00000215057:P40H	.	P	-	2	0	MZF1	63774450	0.000000	0.05858	0.747000	0.31113	0.698000	0.40448	0.333000	0.19768	0.557000	0.29117	0.563000	0.77884	CCT	.	.		0.657	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055	
TGM3	7053	hgsc.bcm.edu	37	20	2290970	2290970	+	Missense_Mutation	SNP	C	C	T	rs139117716	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:2290970C>T	ENST00000381458.5	+	3	391	c.328C>T	c.(328-330)Cgg>Tgg	p.R110W		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	110					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	ACCCATAGGACGGTACACAAT	0.552													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		20392	0.0		0.0	False		,,,				2504	0.0				p.R110W		Atlas-SNP	.											.	TGM3	105	.	0			c.C328T						.	C	TRP/ARG	4,4402	8.1+/-20.4	0,4,2199	197.0	175.0	183.0		328	1.7	0.0	20	dbSNP_134	183	0,8600		0,0,4300	yes	missense	TGM3	NM_003245.3	101	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	benign	110/694	2290970	4,13002	2203	4300	6503	SO:0001583	missense	7053	exon3			ATAGGACGGTACA	L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"""Transglutaminases"""	11779	protein-coding gene	gene with protein product	"""E polypeptide, protein-glutamine-gamma-glutamyltransferase"""	600238	"""transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"""			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.328C>T	chr20.hg19:g.2290970C>T	ENSP00000370867:p.Arg110Trp	143.0	0.0		131.0	51.0	NM_003245	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	hg19	CCDS33435.1	.	.	.	.	.	.	.	.	.	.	C	7.390	0.630671	0.14322	9.08E-4	0.0	ENSG00000125780	ENST00000381458;ENST00000420960	D	0.86230	-2.09	5.34	1.72	0.24424	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	1.329060	0.04642	N	0.405472	D	0.85579	0.5729	M	0.70275	2.135	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.66693	-0.5859	10	0.62326	D	0.03	.	4.5439	0.12071	0.2112:0.5782:0.0:0.2106	.	110	Q08188	TGM3_HUMAN	W	110	ENSP00000370867:R110W	ENSP00000370867:R110W	R	+	1	2	TGM3	2238970	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	0.748000	0.26305	-0.029000	0.13827	0.462000	0.41574	CGG	.	C|1.000;T|0.000		0.552	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245	
VPS16	64601	hgsc.bcm.edu	37	20	2845074	2845074	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:2845074G>T	ENST00000380445.3	+	18	1856	c.1784G>T	c.(1783-1785)cGg>cTg	p.R595L	VPS16_ENST00000380443.3_Missense_Mutation_p.R281L|PTPRA_ENST00000380393.3_5'UTR|VPS16_ENST00000380469.3_Missense_Mutation_p.R451L	NM_022575.2	NP_072097.2	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 homolog (S. cerevisiae)	595					intracellular protein transport (GO:0006886)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|axon (GO:0030424)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	37						ATGACCCTTCGGAATCAGCCC	0.532																																					p.R595L		Atlas-SNP	.											.	VPS16	76	.	0			c.G1784T						.						117.0	112.0	113.0					20																	2845074		2203	4300	6503	SO:0001583	missense	64601	exon18			CCCTTCGGAATCA	AF308801	CCDS13036.1, CCDS13037.1	20p13	2009-07-07	2009-07-07	2009-07-07	ENSG00000215305	ENSG00000215305			14584	protein-coding gene	gene with protein product		608550					Standard	NM_022575		Approved		uc002whe.3	Q9H269	OTTHUMG00000031714	ENST00000380445.3:c.1784G>T	chr20.hg19:g.2845074G>T	ENSP00000369810:p.Arg595Leu	81.0	0.0		74.0	4.0	NM_022575	Q5JUB1|Q8WU31|Q96EE7|Q96N92|Q9H1Q4|Q9H1Q5	Missense_Mutation	SNP	ENST00000380445.3	hg19	CCDS13036.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055831	0.76074	.	.	ENSG00000215305	ENST00000380445;ENST00000380469;ENST00000380443	T;T;T	0.46451	0.87;0.87;0.87	5.2	5.2	0.72013	Vps16, C-terminal (1);	0.110998	0.64402	D	0.000011	T	0.49712	0.1573	M	0.67700	2.07	0.80722	D	1	P;P;P;P	0.47409	0.895;0.895;0.683;0.895	P;P;B;P	0.50970	0.655;0.655;0.145;0.655	T	0.47623	-0.9103	10	0.45353	T	0.12	-25.5608	9.6043	0.39624	0.0921:0.0:0.9079:0.0	.	71;281;451;595	A1A4H0;Q5JUA8;Q9H269-2;Q9H269	.;.;.;VPS16_HUMAN	L	595;451;281	ENSP00000369810:R595L;ENSP00000369836:R451L;ENSP00000369808:R281L	ENSP00000369808:R281L	R	+	2	0	VPS16	2793074	1.000000	0.71417	0.999000	0.59377	0.880000	0.50808	5.600000	0.67599	2.706000	0.92434	0.561000	0.74099	CGG	.	.		0.532	VPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077658.2	NM_022575	
LAMP5	24141	hgsc.bcm.edu	37	20	9496099	9496099	+	Splice_Site	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:9496099G>T	ENST00000246070.2	+	2	556		c.e2-1		RP5-1119D9.4_ENST00000443469.1_RNA|LAMP5_ENST00000427562.2_Splice_Site	NM_012261.3	NP_036393.1	Q9UJQ1	LAMP5_HUMAN	lysosomal-associated membrane protein family, member 5							cytoplasmic vesicle membrane (GO:0030659)|dendrite membrane (GO:0032590)|early endosome membrane (GO:0031901)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|endosome membrane (GO:0010008)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)											TTGTTCCGCAGATACAATGGC	0.493																																					.		Atlas-SNP	.											.	.	.	.	0			c.65-1G>T						.						89.0	85.0	86.0					20																	9496099		2203	4300	6503	SO:0001630	splice_region_variant	24141	exon2			TCCGCAGATACAA	AL121740	CCDS13106.1, CCDS56177.1	20p12	2013-03-14	2011-11-25	2011-11-25	ENSG00000125869	ENSG00000125869			16097	protein-coding gene	gene with protein product	"""brain and dendritic cell associated LAMP"""	614641	"""chromosome 20 open reading frame 103"""	C20orf103		11780052, 21642595	Standard	NM_012261		Approved	dJ1119D9.3, BAD-LAMP, UNC-43	uc002wni.2	Q9UJQ1	OTTHUMG00000031851	ENST00000246070.2:c.65-1G>T	chr20.hg19:g.9496099G>T		73.0	0.0		96.0	5.0	NM_001199897	B4DHZ7|B7Z9Z9	Splice_Site	SNP	ENST00000246070.2	hg19	CCDS13106.1	.	.	.	.	.	.	.	.	.	.	G	19.13	3.766937	0.69878	.	.	ENSG00000125869	ENST00000246070;ENST00000427562	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7362	0.96205	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C20orf103	9444099	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	7.620000	0.83070	2.678000	0.91216	0.655000	0.94253	.	.	.		0.493	LAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077946.2	NM_012261	Intron
RRBP1	6238	hgsc.bcm.edu	37	20	17596120	17596120	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:17596120C>A	ENST00000377813.1	-	23	4309	c.4006G>T	c.(4006-4008)Ggc>Tgc	p.G1336C	RRBP1_ENST00000377807.2_Missense_Mutation_p.G903C|RRBP1_ENST00000455029.2_Missense_Mutation_p.G677C|RRBP1_ENST00000246043.4_Missense_Mutation_p.G1336C|RRBP1_ENST00000470422.1_5'UTR|RRBP1_ENST00000360807.4_Missense_Mutation_p.G903C			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	1336					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						TCTAGGGGGCCGGCTGTGCGG	0.617																																					p.G903C		Atlas-SNP	.											.	RRBP1	157	.	0			c.G2707T						.						50.0	52.0	51.0					20																	17596120		2203	4300	6503	SO:0001583	missense	6238	exon23			GGGGGCCGGCTGT	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"""ribosome binding protein 1 (dog 180kD homolog)"", ""ribosome binding protein 1 homolog 180kDa (dog)"""			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.4006G>T	chr20.hg19:g.17596120C>A	ENSP00000367044:p.Gly1336Cys	76.0	0.0		55.0	4.0	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Missense_Mutation	SNP	ENST00000377813.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.04	2.415869	0.42817	.	.	ENSG00000125844	ENST00000360807;ENST00000377813;ENST00000377807;ENST00000246043;ENST00000455029	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.13	-1.17	0.09648	.	1.187640	0.06414	N	0.721149	T	0.37073	0.0990	L	0.36672	1.1	0.09310	N	1	D;D	0.76494	0.999;0.988	P;P	0.60682	0.878;0.488	T	0.33214	-0.9877	10	0.56958	D	0.05	-1.2695	5.4546	0.16584	0.0:0.3958:0.1451:0.459	.	903;1336	Q9P2E9-3;Q9P2E9	.;RRBP1_HUMAN	C	903;1336;903;1336;677	ENSP00000354045:G903C;ENSP00000367044:G1336C;ENSP00000367038:G903C;ENSP00000246043:G1336C;ENSP00000401206:G677C	ENSP00000246043:G1336C	G	-	1	0	RRBP1	17544120	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.005000	0.13129	-0.106000	0.12110	-0.265000	0.10407	GGC	.	.		0.617	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576	
GGTLC1	92086	hgsc.bcm.edu	37	20	23967085	23967085	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:23967085G>A	ENST00000335694.4	-	2	368	c.164C>T	c.(163-165)aCc>aTc	p.T55I	GGTLC1_ENST00000278765.4_Missense_Mutation_p.T55I|GGTLC1_ENST00000286890.4_Missense_Mutation_p.T55I	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	55					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						GAGGTTGATGGTGCTGGTGGC	0.622																																					p.T55I		Atlas-SNP	.											.	GGTLC1	37	.	0			c.C164T						.						18.0	18.0	18.0					20																	23967085		2201	4279	6480	SO:0001583	missense	92086	exon2			TTGATGGTGCTGG	AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"""Gamma-glutamyltransferases"""	16437	protein-coding gene	gene with protein product		612338	"""gamma-glutamyltransferase-like activity 4"", ""gamma-glutamyltransferase-like activity 3"""	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.164C>T	chr20.hg19:g.23967085G>A	ENSP00000337587:p.Thr55Ile	53.0	0.0		54.0	22.0	NM_178311	D3DW43|Q08246	Missense_Mutation	SNP	ENST00000335694.4	hg19	CCDS13163.1	.	.	.	.	.	.	.	.	.	.	g	12.80	2.045074	0.36085	.	.	ENSG00000149435	ENST00000286890;ENST00000278765;ENST00000335694	T;T;T	0.15603	2.41;2.41;2.41	0.844	0.844	0.18943	.	0.000000	0.85682	D	0.000000	T	0.54631	0.1870	H	0.99516	4.605	0.38367	D	0.944774	D	0.76494	0.999	D	0.70935	0.971	T	0.62478	-0.6846	10	0.87932	D	0	-51.049	7.477	0.27382	1.0E-4:0.0:0.9999:0.0	.	55	Q9BX51	GGTL1_HUMAN	I	55	ENSP00000286890:T55I;ENSP00000278765:T55I;ENSP00000337587:T55I	ENSP00000278765:T55I	T	-	2	0	GGTLC1	23915085	1.000000	0.71417	0.028000	0.17463	0.028000	0.11728	4.489000	0.60309	0.088000	0.17205	0.089000	0.15464	ACC	.	.		0.622	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2	
BPIFB3	359710	hgsc.bcm.edu	37	20	31657761	31657761	+	Splice_Site	SNP	G	G	T	rs372182848		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:31657761G>T	ENST00000375494.3	+	11	1217	c.1217G>T	c.(1216-1218)cGg>cTg	p.R406L		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	406					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCCCTGGAACGGTAACTTGGG	0.562																																					p.R406L		Atlas-SNP	.											.	.	.	.	0			c.G1217T						.						168.0	151.0	156.0					20																	31657761		2203	4300	6503	SO:0001630	splice_region_variant	359710	exon11			TGGAACGGTAACT	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1217+1G>T	chr20.hg19:g.31657761G>T		80.0	0.0		98.0	4.0	NM_182658	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	hg19	CCDS13212.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.021926	0.35701	.	.	ENSG00000186190	ENST00000375494	T	0.10763	2.84	4.43	4.43	0.53597	.	0.000000	0.49916	D	0.000130	T	0.31734	0.0806	M	0.80982	2.52	0.44316	D	0.997196	D	0.69078	0.997	D	0.81914	0.995	T	0.02398	-1.1165	10	0.30078	T	0.28	-19.8272	12.7225	0.57149	0.0:0.0:1.0:0.0	.	406	P59826	BPIB3_HUMAN	L	406	ENSP00000364643:R406L	ENSP00000364643:R406L	R	+	2	0	BPIFB3	31121422	1.000000	0.71417	1.000000	0.80357	0.303000	0.27691	4.189000	0.58358	2.440000	0.82611	0.655000	0.94253	CGG	.	.		0.562	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	Missense_Mutation
RBM12	10137	hgsc.bcm.edu	37	20	34240516	34240516	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:34240516G>A	ENST00000374114.3	-	3	2992	c.2729C>T	c.(2728-2730)gCc>gTc	p.A910V	RBM12_ENST00000359646.1_Missense_Mutation_p.A910V|CPNE1_ENST00000397443.1_Intron|CPNE1_ENST00000317677.5_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.A910V|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000352393.4_Intron|RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317619.3_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	910	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.					nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			AGCAGCTGTGGCTTCATCCCG	0.413																																					p.A910V		Atlas-SNP	.											.	RBM12	93	.	0			c.C2729T						.						89.0	86.0	87.0					20																	34240516		2203	4300	6503	SO:0001583	missense	10137	exon2			GCTGTGGCTTCAT	AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"""RNA binding motif (RRM) containing"""	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.2729C>T	chr20.hg19:g.34240516G>A	ENSP00000363228:p.Ala910Val	131.0	0.0		145.0	6.0	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Missense_Mutation	SNP	ENST00000374114.3	hg19	CCDS13261.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.397344	0.62177	.	.	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	T;T;T	0.18174	2.23;2.23;2.23	5.37	5.37	0.77165	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.49423	0.1556	M	0.84846	2.72	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.54029	-0.8354	10	0.87932	D	0	-4.4997	19.3135	0.94202	0.0:0.0:1.0:0.0	.	910	Q9NTZ6	RBM12_HUMAN	V	910;910;910;709	ENSP00000363228:A910V;ENSP00000352668:A910V;ENSP00000363217:A910V	ENSP00000339879:A709V	A	-	2	0	RBM12	33703930	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.263000	0.95617	2.798000	0.96311	0.650000	0.86243	GCC	.	.		0.413	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047	
KIAA1755	85449	hgsc.bcm.edu	37	20	36841909	36841909	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:36841909C>T	ENST00000279024.4	-	14	3409	c.3138G>A	c.(3136-3138)atG>atA	p.M1046I		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	1046										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				TCTCCAGGAGCATCCGGATCT	0.682																																					p.M1046I		Atlas-SNP	.											.	KIAA1755	145	.	0			c.G3138A						.						38.0	33.0	35.0					20																	36841909		2203	4300	6503	SO:0001583	missense	85449	exon14			CAGGAGCATCCGG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.3138G>A	chr20.hg19:g.36841909C>T	ENSP00000279024:p.Met1046Ile	81.0	0.0		68.0	4.0	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	hg19	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	C	5.886	0.347533	0.11126	.	.	ENSG00000149633	ENST00000279024	T	0.05319	3.46	5.29	0.843	0.18935	.	1.696560	0.03063	N	0.156110	T	0.07188	0.0182	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38929	-0.9638	10	0.38643	T	0.18	.	7.8512	0.29455	0.0963:0.4943:0.4093:0.0	.	1046	Q5JYT7	K1755_HUMAN	I	1046	ENSP00000279024:M1046I	ENSP00000279024:M1046I	M	-	3	0	KIAA1755	36275323	0.424000	0.25490	0.379000	0.26080	0.169000	0.22640	0.516000	0.22817	0.362000	0.24319	-0.304000	0.09214	ATG	.	.		0.682	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
L3MBTL1	26013	hgsc.bcm.edu	37	20	42161426	42161426	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:42161426T>C	ENST00000427442.2	+	12	1391	c.1232T>C	c.(1231-1233)cTg>cCg	p.L411P	L3MBTL1_ENST00000373135.3_Missense_Mutation_p.L343P|L3MBTL1_ENST00000373134.1_Missense_Mutation_p.L343P|L3MBTL1_ENST00000444063.1_Missense_Mutation_p.L343P|L3MBTL1_ENST00000418998.1_Missense_Mutation_p.L411P			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	343					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						CCCCCACCCCTGGGCTTCCAG	0.602																																					p.L411P		Atlas-SNP	.											.	L3MBTL1	105	.	0			c.T1232C						.						92.0	97.0	95.0					20																	42161426		2203	4300	6503	SO:0001583	missense	26013	exon12			CACCCCTGGGCTT	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"""Zinc fingers, C2HC-type containing"", ""Sterile alpha motif (SAM) domain containing"""	15905	protein-coding gene	gene with protein product	"""lethal (3) malignant brain tumor l(3)"""	608802	"""l(3)mbt (Drosophila)-like"", ""l(3)mbt-like (Drosophila)"""	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.1232T>C	chr20.hg19:g.42161426T>C	ENSP00000402107:p.Leu411Pro	159.0	0.0		125.0	5.0	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Missense_Mutation	SNP	ENST00000427442.2	hg19	CCDS46602.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.18|12.18	1.860769|1.860769	0.32884|0.32884	.|.	.|.	ENSG00000185513|ENSG00000185513	ENST00000427442;ENST00000418998;ENST00000373135;ENST00000444063;ENST00000373134;ENST00000422861|ENST00000445228	T;T;T;T;T;T|.	0.43688|.	0.94;0.94;0.94;0.94;0.94;0.94|.	5.09|5.09	3.96|3.96	0.45880|0.45880	.|.	0.531666|.	0.19869|.	N|.	0.104240|.	T|T	0.36468|0.36468	0.0968|0.0968	N|N	0.19112|0.19112	0.55|0.55	0.43226|0.43226	D|D	0.995113|0.995113	B;B;B|.	0.06786|.	0.001;0.001;0.001|.	B;B;B|.	0.09377|.	0.004;0.003;0.004|.	T|T	0.15954|0.15954	-1.0419|-1.0419	10|5	0.29301|.	T|.	0.29|.	.|.	4.2741|4.2741	0.10800|0.10800	0.0:0.2543:0.0:0.7457|0.0:0.2543:0.0:0.7457	.|.	411;343;343|.	Q9Y468-5;Q9Y468-2;Q9Y468-1|.	.;.;.|.	P|R	411;411;343;343;343;129|34	ENSP00000402107:L411P;ENSP00000398516:L411P;ENSP00000362227:L343P;ENSP00000403316:L343P;ENSP00000362226:L343P;ENSP00000410139:L129P|.	ENSP00000362226:L343P|.	L|W	+|+	2|1	0|0	L3MBTL1|L3MBTL1	41594840|41594840	0.487000|0.487000	0.25988|0.25988	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.180000|1.180000	0.32005|0.32005	2.134000|2.134000	0.65973|0.65973	0.482000|0.482000	0.46254|0.46254	CTG|TGG	.	.		0.602	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107	
SLPI	6590	hgsc.bcm.edu	37	20	43882355	43882355	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:43882355A>G	ENST00000338380.2	-	2	125	c.105T>C	c.(103-105)tgT>tgC	p.C35C		NM_003064.2	NP_003055.1	P03973	SLPI_HUMAN	secretory leukocyte peptidase inhibitor	35	Trypsin inhibitory domain.|WAP 1. {ECO:0000255|PROSITE- ProRule:PRU00722}.				negative regulation of protein binding (GO:0032091)|negative regulation of viral genome replication (GO:0045071)	extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			lung(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)				TCTTAGGAGGACAGACTCCAG	0.498																																					p.C35C	GBM(64;162 1089 31780 33427 34538)	Atlas-SNP	.											.	SLPI	13	.	0			c.T105C						.						81.0	82.0	82.0					20																	43882355		2203	4300	6503	SO:0001819	synonymous_variant	6590	exon2			AGGAGGACAGACT	X04502	CCDS13347.1	20q13.12	2013-01-21	2005-08-17		ENSG00000124107	ENSG00000124107		"""WAP four-disulfide core domain containing"""	11092	protein-coding gene	gene with protein product	"""antileukoproteinase"""	107285	"""secretory leukocyte protease inhibitor (antileukoproteinase)"""			3640338, 12206714	Standard	NM_003064		Approved	HUSI-I, ALK1, ALP, BLPI, HUSI, WAP4, WFDC4	uc002xnm.1	P03973	OTTHUMG00000033075	ENST00000338380.2:c.105T>C	chr20.hg19:g.43882355A>G		102.0	0.0		136.0	6.0	NM_003064	B2R5H8|P07757	Silent	SNP	ENST00000338380.2	hg19	CCDS13347.1																																																																																			.	.		0.498	SLPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080494.3		
MMP9	4318	hgsc.bcm.edu	37	20	44640845	44640845	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:44640845A>G	ENST00000372330.3	+	7	1086	c.1067A>G	c.(1066-1068)aAg>aGg	p.K356R	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	356	Fibronectin type-II 3. {ECO:0000255|PROSITE-ProRule:PRU00479}.				collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	TTCCTGGGTAAGGAGTACTCG	0.632																																					p.K356R		Atlas-SNP	.											.	MMP9	84	.	0			c.A1067G						.						73.0	83.0	80.0					20																	44640845		2203	4300	6503	SO:0001583	missense	4318	exon7			TGGGTAAGGAGTA		CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"""matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)"", ""matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"""	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.1067A>G	chr20.hg19:g.44640845A>G	ENSP00000361405:p.Lys356Arg	82.0	0.0		63.0	4.0	NM_004994	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	hg19	CCDS13390.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.962306	0.74016	.	.	ENSG00000100985	ENST00000372330;ENST00000545925	T	0.53206	0.63	4.89	3.76	0.43208	Peptidase M10, metallopeptidase (1);Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);Peptidase, metallopeptidase (1);	0.161334	0.53938	D	0.000047	T	0.43500	0.1250	M	0.64676	1.99	0.39890	D	0.973758	B	0.11235	0.004	B	0.10450	0.005	T	0.48603	-0.9021	10	0.51188	T	0.08	.	9.8817	0.41238	0.9072:0.0:0.0928:0.0	.	356	P14780	MMP9_HUMAN	R	356;19	ENSP00000361405:K356R	ENSP00000361405:K356R	K	+	2	0	MMP9	44074252	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	4.847000	0.62867	2.064000	0.61679	0.459000	0.35465	AAG	.	.		0.632	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1		
SLC13A3	64849	hgsc.bcm.edu	37	20	45239191	45239191	+	Silent	SNP	G	G	T	rs563338890		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:45239191G>T	ENST00000279027.4	-	3	453	c.435C>A	c.(433-435)acC>acA	p.T145T	SLC13A3_ENST00000372121.1_Silent_p.T145T|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000290317.5_Silent_p.T98T|SLC13A3_ENST00000339636.3_Silent_p.T145T|SLC13A3_ENST00000417157.2_Silent_p.T98T|SLC13A3_ENST00000413164.2_Silent_p.T145T|SLC13A3_ENST00000396360.1_Silent_p.T98T|SLC13A3_ENST00000472148.1_Silent_p.T98T|SLC13A3_ENST00000495082.1_Silent_p.T98T	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	145					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)	p.T145T(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	CAGTGGAGGCGGTGTTGCTCA	0.552																																					p.T145T		Atlas-SNP	.											SLC13A3_ENST00000339636,NS,carcinoma,0,1	SLC13A3	88	.	2	Substitution - coding silent(2)	endometrium(2)	c.C435A						.						180.0	161.0	167.0					20																	45239191		2203	4300	6503	SO:0001819	synonymous_variant	64849	exon3			GGAGGCGGTGTTG	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"""Solute carriers"""	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.435C>A	chr20.hg19:g.45239191G>T		88.0	0.0		68.0	3.0	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Silent	SNP	ENST00000279027.4	hg19	CCDS13400.1																																																																																			.	.		0.552	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2		
PCK1	5105	hgsc.bcm.edu	37	20	56137172	56137172	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:56137172C>T	ENST00000319441.4	+	3	434	c.270C>T	c.(268-270)agC>agT	p.S90S	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Intron	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	90					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			GGATCGAAAGCAAGACGGTTA	0.557																																					p.S90S		Atlas-SNP	.											.	PCK1	95	.	0			c.C270T						.						101.0	87.0	92.0					20																	56137172		2203	4300	6503	SO:0001819	synonymous_variant	5105	exon3			CGAAAGCAAGACG		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.270C>T	chr20.hg19:g.56137172C>T		117.0	0.0		95.0	5.0	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	hg19	CCDS13460.1																																																																																			.	.		0.557	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
PMEPA1	56937	hgsc.bcm.edu	37	20	56228121	56228121	+	Nonsense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:56228121C>A	ENST00000341744.3	-	3	605	c.286G>T	c.(286-288)Gag>Tag	p.E96*	PMEPA1_ENST00000265626.4_Nonsense_Mutation_p.E46*|PMEPA1_ENST00000395814.1_Nonsense_Mutation_p.E46*|PMEPA1_ENST00000395816.3_Nonsense_Mutation_p.E46*|PMEPA1_ENST00000347215.4_Nonsense_Mutation_p.E61*	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	96					androgen receptor signaling pathway (GO:0030521)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	R-SMAD binding (GO:0070412)|WW domain binding (GO:0050699)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)	16						ACTGTGCTCTCCGAGGGCCAC	0.632																																					p.E96X		Atlas-SNP	.											PMEPA1,NS,carcinoma,0,1	PMEPA1	29	.	0			c.G286T						.						114.0	69.0	84.0					20																	56228121		2203	4300	6503	SO:0001587	stop_gained	56937	exon3			TGCTCTCCGAGGG	AF224278	CCDS13462.1, CCDS13463.1, CCDS13464.1	20q13.31-q13.33	2008-04-03	2008-04-03	2008-04-03	ENSG00000124225	ENSG00000124225			14107	protein-coding gene	gene with protein product	"""solid tumor-associated 1"""	606564	"""transmembrane, prostate androgen induced RNA"""	TMEPAI		10873380	Standard	NM_020182		Approved	STAG1	uc002xyq.4	Q969W9	OTTHUMG00000032831	ENST00000341744.3:c.286G>T	chr20.hg19:g.56228121C>A	ENSP00000345826:p.Glu96*	83.0	0.0		109.0	35.0	NM_020182	Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Nonsense_Mutation	SNP	ENST00000341744.3	hg19	CCDS13463.1	.	.	.	.	.	.	.	.	.	.	C	37	5.995370	0.97184	.	.	ENSG00000124225	ENST00000341744;ENST00000347215;ENST00000395816;ENST00000265626;ENST00000395814;ENST00000414037;ENST00000395819	.	.	.	4.51	4.51	0.55191	.	0.168609	0.50627	D	0.000104	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-14.1401	16.852	0.85996	0.0:1.0:0.0:0.0	.	.	.	.	X	96;61;46;46;46;68;153	.	ENSP00000265626:E46X	E	-	1	0	PMEPA1	55661527	1.000000	0.71417	0.880000	0.34516	0.820000	0.46376	6.525000	0.73795	2.055000	0.61198	0.655000	0.94253	GAG	.	.		0.632	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	NM_020182	
GNAS	2778	hgsc.bcm.edu	37	20	57428565	57428565	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:57428565A>G	ENST00000371100.4	+	1	797	c.245A>G	c.(244-246)aAc>aGc	p.N82S	GNAS_ENST00000371102.4_Missense_Mutation_p.N82S|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371099.2_Missense_Mutation_p.N82S|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000306120.3_Missense_Mutation_p.T19A|GNAS-AS1_ENST00000424094.2_RNA|GNAS_ENST00000371075.3_Intron|GNAS-AS1_ENST00000598163.1_RNA	NM_001077490.1|NM_080425.2	NP_001070958.1|NP_536350.2	P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			CAGGTCCTCAACCCGGCATTC	0.612			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											p.N82S	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	.	GNAS	867	.	0			c.A245G						.						24.0	27.0	26.0					20																	57428565		1926	4132	6058	SO:0001583	missense	2778	exon1			TCCTCAACCCGGC	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371100.4:c.245A>G	chr20.hg19:g.57428565A>G	ENSP00000360141:p.Asn82Ser	91.0	0.0		81.0	5.0	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371100.4	hg19	CCDS46622.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.014|0.014	-1.575764|-1.575764	0.00887|0.00887	.|.	.|.	ENSG00000087460|ENSG00000087460	ENST00000371099;ENST00000371100;ENST00000371102|ENST00000306120	D;D|.	0.87103|.	-2.21;-2.21|.	4.55|4.55	-6.59|-6.59	0.01830|0.01830	.|.	.|.	.|.	.|.	.|.	T|T	0.08223|0.08223	0.0205|0.0205	N|N	0.02011|0.02011	-0.69|-0.69	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.31806|0.31806	-0.9930|-0.9930	9|6	0.02654|0.22706	T|T	1|0.39	.|.	5.8641|5.8641	0.18765|0.18765	0.4709:0.2422:0.2869:0.0|0.4709:0.2422:0.2869:0.0	.|.	82|.	Q5JWF2|.	GNAS1_HUMAN|.	S|A	82|19	ENSP00000360141:N82S;ENSP00000360143:N82S|.	ENSP00000360140:N82S|ENSP00000302237:T19A	N|T	+|+	2|1	0|0	GNAS|GNAS	56861960|56861960	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.019000|0.019000	0.09904|0.09904	-0.562000|-0.562000	0.05950|0.05950	-0.941000|-0.941000	0.03700|0.03700	-0.410000|-0.410000	0.06199|0.06199	AAC|ACC	.	.		0.612	GNAS-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080417.3	NM_000516	
ZNF831	128611	hgsc.bcm.edu	37	20	57768791	57768791	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:57768791T>C	ENST00000371030.2	+	1	2717	c.2717T>C	c.(2716-2718)cTg>cCg	p.L906P		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	906							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GCTACCCCACTGCATCCTGCA	0.662																																					p.L906P		Atlas-SNP	.											.	ZNF831	287	.	0			c.T2717C						.						29.0	32.0	31.0					20																	57768791		1982	4158	6140	SO:0001583	missense	128611	exon1			CCCCACTGCATCC	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.2717T>C	chr20.hg19:g.57768791T>C	ENSP00000360069:p.Leu906Pro	91.0	0.0		92.0	4.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	T	7.008	0.556245	0.13436	.	.	ENSG00000124203	ENST00000371030	T	0.05258	3.47	4.63	-9.26	0.00662	.	3.549510	0.01228	N	0.008267	T	0.03695	0.0105	N	0.17082	0.46	0.09310	N	0.999996	B	0.09022	0.002	B	0.06405	0.002	T	0.30679	-0.9970	10	0.87932	D	0	3.0326	3.6093	0.08054	0.1793:0.436:0.195:0.1897	.	906	Q5JPB2	ZN831_HUMAN	P	906	ENSP00000360069:L906P	ENSP00000360069:L906P	L	+	2	0	ZNF831	57202186	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.690000	0.00831	-3.191000	0.00219	-1.378000	0.01179	CTG	.	.		0.662	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
MRGBP	55257	hgsc.bcm.edu	37	20	61428015	61428015	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:61428015A>G	ENST00000370487.3	+	1	211	c.140A>G	c.(139-141)aAg>aGg	p.K47R		NM_018270.4	NP_060740.1	Q9NV56	MRGBP_HUMAN	MRG/MORF4L binding protein	47					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	H4/H2A histone acetyltransferase complex (GO:0043189)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CTGGGCCACAAGCCCGTCGGT	0.781																																					p.K47R		Atlas-SNP	.											.	.	.	.	0			c.A140G						.						14.0	14.0	14.0					20																	61428015		2088	4082	6170	SO:0001583	missense	55257	exon1			GCCACAAGCCCGT	AK001776	CCDS13503.1	20q13.33	2012-10-29	2012-10-29	2012-10-29	ENSG00000101189	ENSG00000101189			15866	protein-coding gene	gene with protein product		611157	"""chromosome 20 open reading frame 20"""	C20orf20		12963728	Standard	NM_018270		Approved	FLJ10914, MRG15BP, Eaf7	uc002ydi.3	Q9NV56	OTTHUMG00000032940	ENST00000370487.3:c.140A>G	chr20.hg19:g.61428015A>G	ENSP00000359518:p.Lys47Arg	51.0	0.0		53.0	4.0	NM_018270	A8C4L5	Missense_Mutation	SNP	ENST00000370487.3	hg19	CCDS13503.1	.	.	.	.	.	.	.	.	.	.	A	12.95	2.092136	0.36952	.	.	ENSG00000101189	ENST00000370487	.	.	.	2.96	2.96	0.34315	.	0.200642	0.43110	N	0.000610	T	0.46619	0.1402	L	0.42529	1.33	0.54753	D	0.999989	B	0.20459	0.045	B	0.21360	0.034	T	0.37731	-0.9693	9	0.26408	T	0.33	-10.9024	11.2412	0.48970	1.0:0.0:0.0:0.0	.	47	Q9NV56	MRGBP_HUMAN	R	47	.	ENSP00000359518:K47R	K	+	2	0	C20orf20	60898460	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.332000	0.59279	1.211000	0.43351	0.323000	0.21402	AAG	.	.		0.781	MRGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080080.1	NM_018270	
DIDO1	11083	hgsc.bcm.edu	37	20	61511261	61511261	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:61511261G>T	ENST00000266070.4	-	16	6372	c.6047C>A	c.(6046-6048)cCg>cAg	p.P2016Q	DIDO1_ENST00000395343.1_Missense_Mutation_p.P2016Q	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	2016	Pro-rich.				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)					CATCACCTGCGGGGCCTGGCC	0.687																																					p.P2016Q	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.C6047A						.						36.0	47.0	44.0					20																	61511261		2177	4264	6441	SO:0001583	missense	11083	exon16			ACCTGCGGGGCCT	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.6047C>A	chr20.hg19:g.61511261G>T	ENSP00000266070:p.Pro2016Gln	72.0	0.0		74.0	4.0	NM_001193369	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	.	.	.	.	.	.	.	.	.	.	G	1.534	-0.543597	0.04053	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.08546	3.08;3.08	4.94	3.92	0.45320	.	1.080270	0.07312	N	0.876107	T	0.06645	0.0170	N	0.13098	0.295	0.19300	N	0.99998	B	0.24675	0.109	B	0.19391	0.025	T	0.22661	-1.0210	10	0.32370	T	0.25	-1.6771	12.2577	0.54633	0.0:0.0:0.7274:0.2726	.	2016	Q9BTC0	DIDO1_HUMAN	Q	2016	ENSP00000266070:P2016Q;ENSP00000378752:P2016Q	ENSP00000266070:P2016Q	P	-	2	0	DIDO1	60981706	0.822000	0.29219	0.029000	0.17559	0.088000	0.18126	2.359000	0.44142	2.277000	0.76020	0.561000	0.74099	CCG	.	.		0.687	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
SLC17A9	63910	hgsc.bcm.edu	37	20	61597040	61597040	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr20:61597040G>T	ENST00000370351.4	+	10	1155	c.1024G>T	c.(1024-1026)Gca>Tca	p.A342S	SLC17A9_ENST00000370349.3_Missense_Mutation_p.A336S|SLC17A9_ENST00000488738.1_3'UTR	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	342					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						TGTGGTCTTTGCATCAGCCTC	0.647																																					p.A342S		Atlas-SNP	.											.	SLC17A9	54	.	0			c.G1024T						.						121.0	132.0	128.0					20																	61597040		2110	4231	6341	SO:0001583	missense	63910	exon10			GTCTTTGCATCAG	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.1024G>T	chr20.hg19:g.61597040G>T	ENSP00000359376:p.Ala342Ser	98.0	0.0		97.0	4.0	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Missense_Mutation	SNP	ENST00000370351.4	hg19	CCDS42901.1	.	.	.	.	.	.	.	.	.	.	G	18.10	3.547382	0.65311	.	.	ENSG00000101194	ENST00000370351;ENST00000370349	T;T	0.59638	0.25;0.25	4.8	4.8	0.61643	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.053916	0.85682	D	0.000000	T	0.55257	0.1909	N	0.20685	0.6	0.58432	D	0.999991	B;B;B	0.34241	0.444;0.283;0.24	P;B;B	0.45276	0.475;0.326;0.219	T	0.62001	-0.6946	10	0.66056	D	0.02	.	17.8649	0.88793	0.0:0.0:1.0:0.0	.	362;342;336	B4DPU8;Q9BYT1;Q9BYT1-2	.;S17A9_HUMAN;.	S	342;336	ENSP00000359376:A342S;ENSP00000359374:A336S	ENSP00000359374:A336S	A	+	1	0	SLC17A9	61067485	1.000000	0.71417	0.271000	0.24616	0.089000	0.18198	8.533000	0.90617	2.202000	0.70862	0.561000	0.74099	GCA	.	.		0.647	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082	
ADAMTS5	11096	hgsc.bcm.edu	37	21	28296469	28296469	+	Missense_Mutation	SNP	G	G	A	rs368781824		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:28296469G>A	ENST00000284987.5	-	8	2817	c.2696C>T	c.(2695-2697)aCg>aTg	p.T899M	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	899	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.T899M(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						GCACTGCACCGTTCTGGTGTG	0.542																																					p.T899M	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											ADAMTS5,NS,NS,0,1	ADAMTS5	184	.	1	Substitution - Missense(1)	pancreas(1)	c.C2696T						.	G	MET/THR	0,4406		0,0,2203	92.0	79.0	83.0		2696	5.2	1.0	21		83	2,8598	2.2+/-6.3	0,2,4298	no	missense	ADAMTS5	NM_007038.3	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	899/931	28296469	2,13004	2203	4300	6503	SO:0001583	missense	11096	exon8			TGCACCGTTCTGG	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.2696C>T	chr21.hg19:g.28296469G>A	ENSP00000284987:p.Thr899Met	45.0	0.0		47.0	2.0	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	hg19	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.483244	0.63962	0.0	2.33E-4	ENSG00000154736	ENST00000284987	T	0.54279	0.58	6.07	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.53334	0.1790	L	0.58428	1.81	0.58432	D	0.999998	P	0.44521	0.837	B	0.42593	0.392	T	0.56498	-0.7969	10	0.46703	T	0.11	.	15.649	0.77076	0.0654:0.0:0.9346:0.0	.	899	Q9UNA0	ATS5_HUMAN	M	899	ENSP00000284987:T899M	ENSP00000284987:T899M	T	-	2	0	ADAMTS5	27218340	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.398000	0.79919	1.595000	0.50050	-0.119000	0.15052	ACG	.	.		0.542	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
KCNJ15	3772	hgsc.bcm.edu	37	21	39672189	39672189	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:39672189A>G	ENST00000328656.4	+	4	1309	c.1006A>G	c.(1006-1008)Agc>Ggc	p.S336G	KCNJ15_ENST00000398930.1_Missense_Mutation_p.S336G|KCNJ15_ENST00000398932.1_Missense_Mutation_p.S336G|KCNJ15_ENST00000398934.1_Missense_Mutation_p.S336G|KCNJ15_ENST00000398938.2_Missense_Mutation_p.S336G	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	336					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)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	GATTCGGAAAAGCCCAGATTG	0.433																																					p.T336A		Atlas-SNP	.											.	KCNJ15	43	.	0			c.A1006G						.						63.0	63.0	63.0					21																	39672189		2203	4300	6503	SO:0001583	missense	3772	exon4			CGGAAAAGCCCAG	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.1006A>G	chr21.hg19:g.39672189A>G	ENSP00000331698:p.Ser336Gly	167.0	0.0		150.0	6.0	NM_002243	D3DSH5|O00564|Q96L28|Q99446	Missense_Mutation	SNP	ENST00000328656.4	hg19	CCDS13656.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.772990	0.49680	.	.	ENSG00000157551	ENST00000328656;ENST00000398938;ENST00000398932;ENST00000398930;ENST00000398934	D;D;D;D;D	0.94000	-3.33;-3.33;-3.33;-3.33;-3.33	5.83	5.83	0.93111	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.152159	0.64402	D	0.000020	D	0.90971	0.7161	L	0.46157	1.445	0.38934	D	0.958018	P	0.36086	0.536	B	0.40702	0.338	D	0.89817	0.3986	9	.	.	.	.	11.3152	0.49388	0.8643:0.0:0.0:0.1357	.	336	Q99712	IRK15_HUMAN	G	336	ENSP00000331698:S336G;ENSP00000381911:S336G;ENSP00000381905:S336G;ENSP00000381904:S336G;ENSP00000381907:S336G	.	S	+	1	0	KCNJ15	38594059	1.000000	0.71417	0.994000	0.49952	0.951000	0.60555	4.955000	0.63638	2.236000	0.73375	0.533000	0.62120	AGC	.	.		0.433	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243	
BRWD1	54014	hgsc.bcm.edu	37	21	40568902	40568902	+	Silent	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:40568902C>T	ENST00000333229.2	-	41	6420	c.6093G>A	c.(6091-6093)agG>agA	p.R2031R	BRWD1_ENST00000380800.3_Silent_p.R2031R|BRWD1_ENST00000342449.3_Silent_p.R2031R	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	2031					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TATTGGTATGCCTGTGCTTGT	0.398																																					p.R2031R	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.G6093A						.						165.0	155.0	158.0					21																	40568902		2203	4300	6503	SO:0001819	synonymous_variant	54014	exon41			GGTATGCCTGTGC	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.6093G>A	chr21.hg19:g.40568902C>T		139.0	0.0		113.0	5.0	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	hg19	CCDS13662.1																																																																																			.	.		0.398	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
TFF3	7033	hgsc.bcm.edu	37	21	43733711	43733711	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:43733711T>C	ENST00000518498.1	-	2	389	c.155A>G	c.(154-156)gAc>gGc	p.D52G	TFF3_ENST00000489676.1_5'UTR|TFF3_ENST00000291525.10_Missense_Mutation_p.D88G			Q07654	TFF3_HUMAN	trefoil factor 3 (intestinal)	38	P-type. {ECO:0000255|PROSITE- ProRule:PRU00779}.				defense response (GO:0006952)|digestion (GO:0007586)|response to peptide hormone (GO:0043434)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)				cervix(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	6						GTCCACCCTGTCCTTGGCTGG	0.602																																					p.D52G		Atlas-SNP	.											.	TFF3	9	.	0			c.A155G						.						52.0	46.0	48.0					21																	43733711		2203	4300	6503	SO:0001583	missense	7033	exon2			ACCCTGTCCTTGG	AF432265	CCDS33565.1, CCDS33565.2	21q22.3	2006-05-16			ENSG00000160180	ENSG00000160180			11757	protein-coding gene	gene with protein product		600633				7718582, 9043862	Standard	NM_003226		Approved	HITF, ITF	uc002zav.3	Q07654	OTTHUMG00000086798	ENST00000518498.1:c.155A>G	chr21.hg19:g.43733711T>C	ENSP00000430690:p.Asp52Gly	111.0	0.0		70.0	4.0	NM_003226	E9PBB5|Q96NX0|Q9UDA5	Missense_Mutation	SNP	ENST00000518498.1	hg19	CCDS33565.2	.	.	.	.	.	.	.	.	.	.	T	14.08	2.430026	0.43122	.	.	ENSG00000160180	ENST00000518498;ENST00000291525;ENST00000398431	T;T	0.56275	0.47;0.47	4.31	1.61	0.23674	P-type trefoil (5);	0.774326	0.11500	N	0.557742	T	0.41213	0.1149	.	.	.	0.09310	N	1	P	0.39576	0.679	B	0.41946	0.371	T	0.20806	-1.0264	8	.	.	.	-17.236	5.0381	0.14445	0.358:0.0:0.2324:0.4095	.	38	Q07654	TFF3_HUMAN	G	52;88;40	ENSP00000430690:D52G;ENSP00000291525:D88G	.	D	-	2	0	TFF3	42606780	0.187000	0.23238	0.749000	0.31150	0.918000	0.54935	0.383000	0.20651	0.475000	0.27415	0.459000	0.35465	GAC	.	.		0.602	TFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195358.2	NM_003226	
SIK1	150094	hgsc.bcm.edu	37	21	44839238	44839238	+	Nonsense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:44839238G>A	ENST00000270162.6	-	10	1372	c.1240C>T	c.(1240-1242)Cag>Tag	p.Q414*		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	414					cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	CTCACCCACTGCAGCGAGCTC	0.682																																					p.Q414X		Atlas-SNP	.											.	SIK1	65	.	0			c.C1240T						.						33.0	36.0	35.0					21																	44839238		2196	4296	6492	SO:0001587	stop_gained	150094	exon10			CCCACTGCAGCGA	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"""myocardial SNF1-like kinase"""	605705	"""SNF1-like kinase"""	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.1240C>T	chr21.hg19:g.44839238G>A	ENSP00000270162:p.Gln414*	125.0	0.0		100.0	4.0	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Nonsense_Mutation	SNP	ENST00000270162.6	hg19	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	G	37	6.602117	0.97697	.	.	ENSG00000142178	ENST00000270162	.	.	.	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	15.3475	0.74350	0.0:0.0:1.0:0.0	.	.	.	.	X	414	.	ENSP00000270162:Q414X	Q	-	1	0	SIK1	43663666	1.000000	0.71417	0.956000	0.39512	0.410000	0.31052	6.371000	0.73119	2.289000	0.77006	0.561000	0.74099	CAG	.	.		0.682	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354	
MCM3AP	8888	hgsc.bcm.edu	37	21	47704423	47704423	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:47704423C>T	ENST00000397708.1	-	2	1032	c.778G>A	c.(778-780)Ggc>Agc	p.G260S	YBEY_ENST00000397691.1_5'Flank|YBEY_ENST00000329319.3_5'Flank|YBEY_ENST00000397694.1_5'Flank|YBEY_ENST00000397701.4_5'Flank|MCM3AP_ENST00000291688.1_Missense_Mutation_p.G260S|YBEY_ENST00000339195.6_5'Flank|YBEY_ENST00000397692.1_5'Flank			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	260	FG-repeats.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					AAAGGTTCGCCCAAAACCGCA	0.463																																					p.G260S		Atlas-SNP	.											.	MCM3AP	146	.	0			c.G778A						.						80.0	81.0	80.0					21																	47704423		2203	4300	6503	SO:0001583	missense	8888	exon1			GTTCGCCCAAAAC	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.778G>A	chr21.hg19:g.47704423C>T	ENSP00000380820:p.Gly260Ser	103.0	0.0		99.0	5.0	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	C	7.202	0.593703	0.13875	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.16597	2.33;2.33	4.9	4.9	0.64082	.	0.325990	0.32671	N	0.005784	T	0.13670	0.0331	L	0.29908	0.895	0.09310	N	1	B	0.27823	0.19	B	0.27608	0.081	T	0.15435	-1.0437	10	0.35671	T	0.21	-12.7957	13.3539	0.60617	0.0:0.8405:0.1595:0.0	.	260	O60318	MCM3A_HUMAN	S	260	ENSP00000380820:G260S;ENSP00000291688:G260S	ENSP00000291688:G260S	G	-	1	0	MCM3AP	46528851	0.536000	0.26378	0.051000	0.19133	0.041000	0.13682	1.576000	0.36504	2.537000	0.85549	0.563000	0.77884	GGC	.	.		0.463	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
DIP2A	23181	hgsc.bcm.edu	37	21	47983806	47983806	+	Silent	SNP	C	C	A	rs201790767	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr21:47983806C>A	ENST00000417564.2	+	35	4146	c.4125C>A	c.(4123-4125)acC>acA	p.T1375T	DIP2A_ENST00000318711.7_Silent_p.T1376T|DIP2A_ENST00000479654.1_3'UTR|DIP2A_ENST00000400274.1_Silent_p.T1371T			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1375					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TCGCACACACCGAGACCAAAG	0.562																																					p.T1375T		Atlas-SNP	.											.	DIP2A	332	.	0			c.C4125A						.						64.0	65.0	65.0					21																	47983806		1940	4156	6096	SO:0001819	synonymous_variant	23181	exon35			ACACACCGAGACC	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.4125C>A	chr21.hg19:g.47983806C>A		105.0	0.0		85.0	4.0	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	hg19	CCDS46655.1																																																																																			.	C|0.996;G|0.004		0.562	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
TSSK2	23617	hgsc.bcm.edu	37	22	19119730	19119730	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:19119730A>G	ENST00000399635.2	+	1	1410	c.818A>G	c.(817-819)cAg>cGg	p.Q273R	DGCR14_ENST00000252137.6_3'UTR	NM_053006.4	NP_443732.3	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	273					multicellular organismal development (GO:0007275)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(2)|lung(2)|prostate(4)|stomach(1)	11	Colorectal(54;0.0993)					TCGTGGCTGCAGCCCCCCAAG	0.617																																					p.Q273R		Atlas-SNP	.											.	TSSK2	29	.	0			c.A818G						.						51.0	46.0	48.0					22																	19119730		2203	4300	6503	SO:0001583	missense	23617	exon1			GGCTGCAGCCCCC	AF362953	CCDS13755.1	22q11.21	2007-01-30	2005-03-10	2005-03-12	ENSG00000206203	ENSG00000206203			11401	protein-coding gene	gene with protein product		610710	"""serine/threonine kinase 22B (spermiogenesis associated)"""	STK22B		10591208	Standard	NM_053006		Approved	SPOGA2, FLJ38613	uc002zow.2	Q96PF2	OTTHUMG00000150118	ENST00000399635.2:c.818A>G	chr22.hg19:g.19119730A>G	ENSP00000382544:p.Gln273Arg	94.0	0.0		80.0	4.0	NM_053006	Q8IY55	Missense_Mutation	SNP	ENST00000399635.2	hg19	CCDS13755.1	.	.	.	.	.	.	.	.	.	.	A	10.84	1.464904	0.26335	.	.	ENSG00000206203	ENST00000399635	D	0.82433	-1.61	5.7	5.7	0.88788	Protein kinase-like domain (1);	0.000000	0.48767	D	0.000161	T	0.72938	0.3523	N	0.19112	0.55	0.36448	D	0.865923	B	0.11235	0.004	B	0.15870	0.014	T	0.72846	-0.4169	10	0.46703	T	0.11	.	13.4997	0.61447	1.0:0.0:0.0:0.0	.	273	Q96PF2	TSSK2_HUMAN	R	273	ENSP00000382544:Q273R	ENSP00000382544:Q273R	Q	+	2	0	TSSK2	17499730	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.191000	0.72063	2.172000	0.68678	0.533000	0.62120	CAG	.	.		0.617	TSSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316431.1		
SLC25A1	6576	hgsc.bcm.edu	37	22	19164138	19164138	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:19164138T>C	ENST00000215882.5	-	7	856	c.700A>G	c.(700-702)Agt>Ggt	p.S234G	SLC25A1_ENST00000461267.1_5'Flank|CLTCL1_ENST00000442042.2_5'Flank|SLC25A1_ENST00000451283.1_Missense_Mutation_p.S131G	NM_005984.3	NP_005975.1	P53007	TXTP_HUMAN	solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1	234					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)		CCAAAGACACTGGCTGCGCCT	0.607																																					p.S241G		Atlas-SNP	.											.	SLC25A1	14	.	0			c.A721G						.						47.0	53.0	51.0					22																	19164138		2203	4299	6502	SO:0001583	missense	6576	exon6			AGACACTGGCTGC	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.700A>G	chr22.hg19:g.19164138T>C	ENSP00000215882:p.Ser234Gly	118.0	0.0		99.0	4.0	NM_001256534	A8K8E8|Q9BSK6	Missense_Mutation	SNP	ENST00000215882.5	hg19	CCDS13758.1	.	.	.	.	.	.	.	.	.	.	T	19.94	3.919203	0.73098	.	.	ENSG00000100075	ENST00000215882;ENST00000451283	T;T	0.80123	-1.34;-1.34	5.48	4.44	0.53790	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.83876	0.5349	L	0.42529	1.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.80018	-0.1558	10	0.24483	T	0.36	-12.6986	11.4081	0.49911	0.0:0.0713:0.0:0.9287	.	241;234	D9HTE9;P53007	.;TXTP_HUMAN	G	234;131	ENSP00000215882:S234G;ENSP00000401480:S131G	ENSP00000215882:S234G	S	-	1	0	SLC25A1	17544138	1.000000	0.71417	0.999000	0.59377	0.259000	0.26198	7.983000	0.88140	0.895000	0.36342	0.379000	0.24179	AGT	.	.		0.607	SLC25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316441.1	NM_005984	
TANGO2	128989	hgsc.bcm.edu	37	22	20043483	20043483	+	Missense_Mutation	SNP	T	T	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:20043483T>G	ENST00000327374.4	+	6	576	c.398T>G	c.(397-399)gTc>gGc	p.V133G	TANGO2_ENST00000456048.1_Missense_Mutation_p.V138G|TANGO2_ENST00000434570.2_Missense_Mutation_p.V174G|TANGO2_ENST00000401833.1_Missense_Mutation_p.V174G|TANGO2_ENST00000398042.2_Intron|TANGO2_ENST00000432883.1_Intron|TANGO2_ENST00000420290.2_Missense_Mutation_p.V35G|TANGO2_ENST00000447208.2_Missense_Mutation_p.V133G|TANGO2_ENST00000401886.1_Intron	NM_001283106.1|NM_001283116.1|NM_001283148.1|NM_001283154.1|NM_152906.4	NP_001270035.1|NP_001270045.1|NP_001270077.1|NP_001270083.1|NP_690870.3	Q6ICL3	TNG2_HUMAN	transport and golgi organization 2 homolog (Drosophila)	133																	AAGGGAGACGTCATTTGCTAC	0.587																																					p.V133G		Atlas-SNP	.											C22orf25,colon,carcinoma,0,1	TANGO2	4	.	0			c.T398G						.						141.0	115.0	124.0					22																	20043483		2203	4300	6503	SO:0001583	missense	128989	exon6			GAGACGTCATTTG		CCDS13772.1, CCDS63404.1, CCDS63405.1, CCDS63406.1, CCDS63407.1, CCDS74821.1, CCDS74822.1	22q11.21	2012-12-13	2012-12-13	2012-12-13	ENSG00000183597	ENSG00000183597			25439	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 25"""	C22orf25		12477932	Standard	XM_005261222		Approved	DKFZp761P1121	uc002zrc.1	Q6ICL3	OTTHUMG00000150510	ENST00000327374.4:c.398T>G	chr22.hg19:g.20043483T>G	ENSP00000332721:p.Val133Gly	126.0	0.0		118.0	5.0	NM_152906	A8MUE9|B7WNV6|B7Z583|B7Z730|D3DX23|Q8IW05|Q8NAL0|Q8TCS0|Q96M16	Missense_Mutation	SNP	ENST00000327374.4	hg19	CCDS13772.1	.	.	.	.	.	.	.	.	.	.	T	11.50	1.656608	0.29425	.	.	ENSG00000183597	ENST00000447208;ENST00000450664;ENST00000327374;ENST00000401833;ENST00000434168;ENST00000434570;ENST00000420290;ENST00000456048	T;T;T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98;1.98;1.98	4.52	4.52	0.55395	.	0.475882	0.21803	N	0.068885	T	0.17704	0.0425	N	0.25144	0.715	0.58432	D	0.999999	P;B;P;P;P;B	0.48407	0.709;0.08;0.891;0.91;0.807;0.408	B;B;P;P;B;B	0.48368	0.288;0.036;0.575;0.475;0.215;0.305	T	0.03000	-1.1084	10	0.20519	T	0.43	-21.2036	10.4191	0.44340	0.0:0.0:0.0:1.0	.	133;174;35;174;138;133	B7Z9Q5;B7Z730;B7Z583;B7WNV6;C9JC99;Q6ICL3	.;.;.;.;.;CV025_HUMAN	G	133;133;133;174;133;174;35;138	ENSP00000389797:V133G;ENSP00000415450:V133G;ENSP00000332721:V133G;ENSP00000384827:V174G;ENSP00000411602:V133G;ENSP00000391262:V174G;ENSP00000396182:V35G;ENSP00000403645:V138G	ENSP00000332721:V133G	V	+	2	0	C22orf25	18423483	0.150000	0.22732	0.276000	0.24689	0.919000	0.55068	3.388000	0.52509	2.021000	0.59480	0.460000	0.39030	GTC	.	.		0.587	TANGO2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318689.2	NM_152906	
KLHL22	84861	hgsc.bcm.edu	37	22	20796519	20796519	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:20796519G>A	ENST00000328879.4	-	7	1902	c.1746C>T	c.(1744-1746)tcC>tcT	p.S582S	KLHL22_ENST00000440659.2_Silent_p.S439S	NM_032775.3	NP_116164.2	Q53GT1	KLH22_HUMAN	kelch-like family member 22	582					cell division (GO:0051301)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein monoubiquitination (GO:0006513)	centrosome (GO:0005813)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|polar microtubule (GO:0005827)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|skin(2)|upper_aerodigestive_tract(1)	20	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			GGCCTGAGATGGAGTTGTCCA	0.677																																					p.S582S		Atlas-SNP	.											.	KLHL22	52	.	0			c.C1746T						.						42.0	43.0	43.0					22																	20796519		2202	4300	6502	SO:0001819	synonymous_variant	84861	exon7			TGAGATGGAGTTG		CCDS13780.1	22q11.21	2013-01-30	2013-01-30		ENSG00000099910	ENSG00000099910		"""Kelch-like"", ""BTB/POZ domain containing"""	25888	protein-coding gene	gene with protein product			"""kelch-like 22 (Drosophila)"""			12477932	Standard	NM_032775		Approved	FLJ14360, KELCHL	uc002zsl.2	Q53GT1	OTTHUMG00000150778	ENST00000328879.4:c.1746C>T	chr22.hg19:g.20796519G>A		129.0	0.0		97.0	4.0	NM_032775	A8K3Q4|A8MTV3|B7Z2G1|D3DX30|Q96B68|Q96KC6	Silent	SNP	ENST00000328879.4	hg19	CCDS13780.1																																																																																			.	.		0.677	KLHL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320045.2	NM_032775	
SLC2A11	66035	hgsc.bcm.edu	37	22	24217341	24217341	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:24217341T>C	ENST00000345044.6	+	4	587	c.319T>C	c.(319-321)Tca>Cca	p.S107P	AP000350.10_ENST00000433835.3_Missense_Mutation_p.S72P|SLC2A11_ENST00000405847.1_Missense_Mutation_p.S107P|SLC2A11_ENST00000398356.2_Missense_Mutation_p.S114P|SLC2A11_ENST00000467660.1_3'UTR|SLC2A11_ENST00000316185.8_Missense_Mutation_p.S110P			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11	107					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						CTTTGTGGTGTCAGCAGCAAT	0.532																																					p.S114P		Atlas-SNP	.											.	SLC2A11	32	.	0			c.T340C						.						85.0	77.0	80.0					22																	24217341		2203	4300	6503	SO:0001583	missense	66035	exon5			GTGGTGTCAGCAG	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.319T>C	chr22.hg19:g.24217341T>C	ENSP00000342542:p.Ser107Pro	76.0	0.0		77.0	4.0	NM_030807	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Missense_Mutation	SNP	ENST00000345044.6	hg19	CCDS46673.1	.	.	.	.	.	.	.	.	.	.	T	6.890	0.533609	0.13188	.	.	ENSG00000133460;ENSG00000133460;ENSG00000133460;ENSG00000133460;ENSG00000133460;ENSG00000133460;ENSG00000133460;ENSG00000251357	ENST00000345044;ENST00000398356;ENST00000398363;ENST00000398359;ENST00000405847;ENST00000407566;ENST00000316185;ENST00000433835	T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81	3.68	0.265	0.15612	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.218800	0.05794	N	0.611008	T	0.68357	0.2992	L	0.49126	1.545	0.09310	N	1	B;P;B;B;P;P	0.42203	0.159;0.507;0.082;0.33;0.507;0.773	B;B;B;B;B;B	0.43838	0.116;0.433;0.104;0.319;0.251;0.433	T	0.57670	-0.7771	10	0.72032	D	0.01	.	1.1429	0.01769	0.2177:0.1702:0.4309:0.1812	.	110;114;110;107;114;114	B4E2T0;E7ENI4;Q9BYW1-3;Q9BYW1;E9PH55;Q6P4C1	.;.;.;GTR11_HUMAN;.;.	P	107;114;107;114;107;114;110;72	ENSP00000342542:S107P;ENSP00000381399:S114P;ENSP00000384987:S107P;ENSP00000326748:S110P	ENSP00000400325:S72P	S	+	1	0	AP000350.10;SLC2A11	22547341	0.000000	0.05858	0.112000	0.21494	0.090000	0.18270	-0.347000	0.07750	0.021000	0.15133	-0.526000	0.04340	TCA	.	.		0.532	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319889.3	NM_030807	
UPB1	51733	hgsc.bcm.edu	37	22	24896100	24896100	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:24896100T>C	ENST00000326010.5	+	2	474	c.130T>C	c.(130-132)Ttc>Ctc	p.F44L	UPB1_ENST00000382760.2_Missense_Mutation_p.F44L|UPB1_ENST00000413389.2_Intron	NM_016327.2	NP_057411.1	Q9UBR1	BUP1_HUMAN	ureidopropionase, beta	44					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	beta-ureidopropionase activity (GO:0003837)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	22	Colorectal(2;0.0339)					CAGGGAAGCTTTCGAAGCTGC	0.522																																					p.F44L		Atlas-SNP	.											.	UPB1	60	.	0			c.T130C						.						89.0	87.0	87.0					22																	24896100		2203	4300	6503	SO:0001583	missense	51733	exon2			GAAGCTTTCGAAG	AB013885	CCDS13827.1	22q11.2	2008-04-11			ENSG00000100024	ENSG00000100024			16297	protein-coding gene	gene with protein product		606673				10542323	Standard	XR_244378		Approved	BUP1	uc003aaf.3	Q9UBR1	OTTHUMG00000150749	ENST00000326010.5:c.130T>C	chr22.hg19:g.24896100T>C	ENSP00000324343:p.Phe44Leu	32.0	0.0		36.0	4.0	NM_016327	A3KMF8|Q9UIR3	Missense_Mutation	SNP	ENST00000326010.5	hg19	CCDS13827.1	.	.	.	.	.	.	.	.	.	.	T	4.862	0.160319	0.09287	.	.	ENSG00000100024	ENST00000326010;ENST00000382760;ENST00000426507	T;T	0.74842	-0.88;-0.88	4.73	1.27	0.21489	.	0.877859	0.10274	N	0.694402	T	0.43100	0.1232	N	0.02158	-0.66	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29305	-1.0016	10	0.11182	T	0.66	-0.4431	7.0302	0.24962	0.0:0.3147:0.0:0.6853	.	44	Q9UBR1	BUP1_HUMAN	L	44	ENSP00000324343:F44L;ENSP00000372208:F44L	ENSP00000324343:F44L	F	+	1	0	UPB1	23226100	0.000000	0.05858	0.015000	0.15790	0.043000	0.13939	-0.175000	0.09825	0.264000	0.21851	0.459000	0.35465	TTC	.	.		0.522	UPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319869.1		
CRYBB1	1414	hgsc.bcm.edu	37	22	26997873	26997873	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:26997873C>A	ENST00000215939.2	-	5	675	c.545G>T	c.(544-546)cGc>cTc	p.R182L		NM_001887.3	NP_001878.1	P53674	CRBB1_HUMAN	crystallin, beta B1	182	Beta/gamma crystallin 'Greek key' 3. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			breast(1)|endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(3)|skin(2)|urinary_tract(4)	31						GCTGCCCACGCGGTCACTGAA	0.592																																					p.R182L		Atlas-SNP	.											CRYBB1,NS,carcinoma,0,1	CRYBB1	49	.	0			c.G545T						.						84.0	64.0	71.0					22																	26997873		2203	4300	6503	SO:0001583	missense	1414	exon5			CCCACGCGGTCAC		CCDS13840.1	22q12.1	2008-06-10			ENSG00000100122	ENSG00000100122			2397	protein-coding gene	gene with protein product		600929				8575764, 12360425	Standard	NM_001887		Approved		uc003acy.1	P53674	OTTHUMG00000150980	ENST00000215939.2:c.545G>T	chr22.hg19:g.26997873C>A	ENSP00000215939:p.Arg182Leu	48.0	0.0		56.0	3.0	NM_001887		Missense_Mutation	SNP	ENST00000215939.2	hg19	CCDS13840.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.034186	0.93575	.	.	ENSG00000100122	ENST00000215939	T	0.77620	-1.11	4.8	4.8	0.61643	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.89139	0.6630	H	0.97265	3.97	0.80722	D	1	P	0.52842	0.956	P	0.49887	0.625	D	0.93167	0.6563	10	0.72032	D	0.01	.	17.0174	0.86423	0.0:1.0:0.0:0.0	.	182	P53674	CRBB1_HUMAN	L	182	ENSP00000215939:R182L	ENSP00000215939:R182L	R	-	2	0	CRYBB1	25327873	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	5.383000	0.66219	2.468000	0.83385	0.591000	0.81541	CGC	.	.		0.592	CRYBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320767.1	NM_001887	
THOC5	8563	hgsc.bcm.edu	37	22	29939435	29939435	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:29939435T>C	ENST00000490103.1	-	4	459	c.337A>G	c.(337-339)Aga>Gga	p.R113G	THOC5_ENST00000397873.2_Missense_Mutation_p.R113G|THOC5_ENST00000397872.1_Missense_Mutation_p.R113G|THOC5_ENST00000397871.1_Missense_Mutation_p.R113G	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	113	Interaction with CSF1R. {ECO:0000250}.|Interaction with THOC7.				blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GTCTGATCTCTTCCTTTCTTC	0.388																																					p.R113G		Atlas-SNP	.											.	THOC5	58	.	0			c.A337G						.						149.0	150.0	150.0					22																	29939435		2203	4300	6503	SO:0001583	missense	8563	exon5			GATCTCTTCCTTT	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"""THO complex subunits"""	19074	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 79"""	612733	"""chromosome 22 open reading frame 19"""	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.337A>G	chr22.hg19:g.29939435T>C	ENSP00000420306:p.Arg113Gly	109.0	0.0		182.0	8.0	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	hg19	CCDS13859.1	.	.	.	.	.	.	.	.	.	.	T	18.47	3.630526	0.67015	.	.	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873;ENST00000440771;ENST00000455450;ENST00000428374	T;T;T;T;T	0.56103	1.35;1.35;1.35;1.35;0.48	5.62	1.83	0.25207	.	0.000000	0.85682	D	0.000000	T	0.73466	0.3590	M	0.85462	2.755	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72982	0.963;0.979	T	0.79105	-0.1940	10	0.87932	D	0	-36.245	15.33	0.74200	0.0:0.0:0.4697:0.5302	.	113;113	F8WCP5;Q13769	.;THOC5_HUMAN	G	113;113;113;113;113;109;113	ENSP00000420306:R113G;ENSP00000380970:R113G;ENSP00000380969:R113G;ENSP00000380971:R113G;ENSP00000415425:R109G	ENSP00000444493:R113G	R	-	1	2	THOC5	28269435	0.344000	0.24827	1.000000	0.80357	0.981000	0.71138	-0.158000	0.10070	0.366000	0.24427	0.455000	0.32223	AGA	.	.		0.388	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678	
SEC14L6	730005	hgsc.bcm.edu	37	22	30921660	30921660	+	Silent	SNP	G	G	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:30921660G>C	ENST00000402034.2	-	10	848	c.849C>G	c.(847-849)tcC>tcG	p.S283S		NM_001193336.2	NP_001180265.2	B5MCN3	S14L6_HUMAN	SEC14-like 6 (S. cerevisiae)	283	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			lung(3)	3						CGCGGCCCACGGACCTCGTGT	0.622																																					p.S283S		Atlas-SNP	.											.	SEC14L6	6	.	0			c.C849G						.																																			SO:0001819	synonymous_variant	730005	exon10			GCCCACGGACCTC		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.849C>G	chr22.hg19:g.30921660G>C		110.0	0.0		127.0	19.0	NM_001193336		Silent	SNP	ENST00000402034.2	hg19	CCDS54518.1	.	.	.	.	.	.	.	.	.	.	.	2.721	-0.266633	0.05754	.	.	ENSG00000214491	ENST00000437871	.	.	.	3.99	-7.97	0.01139	.	.	.	.	.	T	0.23133	0.0559	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.15037	-1.0451	4	.	.	.	-19.7776	5.7615	0.18203	0.5084:0.3218:0.0942:0.0757	.	.	.	.	G	88	.	.	R	-	1	0	SEC14L6	29251660	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.221000	0.00552	-3.033000	0.00265	-1.179000	0.01719	CGT	.	.		0.622	SEC14L6-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000322022.2		
SEC14L6	730005	hgsc.bcm.edu	37	22	30928561	30928561	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:30928561A>G	ENST00000402034.2	-	5	373	c.374T>C	c.(373-375)tTc>tCc	p.F125S		NM_001193336.2	NP_001180265.2	B5MCN3	S14L6_HUMAN	SEC14-like 6 (S. cerevisiae)	125	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			lung(3)	3						GCAGCTCCGGAAGCTGTCCCT	0.637																																					p.F125S		Atlas-SNP	.											.	SEC14L6	6	.	0			c.T374C						.																																			SO:0001583	missense	730005	exon5			CTCCGGAAGCTGT		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.374T>C	chr22.hg19:g.30928561A>G	ENSP00000385695:p.Phe125Ser	78.0	0.0		77.0	4.0	NM_001193336		Missense_Mutation	SNP	ENST00000402034.2	hg19	CCDS54518.1	.	.	.	.	.	.	.	.	.	.	.	16.31	3.086308	0.55861	.	.	ENSG00000214491	ENST00000402034	T	0.74632	-0.86	3.38	0.266	0.15617	.	.	.	.	.	T	0.61813	0.2377	L	0.29908	0.895	0.19300	N	0.999971	.	.	.	.	.	.	T	0.53830	-0.8383	7	0.52906	T	0.07	-24.04	4.6796	0.12729	0.6615:0.0:0.0945:0.2441	.	.	.	.	S	125	ENSP00000385695:F125S	ENSP00000385695:F125S	F	-	2	0	SEC14L6	29258561	0.054000	0.20591	0.000000	0.03702	0.147000	0.21601	2.949000	0.49074	-0.192000	0.10432	0.358000	0.22013	TTC	.	.		0.637	SEC14L6-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000322022.2		
RBFOX2	23543	hgsc.bcm.edu	37	22	36152191	36152191	+	Splice_Site	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:36152191A>G	ENST00000438146.2	-	11	1109	c.1110T>C	c.(1108-1110)ggT>ggC	p.G370G	RBFOX2_ENST00000414461.2_Intron|RBFOX2_ENST00000416721.2_Splice_Site_p.G295G|RBFOX2_ENST00000405409.2_Intron|RBFOX2_ENST00000397303.2_Splice_Site_p.G276G|RBFOX2_ENST00000449924.2_Splice_Site_p.G299G|RBFOX2_ENST00000262829.7_Splice_Site_p.G277G|RBFOX2_ENST00000359369.4_Splice_Site_p.G275G	NM_001082578.1|NM_001082579.1	NP_001076047|NP_001076048.1	O43251	RFOX2_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 2	309	Ala-rich.				dendrite morphogenesis (GO:0048813)|intracellular estrogen receptor signaling pathway (GO:0030520)|mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of cell proliferation (GO:0042127)|regulation of definitive erythrocyte differentiation (GO:0010724)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(7)|lung(7)	18						GGTAAACCACACTGCAGAAAA	0.458																																					p.G370G		Atlas-SNP	.											.	RBFOX2	62	.	0			c.T1110C						.						31.0	30.0	31.0					22																	36152191		1890	4105	5995	SO:0001630	splice_region_variant	23543	exon11			AACCACACTGCAG	AL009266	CCDS13921.1, CCDS43013.1, CCDS46699.1, CCDS46700.1, CCDS46701.1	22q12-q13	2013-02-12	2010-09-10	2010-09-10	ENSG00000100320	ENSG00000100320		"""RNA binding motif (RRM) containing"""	9906	protein-coding gene	gene with protein product	"""hexaribonucleotide binding protein 2"""	612149	"""RNA binding motif protein 9"""	RBM9			Standard	NM_014309		Approved	HNRBP2, FOX-2, HRNBP2	uc003aon.4	O43251	OTTHUMG00000150585	ENST00000438146.2:c.1110-1T>C	chr22.hg19:g.36152191A>G		88.0	0.0		88.0	4.0	NM_001082578	A4F5G8|A8K5Z5|B0QYY8|B0QYY9|Q0PRL5|Q0VH35|Q5TF71|Q6IC09|Q8TD00|Q8WYB1|Q96DZ6|Q96NL7|Q9UGW4|Q9UH33	Silent	SNP	ENST00000438146.2	hg19	CCDS43013.1																																																																																			.	.		0.458	RBFOX2-005	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319299.3		Silent
TRIOBP	11078	hgsc.bcm.edu	37	22	38165281	38165281	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:38165281C>A	ENST00000406386.3	+	21	7003	c.6748C>A	c.(6748-6750)Cgc>Agc	p.R2250S	TRIOBP_ENST00000403663.2_Missense_Mutation_p.R537S	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	2250					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GCTGCATGGCCGCCTGTCAGA	0.687																																					p.R2250S		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C6748A						.						15.0	18.0	17.0					22																	38165281		2004	4169	6173	SO:0001583	missense	11078	exon21			CATGGCCGCCTGT	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.6748C>A	chr22.hg19:g.38165281C>A	ENSP00000384312:p.Arg2250Ser	75.0	0.0		70.0	4.0	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.474022	0.63737	.	.	ENSG00000100106	ENST00000406386;ENST00000403663	T;T	0.22539	1.97;1.95	4.44	3.42	0.39159	.	.	.	.	.	T	0.25606	0.0623	L	0.52126	1.63	0.48696	D	0.999691	P;P;P;P	0.49559	0.925;0.841;0.712;0.845	B;P;B;B	0.46685	0.446;0.524;0.363;0.325	T	0.04930	-1.0917	9	0.87932	D	0	.	12.5587	0.56269	0.0:0.9186:0.0:0.0814	.	2152;239;537;2250	Q9H2D6-2;Q8TCM3;F8W6V6;Q9H2D6	.;.;.;TARA_HUMAN	S	2250;537	ENSP00000384312:R2250S;ENSP00000386026:R537S	ENSP00000386026:R537S	R	+	1	0	TRIOBP	36495227	0.885000	0.30320	0.559000	0.28332	0.930000	0.56654	1.999000	0.40806	1.101000	0.41535	0.462000	0.41574	CGC	.	.		0.687	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
MGAT3	4248	hgsc.bcm.edu	37	22	39883658	39883658	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:39883658G>T	ENST00000341184.6	+	2	521	c.306G>T	c.(304-306)gaG>gaT	p.E102D		NM_001098270.1|NM_002409.4	NP_001091740.1|NP_002400.3	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase	102					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)	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0003830)			endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|prostate(1)|skin(1)	24	Melanoma(58;0.04)					TGCTGCCCGAGGACACCACCG	0.697																																					p.E102D		Atlas-SNP	.											.	MGAT3	65	.	0			c.G306T						.						15.0	18.0	17.0					22																	39883658		2196	4293	6489	SO:0001583	missense	4248	exon2			GCCCGAGGACACC	D13789	CCDS13994.2	22q13.1	2013-02-25			ENSG00000128268	ENSG00000128268	2.4.1.144	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7046	protein-coding gene	gene with protein product		604621				8370666	Standard	NM_002409		Approved	GNT-III	uc010gxy.3	Q09327	OTTHUMG00000030185	ENST00000341184.6:c.306G>T	chr22.hg19:g.39883658G>T	ENSP00000345270:p.Glu102Asp	185.0	0.0		152.0	7.0	NM_002409	A6NGD0|Q14CK5|Q6IC49|Q9UH32	Missense_Mutation	SNP	ENST00000341184.6	hg19	CCDS13994.2	.	.	.	.	.	.	.	.	.	.	G	2.247	-0.372506	0.05034	.	.	ENSG00000128268	ENST00000341184;ENST00000429402	.	.	.	4.74	3.72	0.42706	.	0.059458	0.64402	D	0.000004	T	0.24392	0.0591	N	0.11560	0.145	0.34727	D	0.729342	B	0.14438	0.01	B	0.11329	0.006	T	0.19943	-1.0290	9	0.18276	T	0.48	.	7.7287	0.28775	0.2772:0.0:0.7228:0.0	.	102	Q09327	MGAT3_HUMAN	D	102	.	ENSP00000345270:E102D	E	+	3	2	MGAT3	38213604	1.000000	0.71417	1.000000	0.80357	0.190000	0.23558	2.040000	0.41203	0.978000	0.38470	0.467000	0.42956	GAG	.	.		0.697	MGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075039.2	NM_002409	
MCAT	27349	hgsc.bcm.edu	37	22	43529443	43529443	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:43529443G>A	ENST00000290429.6	-	4	824	c.779C>T	c.(778-780)aCc>aTc	p.T260I	MCAT_ENST00000327555.5_3'UTR	NM_173467.4	NP_775738.3	Q8IVS2	FABD_HUMAN	malonyl CoA:ACP acyltransferase (mitochondrial)	260					fatty acid biosynthetic process (GO:0006633)|metabolic process (GO:0008152)	mitochondrion (GO:0005739)	[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	11		Ovarian(80;0.0694)				CAACATCCTGGTGCGTCTGAA	0.537																																					p.T260I		Atlas-SNP	.											.	MCAT	26	.	0			c.C779T						.						31.0	34.0	33.0					22																	43529443		2203	4300	6503	SO:0001583	missense	27349	exon4			ATCCTGGTGCGTC	AL359401	CCDS14045.1, CCDS33660.1	22q13.2	2010-04-27			ENSG00000100294	ENSG00000100294	2.3.1.39		29622	protein-coding gene	gene with protein product		614479				12882974	Standard	NM_173467		Approved	MT, MCT, fabD, FASN2C, NET62	uc003bdl.1	Q8IVS2	OTTHUMG00000150704	ENST00000290429.6:c.779C>T	chr22.hg19:g.43529443G>A	ENSP00000290429:p.Thr260Ile	91.0	0.0		69.0	4.0	NM_173467	B0QY72|O95510|O95511	Missense_Mutation	SNP	ENST00000290429.6	hg19	CCDS33660.1	.	.	.	.	.	.	.	.	.	.	G	2.955	-0.215899	0.06101	.	.	ENSG00000100294	ENST00000290429	T	0.42900	0.96	5.26	4.23	0.50019	Acyl transferase/acyl hydrolase/lysophospholipase (1);Malonyl-CoA ACP transacylase, ACP-binding (1);Acyl transferase (1);	0.344834	0.32273	N	0.006335	T	0.34978	0.0916	L	0.52823	1.66	0.43246	D	0.995169	P	0.46020	0.871	B	0.37304	0.246	T	0.18493	-1.0335	10	0.36615	T	0.2	-19.4544	12.2894	0.54810	0.1349:0.0:0.8651:0.0	.	260	Q8IVS2	FABD_HUMAN	I	260	ENSP00000290429:T260I	ENSP00000290429:T260I	T	-	2	0	MCAT	41859387	1.000000	0.71417	1.000000	0.80357	0.138000	0.21146	3.511000	0.53400	2.620000	0.88729	0.655000	0.94253	ACC	.	.		0.537	MCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319677.2	NM_173467	
SCUBE1	80274	hgsc.bcm.edu	37	22	43610121	43610121	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:43610121A>G	ENST00000360835.4	-	16	2154	c.2028T>C	c.(2026-2028)ggT>ggC	p.G676G	Z82214.3_ENST00000420269.1_RNA	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	676					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				CGTTGCGGGCACCAGGCAGAC	0.647																																					p.G676G		Atlas-SNP	.											.	SCUBE1	105	.	0			c.T2028C						.						58.0	43.0	48.0					22																	43610121		2203	4300	6503	SO:0001819	synonymous_variant	80274	exon16			GCGGGCACCAGGC		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.2028T>C	chr22.hg19:g.43610121A>G		123.0	0.0		107.0	5.0	NM_173050	Q5R336	Silent	SNP	ENST00000360835.4	hg19	CCDS14048.1																																																																																			.	.		0.647	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45218348	45218348	+	Splice_Site	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:45218348C>T	ENST00000389774.2	+	7	718	c.577C>T	c.(577-579)Cgg>Tgg	p.R193W	ARHGAP8_ENST00000356099.6_Splice_Site_p.R162W|ARHGAP8_ENST00000517296.3_Splice_Site_p.R372W|PRR5-ARHGAP8_ENST00000352766.7_Splice_Site_p.R372W|PRR5-ARHGAP8_ENST00000361473.5_Splice_Site_p.R293W|ARHGAP8_ENST00000336963.4_Splice_Site_p.R162W|ARHGAP8_ENST00000389773.5_Splice_Site_p.R284W	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	193	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		CGAAGTTTTGCGGTAAGTGCC	0.458																																					p.R284W		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.C850T						.						101.0	94.0	96.0					22																	45218348		2203	4300	6503	SO:0001630	splice_region_variant	553158	exon9			GTTTTGCGGTAAG	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.578+1C>T	chr22.hg19:g.45218348C>T		126.0	0.0		112.0	5.0	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	hg19	CCDS33664.1	.	.	.	.	.	.	.	.	.	.	C	8.164	0.790205	0.16258	.	.	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000336963;ENST00000356099	T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	4.12	3.09	0.35607	Cellular retinaldehyde-binding/triple function, C-terminal (2);	0.000000	0.30528	U	0.009431	T	0.50222	0.1603	L	0.52011	1.625	0.33698	D	0.614221	B;B;B;B;B;B;P	0.34909	0.309;0.136;0.32;0.309;0.309;0.073;0.475	B;B;B;B;B;B;B	0.32724	0.087;0.052;0.071;0.087;0.052;0.033;0.151	T	0.60989	-0.7153	10	0.56958	D	0.05	.	5.9787	0.19395	0.2048:0.6954:0.0:0.0998	.	198;162;198;193;203;372;293	B7ZMA4;A6ZJ79;A2RU51;P85298;Q6PCC7;B1AHC4;B1AHC3	.;.;.;RHG08_HUMAN;.;.;.	W	293;372;372;284;193;162;162	ENSP00000354732:R293W;ENSP00000262731:R372W;ENSP00000429240:R372W;ENSP00000374423:R284W;ENSP00000374424:R193W;ENSP00000337287:R162W;ENSP00000348407:R162W	ENSP00000337287:R162W	R	+	1	2	PRR5-ARHGAP8;ARHGAP8	43597012	0.424000	0.25490	0.830000	0.32933	0.054000	0.15201	0.781000	0.26774	0.890000	0.36211	0.313000	0.20887	CGG	.	.		0.458	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	Missense_Mutation
PKDREJ	10343	hgsc.bcm.edu	37	22	46657241	46657241	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:46657241T>C	ENST00000253255.5	-	1	1978	c.1979A>G	c.(1978-1980)cAg>cGg	p.Q660R		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	660	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CAAAGTCACCTGAGAAAAAGC	0.458																																					p.Q660R		Atlas-SNP	.											.	PKDREJ	195	.	0			c.A1979G						.						73.0	80.0	77.0					22																	46657241		2203	4300	6503	SO:0001583	missense	10343	exon1			GTCACCTGAGAAA	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.1979A>G	chr22.hg19:g.46657241T>C	ENSP00000253255:p.Gln660Arg	74.0	0.0		70.0	4.0	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	hg19	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.661362	0.67700	.	.	ENSG00000130943	ENST00000253255	T	0.69926	-0.44	5.27	4.22	0.49857	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.107962	0.41396	D	0.000892	T	0.77818	0.4187	M	0.65498	2.005	0.27988	N	0.935773	D	0.89917	1.0	D	0.68943	0.961	T	0.71896	-0.4454	10	0.59425	D	0.04	-15.159	11.9179	0.52776	0.0:0.0:0.1457:0.8543	.	660	Q9NTG1	PKDRE_HUMAN	R	660	ENSP00000253255:Q660R	ENSP00000253255:Q660R	Q	-	2	0	PKDREJ	45035905	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	2.222000	0.42926	0.929000	0.37192	0.533000	0.62120	CAG	.	.		0.458	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
CELSR1	9620	hgsc.bcm.edu	37	22	46930936	46930936	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:46930936G>T	ENST00000262738.3	-	1	2131	c.2132C>A	c.(2131-2133)gCc>gAc	p.A711D	CELSR1_ENST00000497509.1_5'Flank|CELSR1_ENST00000395964.1_Missense_Mutation_p.A711D	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	711	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)		ACGGTCGCGGGCCTGCAGGGT	0.637																																					p.A711D		Atlas-SNP	.											.	CELSR1	242	.	0			c.C2132A						.						52.0	34.0	40.0					22																	46930936		2202	4297	6499	SO:0001583	missense	9620	exon1			TCGCGGGCCTGCA	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.2132C>A	chr22.hg19:g.46930936G>T	ENSP00000262738:p.Ala711Asp	98.0	0.0		50.0	4.0	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.75|16.75	3.209567|3.209567	0.58343|0.58343	.|.	.|.	ENSG00000075275|ENSG00000075275	ENST00000262738;ENST00000395964|ENST00000454637	T;T|.	0.61980|.	0.06;0.06|.	4.51|4.51	4.51|4.51	0.55191|0.55191	Cadherin (4);Cadherin-like (1);|.	0.000000|.	0.64402|.	U|.	0.000003|.	D|D	0.90714|0.90714	0.7086|0.7086	H|H	0.98996|0.98996	4.395|4.395	0.51012|0.51012	D|D	0.999902|0.999902	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.94846|0.94846	0.8009|0.8009	10|5	0.87932|.	D|.	0|.	.|.	16.8582|16.8582	0.86011|0.86011	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	711|.	Q9NYQ6|.	CELR1_HUMAN|.	D|T	711|86	ENSP00000262738:A711D;ENSP00000379293:A711D|.	ENSP00000262738:A711D|.	A|P	-|-	2|1	0|0	CELSR1|CELSR1	45309600|45309600	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.608000|0.608000	0.37181|0.37181	7.506000|7.506000	0.81665|0.81665	2.067000|2.067000	0.61834|0.61834	0.305000|0.305000	0.20034|0.20034	GCC|CCC	.	.		0.637	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
IL17REL	400935	hgsc.bcm.edu	37	22	50439203	50439203	+	Silent	SNP	G	G	T	rs143091006	byFrequency	TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:50439203G>T	ENST00000389983.2	-	5	463	c.199C>A	c.(199-201)Cgg>Agg	p.R67R	IL17REL_ENST00000341280.5_Silent_p.R67R	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	67										endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		CCCTGCTGCCGGTGGGAGGCC	0.706																																					p.R67R		Atlas-SNP	.											.	IL17REL	21	.	0			c.C199A						.						15.0	18.0	17.0					22																	50439203		2198	4291	6489	SO:0001819	synonymous_variant	400935	exon5			GCTGCCGGTGGGA	AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.199C>A	chr22.hg19:g.50439203G>T		99.0	0.0		96.0	5.0	NM_001001694	A6NCN4|A6PVC1	Silent	SNP	ENST00000389983.2	hg19	CCDS33679.1																																																																																			.	G|0.998;A|0.002		0.706	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694	
PANX2	56666	hgsc.bcm.edu	37	22	50615968	50615968	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr22:50615968G>T	ENST00000395842.2	+	2	827	c.827G>T	c.(826-828)cGc>cTc	p.R276L	PANX2_ENST00000159647.5_Missense_Mutation_p.R276L	NM_052839.3	NP_443071.2	Q96RD6	PANX2_HUMAN	pannexin 2	276					ion transport (GO:0006811)|protein hexamerization (GO:0034214)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)	7		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)		CCCGCGGTGCGCGTGAGCTGC	0.667																																					p.R276L		Atlas-SNP	.											PANX2_ENST00000395842,colon,carcinoma,0,2	PANX2	69	.	0			c.G827T						.						43.0	33.0	36.0					22																	50615968		2190	4298	6488	SO:0001583	missense	56666	exon2			CGGTGCGCGTGAG		CCDS14085.2, CCDS54544.1	22q13.33	2011-12-05			ENSG00000073150	ENSG00000073150		"""Ion channels / Pannexins"""	8600	protein-coding gene	gene with protein product		608421				14702039, 14597722	Standard	NM_052839		Approved	hPANX2, PX2	uc003bjn.4	Q96RD6	OTTHUMG00000044649	ENST00000395842.2:c.827G>T	chr22.hg19:g.50615968G>T	ENSP00000379183:p.Arg276Leu	40.0	0.0		28.0	2.0	NM_052839	B7Z684|Q96RD5|Q9UGX8	Missense_Mutation	SNP	ENST00000395842.2	hg19	CCDS14085.2	.	.	.	.	.	.	.	.	.	.	G	15.61	2.883979	0.51908	.	.	ENSG00000073150	ENST00000159647;ENST00000395842	T;T	0.24350	1.86;1.86	4.42	2.32	0.28847	.	0.286325	0.32134	N	0.006531	T	0.15739	0.0379	N	0.14661	0.345	0.35885	D	0.829212	P;P	0.36354	0.493;0.549	B;B	0.38803	0.185;0.282	T	0.18650	-1.0330	10	0.41790	T	0.15	-20.3256	10.3727	0.44064	0.1617:0.0:0.8383:0.0	.	276;276	Q96RD6-1;Q96RD6	.;PANX2_HUMAN	L	276	ENSP00000159647:R276L;ENSP00000379183:R276L	ENSP00000159647:R276L	R	+	2	0	PANX2	48958095	1.000000	0.71417	0.996000	0.52242	0.491000	0.33493	3.218000	0.51192	0.348000	0.23949	-0.327000	0.08410	CGC	.	.		0.667	PANX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075010.3	NM_052839	
MID1	4281	hgsc.bcm.edu	37	X	10437803	10437803	+	Missense_Mutation	SNP	C	C	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:10437803C>T	ENST00000317552.4	-	7	1619	c.1219G>A	c.(1219-1221)Gat>Aat	p.D407N	MID1_ENST00000380785.1_Missense_Mutation_p.D407N|MID1_ENST00000380782.2_Missense_Mutation_p.D407N|MID1_ENST00000380779.1_Missense_Mutation_p.D407N|MID1_ENST00000380780.1_Missense_Mutation_p.D407N|MID1_ENST00000453318.2_Missense_Mutation_p.D407N|MID1_ENST00000380787.1_Missense_Mutation_p.D407N	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1	407	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						CTGAACTCATCATCGGAGGTC	0.483																																					p.D458N		Atlas-SNP	.											.	MID1	72	.	0			c.G1372A						.						173.0	139.0	150.0					X																	10437803		2203	4300	6503	SO:0001583	missense	4281	exon7			ACTCATCATCGGA	Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	7095	protein-coding gene	gene with protein product	"""Opitz/BBB syndrome"""	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.1219G>A	chrX.hg19:g.10437803C>T	ENSP00000312678:p.Asp407Asn	89.0	0.0		85.0	4.0	NM_001193278	B2RCG2|O75361|Q9BZX5	Missense_Mutation	SNP	ENST00000317552.4	hg19	CCDS14138.1	.	.	.	.	.	.	.	.	.	.	C	35	5.518155	0.96416	.	.	ENSG00000101871	ENST00000453318;ENST00000317552;ENST00000380785;ENST00000380779;ENST00000380787;ENST00000380780;ENST00000380782;ENST00000454373;ENST00000413894	T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	5.9	5.9	0.94986	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.59649	0.2209	L	0.59436	1.845	0.80722	D	1	D;D;P	0.54397	0.966;0.966;0.847	D;D;P	0.68039	0.955;0.939;0.905	T	0.50457	-0.8826	10	0.14252	T	0.57	.	19.26	0.93964	0.0:1.0:0.0:0.0	.	407;407;357	A8K5A0;O15344;B4DLX8	.;TRI18_HUMAN;.	N	407;407;407;407;407;407;407;357;407	ENSP00000414521:D407N;ENSP00000312678:D407N;ENSP00000370162:D407N;ENSP00000370156:D407N;ENSP00000370164:D407N;ENSP00000370157:D407N;ENSP00000370159:D407N;ENSP00000391154:D407N	ENSP00000312678:D407N	D	-	1	0	MID1	10397803	1.000000	0.71417	0.974000	0.42286	0.980000	0.70556	7.290000	0.78711	2.500000	0.84329	0.600000	0.82982	GAT	.	.		0.483	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055738.1		
NHS	4810	hgsc.bcm.edu	37	X	17745288	17745288	+	Missense_Mutation	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:17745288C>A	ENST00000380060.3	+	6	3337	c.2999C>A	c.(2998-3000)cCa>cAa	p.P1000Q	NHS_ENST00000398097.3_Missense_Mutation_p.P844Q	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1021					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TTGGCATCTCCATCAAGTGGC	0.468																																					p.P1000Q		Atlas-SNP	.											.	NHS	302	.	0			c.C2999A						.						59.0	54.0	56.0					X																	17745288		2202	4299	6501	SO:0001583	missense	4810	exon6			CATCTCCATCAAG		CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.2999C>A	chrX.hg19:g.17745288C>A	ENSP00000369400:p.Pro1000Gln	104.0	0.0		73.0	4.0	NM_198270	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	hg19	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.560695	0.65538	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	D;D	0.90563	-2.63;-2.69	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	D	0.95726	0.8610	M	0.81802	2.56	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;1.0;0.999	D	0.95841	0.8866	10	0.87932	D	0	-14.6637	19.3108	0.94187	0.0:1.0:0.0:0.0	.	1021;842;844;1000	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	Q	1000;844;842	ENSP00000369400:P1000Q;ENSP00000381170:P844Q	ENSP00000369397:P842Q	P	+	2	0	NHS	17655209	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.794000	0.85869	2.513000	0.84729	0.544000	0.68410	CCA	.	.		0.468	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270	
PPEF1	5475	hgsc.bcm.edu	37	X	18797263	18797263	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:18797263G>T	ENST00000361511.4	+	10	1188	c.694G>T	c.(694-696)Ggg>Tgg	p.G232W	PPEF1_ENST00000349874.5_Missense_Mutation_p.G232W|PPEF1_ENST00000543630.1_Missense_Mutation_p.G232W|PPEF1_ENST00000359763.6_Missense_Mutation_p.G179W|PPEF1_ENST00000544635.1_Missense_Mutation_p.G167W	NM_006240.2|NM_152224.1	NP_006231.2|NP_689410.1	O14829	PPE1_HUMAN	protein phosphatase, EF-hand calcium binding domain 1	232	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|phototransduction, visible light (GO:0007603)|protein dephosphorylation (GO:0006470)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	43	Hepatocellular(33;0.183)					CTTGAACAGAGGGAACCACGA	0.393																																					p.G232W		Atlas-SNP	.											.	PPEF1	89	.	0			c.G694T						.						120.0	111.0	114.0					X																	18797263		2203	4300	6503	SO:0001583	missense	5475	exon10			AACAGAGGGAACC	BC036026	CCDS14188.1, CCDS43920.1	Xp22	2013-01-10			ENSG00000086717	ENSG00000086717		"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""EF-hand domain containing"""	9243	protein-coding gene	gene with protein product	"""protein phosphatase 7, catalytic subunit, alpha isozyme"""	300109		PPEF		9215685, 9326663	Standard	NM_152224		Approved	PPP7CA	uc004cyq.3	O14829	OTTHUMG00000021219	ENST00000361511.4:c.694G>T	chrX.hg19:g.18797263G>T	ENSP00000354871:p.Gly232Trp	84.0	0.0		91.0	4.0	NM_152226	A6NHP4|A8K348|O15253|Q9NU21|Q9UJH0	Missense_Mutation	SNP	ENST00000361511.4	hg19	CCDS14188.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.345829	0.82022	.	.	ENSG00000086717	ENST00000361511;ENST00000359763;ENST00000349874;ENST00000543630;ENST00000544635	D;D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.97;-1.97	5.19	5.19	0.71726	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (3);Metallophosphoesterase domain (1);	0.000000	0.64402	D	0.000007	D	0.96074	0.8721	H	0.99074	4.42	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	0.98385	1.0560	10	0.87932	D	0	-11.704	17.8877	0.88862	0.0:0.0:1.0:0.0	.	232;232;232	O14829-5;O14829;O14829-3	.;PPE1_HUMAN;.	W	232;179;232;232;167	ENSP00000354871:G232W;ENSP00000352806:G179W;ENSP00000341892:G232W;ENSP00000437785:G232W;ENSP00000441289:G167W	ENSP00000341892:G232W	G	+	1	0	PPEF1	18707184	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.417000	0.97391	2.156000	0.67533	0.529000	0.55759	GGG	.	.		0.393	PPEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055953.3	NM_006240	
SMPX	23676	hgsc.bcm.edu	37	X	21761892	21761892	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:21761892T>C	ENST00000379494.3	-	3	341	c.108A>G	c.(106-108)aaA>aaG	p.K36K	SMPX_ENST00000494525.1_5'UTR	NM_014332.2	NP_055147.1	Q9UHP9	SMPX_HUMAN	small muscle protein, X-linked	36					striated muscle contraction (GO:0006941)	costamere (GO:0043034)|M band (GO:0031430)|muscle tendon junction (GO:0005927)|nucleus (GO:0005634)				breast(1)|endometrium(1)	2						GAGTACATTCTTTTCTTCTGG	0.463																																					p.K36K		Atlas-SNP	.											.	SMPX	12	.	0			c.A108G						.						100.0	93.0	95.0					X																	21761892		2203	4300	6503	SO:0001819	synonymous_variant	23676	exon3			ACATTCTTTTCTT		CCDS14200.1	Xp22.2-p22.1	2014-01-28			ENSG00000091482	ENSG00000091482			11122	protein-coding gene	gene with protein product		300226	"""deafness, X-linked 6, sensorineural"""	DFN6		21893181	Standard	NM_014332		Approved	DFNX4	uc004daa.3	Q9UHP9	OTTHUMG00000021235	ENST00000379494.3:c.108A>G	chrX.hg19:g.21761892T>C		60.0	0.0		68.0	4.0	NM_014332	B1AWX2	Silent	SNP	ENST00000379494.3	hg19	CCDS14200.1																																																																																			.	.		0.463	SMPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056023.1	NM_014332	
SMS	6611	hgsc.bcm.edu	37	X	22010832	22010832	+	Splice_Site	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:22010832T>C	ENST00000404933.2	+	10	1313		c.e10+2		SMS_ENST00000379404.1_Splice_Site|SMS_ENST00000415881.2_Splice_Site	NM_004595.4	NP_004586.2	P52788	SPSY_HUMAN	spermine synthase						cellular nitrogen compound metabolic process (GO:0034641)|methionine metabolic process (GO:0006555)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine biosynthetic process (GO:0006597)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	spermidine synthase activity (GO:0004766)|spermine synthase activity (GO:0016768)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(2)	14					Spermine(DB00127)	CTTGGAATTGTATCCTTTGAC	0.408																																					.		Atlas-SNP	.											.	SMS	59	.	0			c.1061+2T>C						.						116.0	87.0	97.0					X																	22010832		2203	4300	6503	SO:0001630	splice_region_variant	6611	exon10			GAATTGTATCCTT	AD001528	CCDS14203.1, CCDS59161.1	Xp22.1	2014-05-16			ENSG00000102172	ENSG00000102172			11123	protein-coding gene	gene with protein product		300105	"""Snyder-Robinson X-linked mental retardation syndrome"""	SRS		7546290, 9299240, 14508504	Standard	NM_004595		Approved	SPMSY, SpS, MRSR	uc004dag.4	P52788	OTTHUMG00000021239	ENST00000404933.2:c.1061+2T>C	chrX.hg19:g.22010832T>C		135.0	0.0		88.0	4.0	NM_004595	A6NHA7|A6NI34|B2R9M0|O00544|Q9UQS1	Splice_Site	SNP	ENST00000404933.2	hg19	CCDS14203.1	.	.	.	.	.	.	.	.	.	.	T	19.82	3.898095	0.72639	.	.	ENSG00000102172	ENST00000404933;ENST00000379404;ENST00000415881	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1664	0.65480	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SMS	21920753	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	5.408000	0.66368	1.723000	0.51488	0.339000	0.21740	.	.	.		0.408	SMS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056032.1	NM_004595	Intron
PCYT1B	9468	hgsc.bcm.edu	37	X	24597452	24597452	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:24597452A>G	ENST00000379144.2	-	6	819	c.689T>C	c.(688-690)cTg>cCg	p.L230P	PCYT1B_ENST00000356768.4_Missense_Mutation_p.L230P|PCYT1B_ENST00000379145.1_Missense_Mutation_p.L212P	NM_004845.4	NP_004836.2	Q9Y5K3	PCY1B_HUMAN	phosphate cytidylyltransferase 1, choline, beta	230					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	choline-phosphate cytidylyltransferase activity (GO:0004105)			breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	17					Choline(DB00122)	GCTGACATTCAGTTCCTTGGC	0.463																																					p.L230P		Atlas-SNP	.											.	PCYT1B	88	.	0			c.T689C						.						277.0	203.0	228.0					X																	24597452		2203	4300	6503	SO:0001583	missense	9468	exon6			ACATTCAGTTCCT	AF052510	CCDS14213.1, CCDS55391.1, CCDS55392.1	Xp22	2008-02-05	2005-09-05		ENSG00000102230	ENSG00000102230	2.7.7.15		8755	protein-coding gene	gene with protein product		604926	"""phosphate cytidylyltransferase 1, choline, beta isoform"""			9593753	Standard	NM_004845		Approved	CCT-beta, CTB	uc004dbi.3	Q9Y5K3	OTTHUMG00000021270	ENST00000379144.2:c.689T>C	chrX.hg19:g.24597452A>G	ENSP00000368439:p.Leu230Pro	185.0	0.0		122.0	5.0	NM_004845	A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9	Missense_Mutation	SNP	ENST00000379144.2	hg19	CCDS14213.1	.	.	.	.	.	.	.	.	.	.	a	12.09	1.835092	0.32421	.	.	ENSG00000102230	ENST00000379145;ENST00000379144;ENST00000356768	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.84866	0.5567	M	0.90870	3.155	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.996	D	0.88435	0.3038	9	0.87932	D	0	-22.5167	14.0852	0.64951	1.0:0.0:0.0:0.0	.	230;212;230	Q9Y5K3-2;E9PD84;Q9Y5K3	.;.;PCY1B_HUMAN	P	212;230;230	.	ENSP00000349211:L230P	L	-	2	0	PCYT1B	24507373	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	8.753000	0.91637	1.901000	0.55032	0.427000	0.28365	CTG	.	.		0.463	PCYT1B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056103.1	NM_004845	
MAGEB2	4113	hgsc.bcm.edu	37	X	30236769	30236769	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:30236769T>C	ENST00000378988.4	+	2	173	c.72T>C	c.(70-72)ggT>ggC	p.G24G		NM_002364.4	NP_002355.2	O15479	MAGB2_HUMAN	melanoma antigen family B, 2	24										breast(1)|large_intestine(3)|lung(17)|ovary(1)|skin(1)	23						AGACCCGGGGTCTCAATGTTC	0.577																																					p.G24G		Atlas-SNP	.											.	MAGEB2	133	.	0			c.T72C						.						38.0	36.0	37.0					X																	30236769		2202	4300	6502	SO:0001819	synonymous_variant	4113	exon2			CCGGGGTCTCAAT	AF015766	CCDS14219.1	Xp21.3	2009-03-17			ENSG00000099399	ENSG00000099399			6809	protein-coding gene	gene with protein product	"""DSS/AHC critical interval MAGE superfamily 6"", ""melanoma-associated antigen B2"", ""cancer/testis antigen family 3, member 2"""	300098				9441743	Standard	NM_002364		Approved	DAM6, MAGE-XP-2, MGC26438, CT3.2	uc004dbz.3	O15479	OTTHUMG00000021319	ENST00000378988.4:c.72T>C	chrX.hg19:g.30236769T>C		125.0	0.0		96.0	4.0	NM_002364	O75860	Silent	SNP	ENST00000378988.4	hg19	CCDS14219.1																																																																																			.	.		0.577	MAGEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056157.1	NM_002364	
DMD	1756	hgsc.bcm.edu	37	X	32328324	32328324	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:32328324A>G	ENST00000357033.4	-	42	6198	c.5992T>C	c.(5992-5994)Tct>Cct	p.S1998P	DMD_ENST00000378677.2_Missense_Mutation_p.S1994P	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	1998					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)				AAATAAGTAGAAGGCACATAA	0.388																																					p.S1998P		Atlas-SNP	.											.	DMD	2127	.	0			c.T5992C						.						116.0	95.0	102.0					X																	32328324		2202	4300	6502	SO:0001583	missense	1756	exon42			AAGTAGAAGGCAC	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.5992T>C	chrX.hg19:g.32328324A>G	ENSP00000354923:p.Ser1998Pro	223.0	0.0		140.0	6.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.296552	0.81025	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.62639	0.01;0.01	6.16	6.16	0.99307	.	0.000000	0.37095	U	0.002258	T	0.76133	0.3945	L	0.61218	1.895	0.80722	D	1	D;D;D;D;D	0.69078	0.997;0.997;0.997;0.997;0.997	D;D;D;D;D	0.81914	0.991;0.995;0.995;0.995;0.995	T	0.76506	-0.2934	10	0.46703	T	0.11	.	14.25	0.66013	1.0:0.0:0.0:0.0	.	1990;1998;1994;657;654	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	P	1990;657;654;1994;1998;1998;1875	ENSP00000367948:S1994P;ENSP00000354923:S1998P	ENSP00000354923:S1998P	S	-	1	0	DMD	32238245	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.711000	0.74675	2.085000	0.62840	0.481000	0.45027	TCT	.	.		0.388	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
CHDC2	286464	hgsc.bcm.edu	37	X	36156116	36156116	+	Missense_Mutation	SNP	G	G	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:36156116G>C	ENST00000313548.4	+	9	1273	c.1087G>C	c.(1087-1089)Gac>Cac	p.D363H		NM_173695.2	NP_775966.1	Q8N9S7	CHDC2_HUMAN	calponin homology domain containing 2	363	CH.					integral component of membrane (GO:0016021)											TTTTGACAAAGACCTTTCAGA	0.323																																					p.D363H		Atlas-SNP	.											.	.	.	.	0			c.G1087C						.						89.0	78.0	82.0					X																	36156116		2202	4298	6500	SO:0001583	missense	286464	exon9			GACAAAGACCTTT	AK093920	CCDS14238.1	Xp21.1	2014-08-07	2012-11-28	2012-11-28	ENSG00000176034	ENSG00000176034			26708	protein-coding gene	gene with protein product			"""chromosome X open reading frame 59"""	CXorf59			Standard	NM_173695		Approved	FLJ36601, RP13-11B7.1	uc004ddk.1	Q8N9S7	OTTHUMG00000021351	ENST00000313548.4:c.1087G>C	chrX.hg19:g.36156116G>C	ENSP00000324767:p.Asp363His	244.0	0.0		176.0	10.0	NM_173695		Missense_Mutation	SNP	ENST00000313548.4	hg19	CCDS14238.1	.	.	.	.	.	.	.	.	.	.	G	10.80	1.453015	0.26161	.	.	ENSG00000176034	ENST00000378660;ENST00000313548	D;D	0.96745	-4.11;-4.11	5.22	4.34	0.51931	Calponin homology domain (3);	0.093856	0.35585	N	0.003102	D	0.97402	0.9150	M	0.76002	2.32	0.23712	N	0.997049	D	0.65815	0.995	P	0.61397	0.888	D	0.93320	0.6692	10	0.87932	D	0	-6.8663	14.0852	0.64951	0.0:0.1475:0.8525:0.0	.	363	Q8N9S7	CX059_HUMAN	H	363	ENSP00000367929:D363H;ENSP00000324767:D363H	ENSP00000324767:D363H	D	+	1	0	CXorf59	36066037	1.000000	0.71417	0.034000	0.17996	0.068000	0.16541	5.232000	0.65332	0.989000	0.38761	0.529000	0.55759	GAC	.	.		0.323	CHDC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173695	
PRRG1	5638	hgsc.bcm.edu	37	X	37312753	37312753	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:37312753T>C	ENST00000542554.1	+	5	808	c.536T>C	c.(535-537)gTg>gCg	p.V179A	PRRG1_ENST00000378628.4_Missense_Mutation_p.V179A|PRRG1_ENST00000491253.1_3'UTR|PRRG1_ENST00000449135.2_Missense_Mutation_p.V179A|PRRG1_ENST00000543642.1_Missense_Mutation_p.V179A|TM4SF2_ENST00000465127.1_Intron	NM_001173489.1	NP_001166960.1	O14668	TMG1_HUMAN	proline rich Gla (G-carboxyglutamic acid) 1	179						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	15						ACTGGCCAAGTGAACCTGCAG	0.532																																					p.V179A		Atlas-SNP	.											.	PRRG1	42	.	0			c.T536C						.						76.0	60.0	65.0					X																	37312753		2202	4300	6502	SO:0001583	missense	5638	exon4			GCCAAGTGAACCT	AF009242	CCDS14239.1, CCDS55397.1	Xp21.1	2010-08-13	2004-05-27		ENSG00000130962	ENSG00000130962			9469	protein-coding gene	gene with protein product		604428	"""proline-rich Gla (G-carboxyglutamic acid) polypeptide 1"""			9256434	Standard	NM_000950		Approved	PRGP1	uc004ddo.3	O14668	OTTHUMG00000021360	ENST00000542554.1:c.536T>C	chrX.hg19:g.37312753T>C	ENSP00000444278:p.Val179Ala	66.0	0.0		55.0	4.0	NM_001173490	B2R7A3|C9JXL7|D3DWA9|Q5JT66	Missense_Mutation	SNP	ENST00000542554.1	hg19	CCDS14239.1	.	.	.	.	.	.	.	.	.	.	T	2.735	-0.263540	0.05754	.	.	ENSG00000130962	ENST00000378628;ENST00000542554;ENST00000543642;ENST00000449135	D;D;D;D	0.98701	-5.08;-5.08;-5.08;-5.08	5.96	1.87	0.25490	.	0.984876	0.08327	N	0.962944	D	0.91975	0.7458	N	0.02539	-0.55	0.20563	N	0.999886	B	0.06786	0.001	B	0.09377	0.004	D	0.86637	0.1889	10	0.07482	T	0.82	-0.158	5.6786	0.17763	0.0:0.2582:0.1376:0.6043	.	179	O14668	TMG1_HUMAN	A	179	ENSP00000367894:V179A;ENSP00000444278:V179A;ENSP00000443271:V179A;ENSP00000390332:V179A	ENSP00000367894:V179A	V	+	2	0	PRRG1	37197674	0.958000	0.32768	1.000000	0.80357	0.996000	0.88848	0.102000	0.15272	0.341000	0.23771	0.486000	0.48141	GTG	.	.		0.532	PRRG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056228.2	NM_000950	
BCOR	54880	hgsc.bcm.edu	37	X	39913172	39913172	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:39913172G>T	ENST00000378444.4	-	14	5171	c.4943C>A	c.(4942-4944)cCg>cAg	p.P1648Q	BCOR_ENST00000378463.1_Missense_Mutation_p.P491Q|BCOR_ENST00000342274.4_Missense_Mutation_p.P1614Q|BCOR_ENST00000397354.3_Missense_Mutation_p.P1614Q|BCOR_ENST00000378455.4_Missense_Mutation_p.P1596Q	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1648	Necessary and sufficient for interaction with PCGF1.				heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						GTTATAACACGGTAAGAGGGG	0.468			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																														p.P1648Q		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.C4943A						.						47.0	41.0	43.0					X																	39913172		2202	4300	6502	SO:0001583	missense	54880	exon14			TAACACGGTAAGA	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.4943C>A	chrX.hg19:g.39913172G>T	ENSP00000367705:p.Pro1648Gln	135.0	0.0		86.0	4.0	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	hg19	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.140948	0.56936	.	.	ENSG00000183337	ENST00000413905;ENST00000378463;ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000442018	T;T;T;T;T;T;T	0.75260	-0.92;0.36;0.6;0.59;0.49;0.59;-0.83	5.85	5.85	0.93711	.	.	.	.	.	D	0.86356	0.5913	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.87140	0.2202	9	0.72032	D	0.01	-10.4304	19.0962	0.93253	0.0:0.0:1.0:0.0	.	1596;1648;1614	Q6W2J9-4;Q6W2J9;Q6W2J9-2	.;BCOR_HUMAN;.	Q	518;491;1596;1614;1648;1614;321	ENSP00000408006:P518Q;ENSP00000367724:P491Q;ENSP00000367716:P1596Q;ENSP00000380512:P1614Q;ENSP00000367705:P1648Q;ENSP00000345923:P1614Q;ENSP00000387552:P321Q	ENSP00000345923:P1614Q	P	-	2	0	BCOR	39798116	1.000000	0.71417	0.092000	0.20876	0.024000	0.10985	9.476000	0.97823	2.459000	0.83118	0.600000	0.82982	CCG	.	.		0.468	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
MED14	9282	hgsc.bcm.edu	37	X	40522223	40522223	+	Missense_Mutation	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:40522223G>A	ENST00000324817.1	-	26	3756	c.3638C>T	c.(3637-3639)tCa>tTa	p.S1213L		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	1213					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|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)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	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 coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CATGATGACTGATCCAAGGAA	0.443																																					p.S1213L		Atlas-SNP	.											.	MED14	108	.	0			c.C3638T						.						82.0	66.0	71.0					X																	40522223		2203	4300	6503	SO:0001583	missense	9282	exon26			ATGACTGATCCAA	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"""cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"""	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.3638C>T	chrX.hg19:g.40522223G>A	ENSP00000323720:p.Ser1213Leu	115.0	0.0		95.0	5.0	NM_004229	Q4KMR7|Q9UNB3	Missense_Mutation	SNP	ENST00000324817.1	hg19	CCDS14254.1	.	.	.	.	.	.	.	.	.	.	G	31	5.086900	0.94100	.	.	ENSG00000180182	ENST00000324817;ENST00000433003	T;T	0.57273	0.41;0.41	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.56963	0.2021	L	0.58101	1.795	0.80722	D	1	P;P	0.47762	0.9;0.9	P;P	0.44518	0.452;0.452	T	0.62534	-0.6834	10	0.66056	D	0.02	.	18.6702	0.91508	0.0:0.0:1.0:0.0	.	1213;1213	A8KAK5;O60244	.;MED14_HUMAN	L	1213;112	ENSP00000323720:S1213L;ENSP00000411357:S112L	ENSP00000323720:S1213L	S	-	2	0	MED14	40407167	1.000000	0.71417	0.977000	0.42913	0.997000	0.91878	9.476000	0.97823	2.353000	0.79882	0.529000	0.55759	TCA	.	.		0.443	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229	
ZNF182	7569	hgsc.bcm.edu	37	X	47836310	47836310	+	Silent	SNP	G	G	A	rs376875839		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:47836310G>A	ENST00000396965.1	-	7	1526	c.1176C>T	c.(1174-1176)caC>caT	p.H392H	ZNF182_ENST00000376943.3_Silent_p.H373H|ZNF182_ENST00000305127.6_Silent_p.H392H	NM_001178099.1	NP_001171570.1	P17025	ZN182_HUMAN	zinc finger protein 182	392					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(5)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)	22						GAGTTCTCTGGTGTATAATGA	0.368																																					p.H392H		Atlas-SNP	.											.	ZNF182	117	.	0			c.C1176T						.	G	,,	1,3834		0,0,1,1632,570	106.0	100.0	102.0		1119,1176,1176	1.9	1.0	X		102	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF182	NM_001007088.1,NM_001178099.1,NM_006962.1	,,	0,0,1,4060,2442	AA,AG,A,GG,G		0.0,0.0261,0.0095	,,	373/621,392/640,392/640	47836310	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	7569	exon7			TCTCTGGTGTATA	AK122874, R98366	CCDS35235.1, CCDS35236.1	Xp11.23	2013-01-08	2006-05-10	2006-05-10	ENSG00000147118	ENSG00000147118		"""Zinc fingers, C2H2-type"", ""-"""	13001	protein-coding gene	gene with protein product		314993	"""zinc finger protein 182 (HHZ150)"", ""zinc finger protein 21 (KOX 14)"""	ZNF21		8088786, 2014798, 8914609	Standard	NM_001178099		Approved	KOX14, HHZ150, Zfp182	uc004dit.3	P17025	OTTHUMG00000021460	ENST00000396965.1:c.1176C>T	chrX.hg19:g.47836310G>A		148.0	0.0		96.0	5.0	NM_006962	A2IDD7|Q3KP67|Q96QH7	Silent	SNP	ENST00000396965.1	hg19	CCDS35236.1																																																																																			.	.		0.368	ZNF182-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277055.1	NM_006962	
HDAC6	10013	hgsc.bcm.edu	37	X	48661183	48661183	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:48661183T>C	ENST00000334136.5	+	2	262	c.84T>C	c.(82-84)agT>agC	p.S28S	HDAC6_ENST00000469223.1_Intron|HDAC6_ENST00000444343.2_Silent_p.S42S|HDAC6_ENST00000376619.2_Silent_p.S28S|HDAC6_ENST00000413163.2_Intron			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	28					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|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)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	AGGACTCCAGTGTCACTTCGG	0.597																																					p.S28S	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.T84C						.						45.0	37.0	40.0					X																	48661183		2201	4299	6500	SO:0001819	synonymous_variant	10013	exon2			CTCCAGTGTCACT	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 90"""	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.84T>C	chrX.hg19:g.48661183T>C		168.0	0.0		110.0	5.0	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Silent	SNP	ENST00000334136.5	hg19	CCDS14306.1																																																																																			.	.		0.597	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044	
PPP1R3F	89801	hgsc.bcm.edu	37	X	49143280	49143280	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:49143280T>C	ENST00000055335.6	+	4	2144	c.2128T>C	c.(2128-2130)Ttg>Ctg	p.L710L	PPP1R3F_ENST00000438316.1_Silent_p.L381L|PPP1R3F_ENST00000466508.1_Silent_p.L364L|PPP1R3F_ENST00000495799.1_Silent_p.L364L|PPP1R3F_ENST00000376188.1_Silent_p.L364L	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	710					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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					CCTCAGTCCCTTGGGGGCCGA	0.592																																					p.L710L		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.T2128C						.						50.0	33.0	38.0					X																	49143280		2202	4300	6502	SO:0001819	synonymous_variant	89801	exon4			AGTCCCTTGGGGG		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.2128T>C	chrX.hg19:g.49143280T>C		140.0	0.0		81.0	4.0	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Silent	SNP	ENST00000055335.6	hg19	CCDS35254.1																																																																																			.	.		0.592	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215	
CLCN5	1184	hgsc.bcm.edu	37	X	49855056	49855056	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:49855056A>G	ENST00000307367.2	+	10	2109	c.1818A>G	c.(1816-1818)gaA>gaG	p.E606E	CLCN5_ENST00000376091.3_Silent_p.E676E|CLCN5_ENST00000376088.3_Silent_p.E676E|CLCN5_ENST00000376108.3_Silent_p.E606E			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	606	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					TGACTGTGGAAGATGTAGAGA	0.478																																					p.E676E		Atlas-SNP	.											.	CLCN5	137	.	0			c.A2028G						.						86.0	71.0	76.0					X																	49855056		2203	4300	6503	SO:0001819	synonymous_variant	1184	exon13			TGTGGAAGATGTA	X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"""Ion channels / Chloride channels : Voltage-sensitive"""	2023	protein-coding gene	gene with protein product	"""Dent disease"""	300008	"""nephrolithiasis 2, X-linked"", ""nephrolithiasis 1 (X-linked)"", ""chloride channel 5"""	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.1818A>G	chrX.hg19:g.49855056A>G		115.0	0.0		96.0	4.0	NM_001127898	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Silent	SNP	ENST00000307367.2	hg19	CCDS14328.1																																																																																			.	.		0.478	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1		
AKAP4	8852	hgsc.bcm.edu	37	X	49955744	49955744	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:49955744T>C	ENST00000376056.2	-	6	2547	c.2397A>G	c.(2395-2397)tcA>tcG	p.S799S	AKAP4_ENST00000358526.2_Silent_p.S808S|AKAP4_ENST00000376064.3_Silent_p.S799S|AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Silent_p.S425S					A kinase (PRKA) anchor protein 4											NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(6)|lung(14)|ovary(1)|skin(4)	41	Ovarian(276;0.236)					CTGCTTTAGCTGAAACCTGAG	0.512																																					p.S808S		Atlas-SNP	.											.	AKAP4	131	.	0			c.A2424G						.						148.0	130.0	136.0					X																	49955744		2203	4300	6503	SO:0001819	synonymous_variant	8852	exon6			TTTAGCTGAAACC	AF072756	CCDS14329.1, CCDS14330.1	Xp11.2	2009-03-12			ENSG00000147081	ENSG00000147081		"""A-kinase anchor proteins"""	374	protein-coding gene	gene with protein product	"""A-kinase anchor protein 82 kDa"", ""testis-specific gene HI"", ""protein kinase A anchoring protein 4"", ""cancer/testis antigen 99"""	300185				9822690, 9514854	Standard	NM_003886		Approved	p82, hAKAP82, AKAP82, Fsc1, HI, CT99	uc004dow.1	Q5JQC9	OTTHUMG00000021517	ENST00000376056.2:c.2397A>G	chrX.hg19:g.49955744T>C		132.0	0.0		83.0	4.0	NM_003886		Silent	SNP	ENST00000376056.2	hg19	CCDS14330.1																																																																																			.	.		0.512	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886	
SMC1A	8243	hgsc.bcm.edu	37	X	53432729	53432729	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:53432729T>C	ENST00000322213.4	-	10	1832	c.1705A>G	c.(1705-1707)Acc>Gcc	p.T569A	SMC1A_ENST00000375340.6_Missense_Mutation_p.T335A	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	569	Flexible hinge.				DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						GGCAAGAAGGTCTCAGGCTCC	0.537																																					p.T569A		Atlas-SNP	.											.	SMC1A	112	.	0			c.A1705G						.						69.0	53.0	58.0					X																	53432729		2203	4300	6503	SO:0001583	missense	8243	exon10			AGAAGGTCTCAGG	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"""Structural maintenance of chromosomes proteins"""	11111	protein-coding gene	gene with protein product		300040	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"""	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.1705A>G	chrX.hg19:g.53432729T>C	ENSP00000323421:p.Thr569Ala	110.0	0.0		98.0	4.0	NM_006306	O14995|Q16351|Q2M228	Missense_Mutation	SNP	ENST00000322213.4	hg19	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.289515	0.80914	.	.	ENSG00000072501	ENST00000322213;ENST00000375340	D;D	0.89050	-2.46;-2.46	5.15	5.15	0.70609	SMCs flexible hinge (3);RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.95201	0.8444	M	0.91818	3.245	0.80722	D	1	B;D;D	0.89917	0.301;1.0;0.998	B;D;D	0.73380	0.086;0.98;0.941	D	0.96038	0.9022	10	0.87932	D	0	.	13.4318	0.61059	0.0:0.0:0.0:1.0	.	335;547;569	B7Z709;Q6MZR8;Q14683	.;.;SMC1A_HUMAN	A	569;335	ENSP00000323421:T569A;ENSP00000364489:T335A	ENSP00000323421:T569A	T	-	1	0	SMC1A	53449454	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.704000	0.84595	1.976000	0.57569	0.486000	0.48141	ACC	.	.		0.537	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306	
HUWE1	10075	hgsc.bcm.edu	37	X	53579842	53579842	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:53579842G>T	ENST00000342160.3	-	61	8964	c.8507C>A	c.(8506-8508)cCa>cAa	p.P2836Q	HUWE1_ENST00000262854.6_Missense_Mutation_p.P2836Q			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2836					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						AGCTCTCTCTGGGGAAAGTGA	0.507																																					p.P2836Q		Atlas-SNP	.											.	HUWE1	724	.	0			c.C8507A						.						45.0	44.0	44.0					X																	53579842		2203	4300	6503	SO:0001583	missense	10075	exon62			CTCTCTGGGGAAA	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.8507C>A	chrX.hg19:g.53579842G>T	ENSP00000340648:p.Pro2836Gln	115.0	0.0		83.0	4.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	G	17.55	3.418814	0.62622	.	.	ENSG00000086758	ENST00000342160;ENST00000262854	T;T	0.37235	1.21;1.21	5.74	5.74	0.90152	.	0.592639	0.17254	N	0.181031	T	0.48519	0.1504	L	0.27053	0.805	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.83275	0.991;0.996	T	0.31971	-0.9924	10	0.27785	T	0.31	.	17.5784	0.87957	0.0:0.0:1.0:0.0	.	2836;2836	Q7Z6Z7;Q7Z6Z7-2	HUWE1_HUMAN;.	Q	2836	ENSP00000340648:P2836Q;ENSP00000262854:P2836Q	ENSP00000262854:P2836Q	P	-	2	0	HUWE1	53596567	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.813000	0.91963	2.422000	0.82143	0.600000	0.82982	CCA	.	.		0.507	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
KLF8	11279	hgsc.bcm.edu	37	X	56291711	56291711	+	Silent	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:56291711A>G	ENST00000468660.1	+	3	468	c.180A>G	c.(178-180)ccA>ccG	p.P60P	KLF8_ENST00000374928.3_Silent_p.P60P	NM_007250.4	NP_009181.2	O95600	KLF8_HUMAN	Kruppel-like factor 8	60					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(4)|large_intestine(6)|lung(5)|ovary(1)	16						TGGAGAACCCAGCACTGTTTA	0.483																																					p.P60P		Atlas-SNP	.											.	KLF8	38	.	0			c.A180G						.						48.0	42.0	44.0					X																	56291711		2203	4300	6503	SO:0001819	synonymous_variant	11279	exon4			GAACCCAGCACTG	U28282	CCDS14373.1, CCDS55428.1	Xp11.21	2013-01-08			ENSG00000102349	ENSG00000102349		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	6351	protein-coding gene	gene with protein product		300286					Standard	NM_007250		Approved	BKLF3, ZNF741, DXS741	uc004dur.3	O95600	OTTHUMG00000021666	ENST00000468660.1:c.180A>G	chrX.hg19:g.56291711A>G		138.0	0.0		96.0	4.0	NM_001159296	B4DJN3|E7EQQ8|L0R3U8|L0R4U2|Q2M246|Q59GV5|Q5HYQ5|Q5JXP7|Q6MZJ7|Q9UGC4	Silent	SNP	ENST00000468660.1	hg19	CCDS14373.1																																																																																			.	.		0.483	KLF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056887.2	NM_007250	
LAS1L	81887	hgsc.bcm.edu	37	X	64744928	64744928	+	Missense_Mutation	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:64744928T>C	ENST00000374811.3	-	8	999	c.959A>G	c.(958-960)gAg>gGg	p.E320G	LAS1L_ENST00000312391.8_Silent_p.G283G|LAS1L_ENST00000374807.5_Missense_Mutation_p.E320G|LAS1L_ENST00000374804.5_Missense_Mutation_p.E278G	NM_031206.4	NP_112483.1	Q9Y4W2	LAS1L_HUMAN	LAS1-like (S. cerevisiae)	320					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	33						CAGCACAGCCTCCCTGGAACA	0.512																																					p.E320G		Atlas-SNP	.											.	LAS1L	72	.	0			c.A959G						.						101.0	77.0	85.0					X																	64744928		2203	4300	6503	SO:0001583	missense	81887	exon8			ACAGCCTCCCTGG	BC014545	CCDS14381.1, CCDS55433.1, CCDS55434.1	Xq12	2008-02-05			ENSG00000001497	ENSG00000001497			25726	protein-coding gene	gene with protein product						12477932	Standard	NM_031206		Approved	FLJ12525	uc004dwa.2	Q9Y4W2	OTTHUMG00000021720	ENST00000374811.3:c.959A>G	chrX.hg19:g.64744928T>C	ENSP00000363944:p.Glu320Gly	54.0	0.0		65.0	4.0	NM_031206	A9X410|Q5JXQ0|Q8TEN5|Q9H9V5	Missense_Mutation	SNP	ENST00000374811.3	hg19	CCDS14381.1	.	.	.	.	.	.	.	.	.	.	T	8.332	0.826680	0.16749	.	.	ENSG00000001497	ENST00000374807;ENST00000374811;ENST00000374804	.	.	.	5.35	2.85	0.33270	.	0.742114	0.12835	N	0.435334	T	0.27629	0.0679	L	0.38175	1.15	0.28833	N	0.89703	B;B;B	0.19583	0.001;0.037;0.006	B;B;B	0.15052	0.005;0.012;0.004	T	0.10776	-1.0615	8	.	.	.	.	4.2525	0.10702	0.0:0.1073:0.2042:0.6885	.	278;320;320	Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2	.;.;LAS1L_HUMAN	G	320;320;278	.	.	E	-	2	0	LAS1L	64661653	0.456000	0.25744	0.989000	0.46669	0.953000	0.61014	0.464000	0.21988	1.785000	0.52413	0.486000	0.48141	GAG	.	.		0.512	LAS1L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056974.1	NM_031206	
SLC7A3	84889	hgsc.bcm.edu	37	X	70149744	70149744	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:70149744A>G	ENST00000374299.3	-	2	248	c.104T>C	c.(103-105)cTg>cCg	p.L35P	SLC7A3_ENST00000298085.4_Missense_Mutation_p.L35P			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	35					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CACTAAATCCAGGGTGCTTAG	0.562																																					p.L35P		Atlas-SNP	.											.	SLC7A3	76	.	0			c.T104C						.						79.0	62.0	68.0					X																	70149744		2203	4300	6503	SO:0001583	missense	84889	exon2			AAATCCAGGGTGC	AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"""Solute carriers"""	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.104T>C	chrX.hg19:g.70149744A>G	ENSP00000363417:p.Leu35Pro	89.0	0.0		96.0	4.0	NM_032803	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Missense_Mutation	SNP	ENST00000374299.3	hg19	CCDS14404.1	.	.	.	.	.	.	.	.	.	.	A	16.01	3.002570	0.54254	.	.	ENSG00000165349	ENST00000374299;ENST00000298085	D;D	0.91631	-2.88;-2.88	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.91825	0.7413	M	0.75777	2.31	0.80722	D	1	B	0.25007	0.116	B	0.32289	0.143	D	0.90740	0.4649	10	0.66056	D	0.02	.	12.6897	0.56968	1.0:0.0:0.0:0.0	.	35	Q8WY07	CTR3_HUMAN	P	35	ENSP00000363417:L35P;ENSP00000298085:L35P	ENSP00000298085:L35P	L	-	2	0	SLC7A3	70066469	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	8.947000	0.93000	1.787000	0.52448	0.430000	0.28490	CTG	.	.		0.562	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803	
MED12	9968	hgsc.bcm.edu	37	X	70352238	70352238	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:70352238G>T	ENST00000374080.3	+	31	4297	c.4265G>T	c.(4264-4266)cGc>cTc	p.R1422L	MED12_ENST00000333646.6_Missense_Mutation_p.R1422L|MED12_ENST00000374102.1_Missense_Mutation_p.R1422L			Q93074	MED12_HUMAN	mediator complex subunit 12	1422					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|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)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					TCTCTAGAGCGCTCTGGTGTA	0.562			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.R1422L		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.G4265T						.						65.0	60.0	62.0					X																	70352238		2009	4163	6172	SO:0001583	missense	9968	exon31			TAGAGCGCTCTGG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.4265G>T	chrX.hg19:g.70352238G>T	ENSP00000363193:p.Arg1422Leu	59.0	0.0		76.0	4.0	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	hg19	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.903756	0.92035	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072;ENST00000439750	T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.71651	0.3365	L	0.60455	1.87	0.80722	D	1	P;D;P;P	0.57571	0.939;0.98;0.78;0.948	P;P;P;P	0.51355	0.643;0.654;0.535;0.667	T	0.73084	-0.4094	10	0.40728	T	0.16	-12.3509	16.9533	0.86251	0.0:0.0:1.0:0.0	.	1422;1269;1422;1422	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	L	1422;1422;1422;1422;1390;167	ENSP00000333125:R1422L;ENSP00000363215:R1422L;ENSP00000363193:R1422L;ENSP00000414203:R1390L;ENSP00000408388:R167L	ENSP00000333125:R1422L	R	+	2	0	MED12	70268963	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	8.947000	0.93000	2.267000	0.75376	0.523000	0.50628	CGC	.	.		0.562	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
TBX22	50945	hgsc.bcm.edu	37	X	79282236	79282236	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:79282236C>A	ENST00000373294.5	+	5	695	c.667C>A	c.(667-669)Cga>Aga	p.R223R	TBX22_ENST00000373291.1_Silent_p.R103R|TBX22_ENST00000373296.3_Silent_p.R223R|TBX22_ENST00000442340.1_Silent_p.R103R	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	223					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R223*(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						GTACAAACCCCGAGTGCACGT	0.453																																					p.R223R		Atlas-SNP	.											.	TBX22	118	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C667A	GRCh37	CD013205	TBX22	D		.						158.0	128.0	138.0					X																	79282236		2203	4300	6503	SO:0001819	synonymous_variant	50945	exon5			AAACCCCGAGTGC	AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"""T-boxes"""	11600	protein-coding gene	gene with protein product		300307	"""cleft palate and/or ankyloglossia"""	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.667C>A	chrX.hg19:g.79282236C>A		83.0	0.0		93.0	4.0	NM_016954	Q5JZ06|Q96LC0|Q9HBF1	Silent	SNP	ENST00000373294.5	hg19	CCDS14445.1																																																																																			.	.		0.453	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954	
IRS4	8471	hgsc.bcm.edu	37	X	107975816	107975816	+	Silent	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:107975816G>T	ENST00000372129.2	-	1	3835	c.3759C>A	c.(3757-3759)ccC>ccA	p.P1253P	RP6-24A23.6_ENST00000563887.1_Silent_p.P34P	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	1253					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						GACCTCTTTTGGGAGAGTCGA	0.448																																					p.P1253P		Atlas-SNP	.											.	IRS4	253	.	0			c.C3759A						.						96.0	95.0	95.0					X																	107975816		2203	4300	6503	SO:0001819	synonymous_variant	8471	exon1			TCTTTTGGGAGAG	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.3759C>A	chrX.hg19:g.107975816G>T		77.0	0.0		89.0	4.0	NM_003604		Silent	SNP	ENST00000372129.2	hg19	CCDS14544.1																																																																																			.	.		0.448	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
NKRF	55922	hgsc.bcm.edu	37	X	118725226	118725226	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:118725226T>C	ENST00000371527.1	-	2	814	c.162A>G	c.(160-162)agA>agG	p.R54R	NKRF_ENST00000487600.1_5'UTR|NKRF_ENST00000542113.1_Silent_p.R69R|NKRF_ENST00000304449.5_Silent_p.R54R	NM_001173488.1	NP_001166959.1	O15226	NKRF_HUMAN	NFKB repressing factor	54	Active repression domain.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	30						CAAAACGAGGTCTCGCATGGA	0.363																																					p.R69R		Atlas-SNP	.											.	NKRF	121	.	0			c.A207G						.						90.0	82.0	85.0					X																	118725226		2203	4300	6503	SO:0001819	synonymous_variant	55922	exon4			ACGAGGTCTCGCA	AJ011812	CCDS35375.1, CCDS55486.1	Xq24	2013-01-28	2008-03-26		ENSG00000186416	ENSG00000186416		"""G patch domain containing"""	19374	protein-coding gene	gene with protein product		300440	"""NF-kappaB repressing factor"""			10562553	Standard	NM_017544		Approved	ITBA4, NRF	uc022cdk.1	O15226	OTTHUMG00000022277	ENST00000371527.1:c.162A>G	chrX.hg19:g.118725226T>C		60.0	0.0		85.0	4.0	NM_001173487	G3V1N1|Q4VC41|Q9UJ91	Silent	SNP	ENST00000371527.1	hg19	CCDS35375.1																																																																																			.	.		0.363	NKRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058044.1	NM_017544	
C1GALT1C1	29071	hgsc.bcm.edu	37	X	119760344	119760344	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:119760344G>A	ENST00000304661.5	-	2	916	c.678C>T	c.(676-678)tgC>tgT	p.C226C	C1GALT1C1_ENST00000371313.2_Silent_p.C226C	NM_001011551.2	NP_001011551.1	Q96EU7	C1GLC_HUMAN	C1GALT1-specific chaperone 1	226					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	11						CATATTTCAGGCAAACTGCTA	0.378																																					p.C226C		Atlas-SNP	.											.	C1GALT1C1	22	.	0			c.C678T						.						113.0	107.0	109.0					X																	119760344		2203	4300	6503	SO:0001819	synonymous_variant	29071	exon3			TTTCAGGCAAACT	AJ238398	CCDS14602.1	Xq24	2008-02-05			ENSG00000171155	ENSG00000171155			24338	protein-coding gene	gene with protein product		300611				11042152, 12361956	Standard	NM_152692		Approved	COSMC, C1GALT2	uc004esz.3	Q96EU7	OTTHUMG00000022305	ENST00000304661.5:c.678C>T	chrX.hg19:g.119760344G>A		93.0	0.0		107.0	6.0	NM_152692	A8K246|Q8WWS3|Q9NZX1	Silent	SNP	ENST00000304661.5	hg19	CCDS14602.1																																																																																			.	.		0.378	C1GALT1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058117.1	NM_152692	
STAG2	10735	hgsc.bcm.edu	37	X	123190045	123190045	+	Silent	SNP	C	C	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:123190045C>A	ENST00000371160.1	+	14	1554	c.1264C>A	c.(1264-1266)Cgg>Agg	p.R422R	STAG2_ENST00000371144.3_Silent_p.R422R|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000354548.5_Silent_p.R353R|STAG2_ENST00000371145.3_Silent_p.R422R|STAG2_ENST00000218089.9_Silent_p.R422R|STAG2_ENST00000371157.3_Silent_p.R422R	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	422					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						TTCAGCTCACCGGCCAGTAGC	0.353																																					p.R422R		Atlas-SNP	.											.	STAG2	309	.	0			c.C1264A						.						93.0	88.0	89.0					X																	123190045		2203	4300	6503	SO:0001819	synonymous_variant	10735	exon14			GCTCACCGGCCAG	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1264C>A	chrX.hg19:g.123190045C>A		79.0	0.0		88.0	4.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.		0.353	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
STAG2	10735	hgsc.bcm.edu	37	X	123190067	123190067	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:123190067G>T	ENST00000371160.1	+	14	1576	c.1286G>T	c.(1285-1287)gGa>gTa	p.G429V	STAG2_ENST00000371144.3_Missense_Mutation_p.G429V|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000354548.5_Missense_Mutation_p.G360V|STAG2_ENST00000371145.3_Missense_Mutation_p.G429V|STAG2_ENST00000218089.9_Missense_Mutation_p.G429V|STAG2_ENST00000371157.3_Missense_Mutation_p.G429V	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	429					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						GTAGCAGCTGGAGAATTTCTC	0.333																																					p.G429V		Atlas-SNP	.											.	STAG2	309	.	0			c.G1286T						.						74.0	71.0	72.0					X																	123190067		2203	4300	6503	SO:0001583	missense	10735	exon14			CAGCTGGAGAATT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1286G>T	chrX.hg19:g.123190067G>T	ENSP00000360202:p.Gly429Val	67.0	0.0		74.0	4.0	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.465602	0.84425	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58	5.2	5.2	0.72013	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.56615	0.1997	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.986	T	0.58272	-0.7665	10	0.51188	T	0.08	-17.3276	18.0609	0.89377	0.0:0.0:1.0:0.0	.	429;429	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	V	429;429;360;429;429;429;429	ENSP00000218089:G429V;ENSP00000397265:G429V;ENSP00000346555:G360V;ENSP00000360202:G429V;ENSP00000360199:G429V;ENSP00000360187:G429V;ENSP00000360186:G429V	ENSP00000218089:G429V	G	+	2	0	STAG2	123017748	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.809000	0.99208	2.288000	0.76882	0.544000	0.68410	GGA	.	.		0.333	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
GPR119	139760	hgsc.bcm.edu	37	X	129519158	129519158	+	Silent	SNP	G	G	T	rs200469524		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:129519158G>T	ENST00000276218.2	-	1	353	c.264C>A	c.(262-264)tcC>tcA	p.S88S		NM_178471.2	NP_848566.1	Q8TDV5	GP119_HUMAN	G protein-coupled receptor 119	88					insulin secretion (GO:0030073)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(3)|prostate(1)	11						AGGCAGCTGCGGAGGAAGTGA	0.577																																					p.S88S		Atlas-SNP	.											.	GPR119	34	.	0			c.C264A						.						116.0	111.0	113.0					X																	129519158		2203	4300	6503	SO:0001819	synonymous_variant	139760	exon1			AGCTGCGGAGGAA	AY288416	CCDS14625.1	Xq26.1	2014-01-30			ENSG00000147262	ENSG00000147262		"""GPCR / Class A : Orphans"""	19060	protein-coding gene	gene with protein product		300513				12044878, 14623098	Standard	NM_178471		Approved	hGPCR2, GPCR2	uc011muv.2	Q8TDV5	OTTHUMG00000022397	ENST00000276218.2:c.264C>A	chrX.hg19:g.129519158G>T		80.0	0.0		90.0	5.0	NM_178471	Q495H7|Q4VBN3	Silent	SNP	ENST00000276218.2	hg19	CCDS14625.1																																																																																			.	.		0.577	GPR119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058270.1	NM_178471	
SLC9A6	10479	hgsc.bcm.edu	37	X	135067790	135067790	+	Silent	SNP	G	G	A			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:135067790G>A	ENST00000370698.3	+	1	164	c.129G>A	c.(127-129)tcG>tcA	p.S43S	SLC9A6_ENST00000370695.4_Silent_p.S43S|SLC9A6_ENST00000370701.1_5'UTR	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6	43					axon extension (GO:0048675)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|dendrite extension (GO:0097484)|dendritic spine development (GO:0060996)|ion transport (GO:0006811)|neuron projection morphogenesis (GO:0048812)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon terminus (GO:0043679)|axonal spine (GO:0044308)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)	sodium:proton antiporter activity (GO:0015385)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(18)|ovary(2)|upper_aerodigestive_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CAGGGGCTTCGGACGGCGGCG	0.687																																					p.S43S		Atlas-SNP	.											.	SLC9A6	64	.	0			c.G129A						.						41.0	44.0	43.0					X																	135067790		2201	4297	6498	SO:0001819	synonymous_variant	10479	exon1			GGCTTCGGACGGC	AF030409	CCDS14654.1, CCDS44003.1, CCDS55504.1	Xq26.3	2013-05-22	2012-03-22		ENSG00000198689	ENSG00000198689		"""Solute carriers"""	11079	protein-coding gene	gene with protein product		300231	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 6"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 6"""			9507001	Standard	NM_001042537		Approved	NHE6, KIAA0267	uc004ezk.3	Q92581	OTTHUMG00000022498	ENST00000370698.3:c.129G>A	chrX.hg19:g.135067790G>A		63.0	0.0		66.0	4.0	NM_006359	A6NIQ9|A8K160|B4DU30|B7ZAE0|Q3ZCW7|Q5JPP8|Q5JPP9|Q86VS0	Silent	SNP	ENST00000370698.3	hg19	CCDS14654.1																																																																																			.	.		0.687	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058450.1	NM_006359	
AFF2	2334	hgsc.bcm.edu	37	X	148062276	148062276	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:148062276T>C	ENST00000370460.2	+	19	4058	c.3579T>C	c.(3577-3579)gcT>gcC	p.A1193A	AFF2_ENST00000286437.5_Silent_p.A834A|AFF2_ENST00000342251.3_Silent_p.A1160A|AFF2_ENST00000370457.5_Silent_p.A1158A	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	1193					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					AGCAAAATGCTTCAAAAGTCG	0.353																																					p.A1193A		Atlas-SNP	.											.	AFF2	679	.	0			c.T3579C						.						82.0	81.0	82.0					X																	148062276		2203	4300	6503	SO:0001819	synonymous_variant	2334	exon19			AAATGCTTCAAAA	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.3579T>C	chrX.hg19:g.148062276T>C		48.0	0.0		73.0	4.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	hg19	CCDS14684.1																																																																																			.	.		0.353	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	
FATE1	89885	hgsc.bcm.edu	37	X	150889973	150889973	+	Splice_Site	SNP	G	G	T	rs149441058		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:150889973G>T	ENST00000370350.3	+	3	426	c.341G>T	c.(340-342)cGc>cTc	p.R114L		NM_033085.2	NP_149076.1	Q969F0	FATE1_HUMAN	fetal and adult testis expressed 1	114						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(6)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)					CATTATGATCGGTAAGAGCTG	0.602																																					p.R114L		Atlas-SNP	.											.	FATE1	30	.	0			c.G341T						.						76.0	60.0	65.0					X																	150889973		2203	4300	6503	SO:0001630	splice_region_variant	89885	exon3			ATGATCGGTAAGA	AF249872	CCDS14700.1	Xq28	2009-03-25			ENSG00000147378	ENSG00000147378			24683	protein-coding gene	gene with protein product	"""cancer/testis antigen 43"""	300450				11694338	Standard	NM_033085		Approved	FATE, CT43	uc004fex.3	Q969F0	OTTHUMG00000024172	ENST00000370350.3:c.341+1G>T	chrX.hg19:g.150889973G>T		66.0	0.0		90.0	4.0	NM_033085		Missense_Mutation	SNP	ENST00000370350.3	hg19	CCDS14700.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.630216	0.46944	.	.	ENSG00000147378	ENST00000370350	T	0.48836	0.8	3.92	1.14	0.20703	.	1.132520	0.06614	N	0.756234	T	0.40297	0.1111	L	0.29908	0.895	0.80722	D	1	P	0.49090	0.919	P	0.46172	0.506	T	0.20240	-1.0281	10	0.59425	D	0.04	-0.0367	5.8408	0.18633	0.3632:0.0:0.6368:0.0	.	114	Q969F0	FATE1_HUMAN	L	114	ENSP00000359375:R114L	ENSP00000359375:R114L	R	+	2	0	FATE1	150640629	0.516000	0.26218	0.017000	0.16124	0.023000	0.10783	0.465000	0.22004	0.114000	0.18032	0.529000	0.55759	CGC	.	G|1.000;A|0.000		0.602	FATE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060885.1	NM_033085	Missense_Mutation
ATP2B3	492	hgsc.bcm.edu	37	X	152821529	152821529	+	Missense_Mutation	SNP	G	G	T			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:152821529G>T	ENST00000349466.2	+	13	2407	c.2081G>T	c.(2080-2082)tGc>tTc	p.C694F	ATP2B3_ENST00000393842.1_Missense_Mutation_p.C680F|ATP2B3_ENST00000359149.3_Missense_Mutation_p.C694F|ATP2B3_ENST00000263519.4_Missense_Mutation_p.C694F|ATP2B3_ENST00000370186.1_Missense_Mutation_p.C680F|ATP2B3_ENST00000370181.2_Missense_Mutation_p.C680F			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	694					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ATCCGAAAATGCCAGCGTGCT	0.597																																					p.C694F		Atlas-SNP	.											.	ATP2B3	552	.	0			c.G2081T						.						129.0	129.0	129.0					X																	152821529		2203	4300	6503	SO:0001583	missense	492	exon12			GAAAATGCCAGCG	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"""ATPases / P-type"""	816	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 3"", ""cilia and flagella associated protein 39"""	300014	"""spinocerebellar ataxia, X-linked 1"", ""cerebellar ataxia 2 (X-linked)"""	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.2081G>T	chrX.hg19:g.152821529G>T	ENSP00000343886:p.Cys694Phe	72.0	0.0		95.0	4.0	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Missense_Mutation	SNP	ENST00000349466.2	hg19	CCDS35440.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.430579	0.83776	.	.	ENSG00000067842	ENST00000370186;ENST00000349466;ENST00000393842;ENST00000359149;ENST00000263519;ENST00000370181	D;D;D;D;D;D	0.96168	-3.93;-3.93;-3.93;-3.93;-3.93;-3.93	4.87	4.87	0.63330	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.97996	0.9340	M	0.90309	3.105	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.973	D	0.99198	1.0872	10	0.87932	D	0	-27.3007	16.1639	0.81739	0.0:0.0:1.0:0.0	.	694;694	Q16720;Q16720-2	AT2B3_HUMAN;.	F	680;694;680;694;694;680	ENSP00000359205:C680F;ENSP00000343886:C694F;ENSP00000377425:C680F;ENSP00000352062:C694F;ENSP00000263519:C694F;ENSP00000359200:C680F	ENSP00000263519:C694F	C	+	2	0	ATP2B3	152474723	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.721000	0.98766	2.155000	0.67459	0.529000	0.55759	TGC	.	.		0.597	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949	
TKTL1	8277	hgsc.bcm.edu	37	X	153543546	153543546	+	Silent	SNP	T	T	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:153543546T>C	ENST00000369915.3	+	7	1077	c.888T>C	c.(886-888)ggT>ggC	p.G296G	TKTL1_ENST00000217905.7_Silent_p.G36G|TKTL1_ENST00000369912.2_Silent_p.G240G	NM_001145933.1|NM_012253.3	NP_001139405.1|NP_036385.3	P51854	TKTL1_HUMAN	transketolase-like 1	296					glucose catabolic process (GO:0006007)|thiamine metabolic process (GO:0006772)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			NS(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(5)|prostate(1)|skin(1)|urinary_tract(2)	34	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-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)					AAGCATGCGGTCTGGCTCTGG	0.473																																					p.G296G		Atlas-SNP	.											.	TKTL1	61	.	0			c.T888C						.						171.0	138.0	149.0					X																	153543546		2203	4300	6503	SO:0001819	synonymous_variant	8277	exon7			ATGCGGTCTGGCT	X91817	CCDS35448.1, CCDS55541.1	Xq28	2008-02-05			ENSG00000007350	ENSG00000007350			11835	protein-coding gene	gene with protein product		300044				8838793	Standard	NM_012253		Approved	TKR, TKT2	uc004fkg.3	P51854	OTTHUMG00000022707	ENST00000369915.3:c.888T>C	chrX.hg19:g.153543546T>C		84.0	0.0		78.0	4.0	NM_012253	A8K896|Q5TYJ8|Q5TYJ9|Q8TC75	Silent	SNP	ENST00000369915.3	hg19	CCDS35448.1																																																																																			.	.		0.473	TKTL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058923.1	NM_012253	
DNASE1L1	1774	hgsc.bcm.edu	37	X	153631431	153631431	+	Missense_Mutation	SNP	A	A	G			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:153631431A>G	ENST00000393638.1	-	7	912	c.626T>C	c.(625-627)gTg>gCg	p.V209A	DNASE1L1_ENST00000369809.1_Missense_Mutation_p.V209A|SNORA70_ENST00000384436.1_RNA	NM_001009934.1	NP_001009934.1	P49184	DNSL1_HUMAN	deoxyribonuclease I-like 1	209					DNA metabolic process (GO:0006259)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			lung(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)					ATCGGCAATCACCCAGTGGAA	0.627																																					p.V209A		Atlas-SNP	.											.	DNASE1L1	20	.	0			c.T626C						.						58.0	55.0	56.0					X																	153631431		2203	4300	6503	SO:0001583	missense	1774	exon7			GCAATCACCCAGT	L40817	CCDS14747.1	Xq28	2008-02-05			ENSG00000013563	ENSG00000013563			2957	protein-coding gene	gene with protein product	"""DNase X"""	300081		DNL1L		8541839, 8654957	Standard	XM_005277829		Approved	DNAS1L1, XIB, DNASEX	uc004fkw.1	P49184	OTTHUMG00000033188	ENST00000393638.1:c.626T>C	chrX.hg19:g.153631431A>G	ENSP00000377255:p.Val209Ala	73.0	0.0		84.0	5.0	NM_006730	D3DWW7|Q5HY41	Missense_Mutation	SNP	ENST00000393638.1	hg19	CCDS14747.1	.	.	.	.	.	.	.	.	.	.	A	13.86	2.362903	0.41902	.	.	ENSG00000013563	ENST00000369809;ENST00000393638;ENST00000014935;ENST00000369808;ENST00000369807;ENST00000309585	T;T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75;0.75	4.93	-2.34	0.06704	Endonuclease/exonuclease/phosphatase (2);	0.572650	0.16380	N	0.216952	T	0.27169	0.0666	N	0.17312	0.475	0.26270	N	0.978448	B	0.02656	0.0	B	0.06405	0.002	T	0.13980	-1.0489	10	0.51188	T	0.08	-15.7171	9.5875	0.39526	0.698:0.0:0.302:0.0	.	209	P49184	DNSL1_HUMAN	A	209	ENSP00000358824:V209A;ENSP00000377255:V209A;ENSP00000014935:V209A;ENSP00000358823:V209A;ENSP00000358822:V209A;ENSP00000309168:V209A	ENSP00000014935:V209A	V	-	2	0	DNASE1L1	153284625	0.868000	0.29978	0.129000	0.21949	0.873000	0.50193	1.545000	0.36169	-0.452000	0.07087	-0.327000	0.08410	GTG	.	.		0.627	DNASE1L1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080928.2		
GSDMB	55876	hgsc.bcm.edu	37	17	38068744	38068746	+	In_Frame_Del	DEL	TTT	TTT	-			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr17:38068744_38068746delTTT	ENST00000394179.1	-	3	370_372	c.240_242delAAA	c.(238-243)caaaag>cag	p.K81del	GSDMB_ENST00000520542.1_In_Frame_Del_p.K81del|GSDMB_ENST00000418519.1_In_Frame_Del_p.K81del|GSDMB_ENST00000394175.2_In_Frame_Del_p.K81del|GSDMB_ENST00000309481.7_In_Frame_Del_p.K81del|GSDMB_ENST00000360317.3_In_Frame_Del_p.K81del			Q8TAX9	GSDMB_HUMAN	gasdermin B	81						cytoplasm (GO:0005737)				breast(2)|endometrium(3)|large_intestine(6)|lung(6)|pancreas(1)|prostate(1)|stomach(2)	21						AAACTCAGCCTTTTGACCTGGAA	0.478																																					p.81_81del		Atlas-Indel,Pindel	.											.	GSDMB	87	.	0			c.241_243del						.																																			SO:0001651	inframe_deletion	55876	exon3			.	AF119884	CCDS11354.1, CCDS42313.1, CCDS54119.1, CCDS54120.1	17q21.2	2008-07-31	2008-07-31	2008-07-31	ENSG00000073605	ENSG00000073605			23690	protein-coding gene	gene with protein product		611221	"""gasdermin-like"""	GSDML		12883658, 15010812, 17350798	Standard	NM_001042471		Approved	PRO2521	uc010cwj.3	Q8TAX9	OTTHUMG00000133248	ENST00000394179.1:c.240_242delAAA	chr17.hg19:g.38068744_38068746delTTT	ENSP00000377733:p.Lys81del	216.0	0.0		213.0	104.0	NM_001042471	B4DKK7|Q7Z377|Q8WY76|Q9NX71|Q9P163	In_Frame_Del	DEL	ENST00000394179.1	hg19																																																																																				.	.		0.478	GSDMB-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_018530	
AXIN1	8312	hgsc.bcm.edu	37	16	364562	364563	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr16:364562_364563delAC	ENST00000262320.3	-	3	1370_1371	c.999_1000delGT	c.(997-1002)ctgtccfs	p.S334fs	AXIN1_ENST00000481769.1_5'UTR|AXIN1_ENST00000354866.3_Frame_Shift_Del_p.S334fs	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	334	Interaction with TP53. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)	p.T336fs*17(1)		biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				TCCGTGAGGGACAGGGTGTCTG	0.614																																					p.334_334del		Atlas-Indel,Pindel	.											.	AXIN1	290	.	1	Insertion - Frameshift(1)	liver(1)	c.1000_1001del						.																																			SO:0001589	frameshift_variant	8312	exon3			.	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	903	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 49"""	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.999_1000delGT	chr16.hg19:g.364562_364563delAC	ENSP00000262320:p.Ser334fs	135.0	0.0		52.0	23.0	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Frame_Shift_Del	DEL	ENST00000262320.3	hg19	CCDS10405.1																																																																																			.	.		0.614	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		
RBM10	8241	hgsc.bcm.edu	37	X	47041174	47041185	+	In_Frame_Del	DEL	GCTCAAATCTGA	GCTCAAATCTGA	-	rs150665564		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	GCTCAAATCTGA	GCTCAAATCTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:47041174_47041185delGCTCAAATCTGA	ENST00000377604.3	+	15	2344_2355	c.1602_1613delGCTCAAATCTGA	c.(1600-1614)gtgctcaaatctgag>gtg	p.LKSE535del	RBM10_ENST00000329236.7_In_Frame_Del_p.LKSE457del|RBM10_ENST00000345781.6_In_Frame_Del_p.LKSE458del	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	535					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						CACCCGCTGTGCTCAAATCTGAGCTCCAGAGC	0.618																																					p.599_603del	Melanoma(171;120 2705 19495 39241)	Atlas-INDEL	.											.	RBM10	117	.	0			c.1796_1807del						.																																			SO:0001651	inframe_deletion	8241	exon15			.	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"""Zinc fingers, RAN-binding domain containing"", ""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.1602_1613delGCTCAAATCTGA	chrX.hg19:g.47041174_47041185delGCTCAAATCTGA	ENSP00000366829:p.Leu535_Glu538del	109.0	0.0		31.0	18.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	In_Frame_Del	DEL	ENST00000377604.3	hg19	CCDS14274.1																																																																																			.	.		0.618	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676	
ALB	213	hgsc.bcm.edu	37	4	74275125	74275126	+	Frame_Shift_Ins	INS	-	-	C			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chr4:74275125_74275126insC	ENST00000503124.1	+	3	293_294	c.86_87insC	c.(85-90)cttttcfs	p.LF29fs	ALB_ENST00000509063.1_Frame_Shift_Ins_p.LF179fs|ALB_ENST00000415165.2_Intron|ALB_ENST00000401494.3_Frame_Shift_Ins_p.LF64fs|ALB_ENST00000295897.4_Frame_Shift_Ins_p.LF179fs|ALB_ENST00000505649.1_3'UTR			Q8TES7	FBF1_HUMAN	albumin	0					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)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CCGGAACTCCTTTTCTTTGCTA	0.351																																					p.L179fs		Atlas-INDEL	.											.	ALB	132	.	0			c.536_537insC						.																																			SO:0001589	frameshift_variant	213	exon5			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	Exception_encountered	chr4.hg19:g.74275125_74275126insC	ENSP00000421027:p.Leu29fs	388.0	0.0		297.0	154.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Ins	INS	ENST00000503124.1	hg19																																																																																				.	.		0.351	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	
VCX2	51480	hgsc.bcm.edu	37	X	8138170	8138171	+	Frame_Shift_Del	DEL	CT	CT	-	rs75657421|rs78723459		TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:8138170_8138171delCT	ENST00000317103.4	-	3	628_629	c.322_323delAG	c.(322-324)agcfs	p.S108fs		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	108	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.			S -> A (in Ref. 1; AAG41765, 2; AAF28172 and 4; AAH98113/AAH96715/AAH98163). {ECO:0000305}.						endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				TTCCACCTCGCTCTCCTGACTC	0.644																																					p.108_108del		Pindel	.											.	VCX2	16	.	0			c.323_324del						.																																			SO:0001589	frameshift_variant	51480	exon3			.	AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.322_323delAG	chrX.hg19:g.8138172_8138173delCT	ENSP00000321309:p.Ser108fs	186.0	0.0		110.0	12.0	NM_016378	A3KPB6|Q4V9T2|Q9P0H5	Frame_Shift_Del	DEL	ENST00000317103.4	hg19	CCDS35200.1																																																																																			.	.		0.644	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378	
RBM10	8241	hgsc.bcm.edu	37	X	47041175	47041186	+	In_Frame_Del	DEL	CTCAAATCTGAG	CTCAAATCTGAG	-			TCGA-ES-A2HS-01A-11D-A183-10	TCGA-ES-A2HS-11A-11D-A183-10	CTCAAATCTGAG	CTCAAATCTGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dcf45005-7e6d-4c26-9994-f973da7e814f	a9c45810-b691-4963-b215-977e8f93d1c2	g.chrX:47041175_47041186delCTCAAATCTGAG	ENST00000377604.3	+	15	2345_2356	c.1603_1614delCTCAAATCTGAG	c.(1603-1614)ctcaaatctgagdel	p.LKSE535del	RBM10_ENST00000329236.7_In_Frame_Del_p.LKSE457del|RBM10_ENST00000345781.6_In_Frame_Del_p.LKSE458del	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	535					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						ACCCGCTGTGCTCAAATCTGAGCTCCAGAGCC	0.618																																					p.599_603del	Melanoma(171;120 2705 19495 39241)	Pindel	.											.	RBM10	117	.	0			c.1797_1808del						.																																			SO:0001651	inframe_deletion	8241	exon15			.	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"""Zinc fingers, RAN-binding domain containing"", ""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.1603_1614delCTCAAATCTGAG	chrX.hg19:g.47041175_47041186delCTCAAATCTGAG	ENSP00000366829:p.Leu535_Glu538del	109.0	0.0		31.0	19.0	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	In_Frame_Del	DEL	ENST00000377604.3	hg19	CCDS14274.1																																																																																			.	.		0.618	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676	
