#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
PLEKHN1	84069	hgsc.bcm.edu	37	1	909218	909218	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:909218C>T	ENST00000379409.2	+	13	1626	c.1596C>T	c.(1594-1596)ctC>ctT	p.L532L	PLEKHN1_ENST00000379410.3_Silent_p.L480L|PLEKHN1_ENST00000379407.3_Silent_p.L445L			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	532										central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9	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;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		TGCAGTTCCTCAGTGCCATGC	0.682																																					p.L480L		Atlas-SNP	.											.	PLEKHN1	49	.	0			c.C1440T						.						23.0	28.0	27.0					1																	909218		2195	4294	6489	SO:0001819	synonymous_variant	84069	exon14			GTTCCTCAGTGCC	AL136730	CCDS4.1, CCDS53256.1	1p36.33	2013-01-11			ENSG00000187583	ENSG00000187583		"""Pleckstrin homology (PH) domain containing"""	25284	protein-coding gene	gene with protein product						11230166	Standard	NM_032129		Approved	DKFZP434H2010	uc001acd.3	Q494U1	OTTHUMG00000040756	ENST00000379409.2:c.1596C>T	chr1.hg19:g.909218C>T		89.0	0.0		72.0	4.0	NM_032129	Q494U2|Q5SV98|Q9H0M7	Silent	SNP	ENST00000379409.2	hg19																																																																																				.	.		0.682	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129	
FAM132A	388581	hgsc.bcm.edu	37	1	1178923	1178923	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:1178923G>A	ENST00000330388.2	-	5	572	c.541C>T	c.(541-543)Caa>Taa	p.Q181*		NM_001014980.2	NP_001014980.1	Q5T7M4	ADIPL_HUMAN	family with sequence similarity 132, member A	181	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				negative regulation of gluconeogenesis (GO:0045721)|negative regulation of inflammatory response (GO:0050728)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of glucose import (GO:0046324)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|lung(1)	2	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)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.22e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AAGGCACCTTGGGCAGCAGGC	0.711																																					p.Q181X		Atlas-SNP	.											.	FAM132A	12	.	0			c.C541T						.						16.0	14.0	15.0					1																	1178923		2086	4136	6222	SO:0001587	stop_gained	388581	exon5			CACCTTGGGCAGC	BC089443	CCDS30554.1	1p36.33	2012-03-26	2007-03-27	2007-03-27	ENSG00000184163	ENSG00000184163			32308	protein-coding gene	gene with protein product	"""adipolin"", ""adipose-derived insulin-sensitizing factor"""		"""C1q domain containing 2"""	C1QDC2		21849507	Standard	NM_001014980		Approved	MGC105127, C1QTNF12, CTRP12	uc001adl.2	Q5T7M4	OTTHUMG00000001412	ENST00000330388.2:c.541C>T	chr1.hg19:g.1178923G>A	ENSP00000329137:p.Gln181*	38.0	0.0		43.0	4.0	NM_001014980	Q5EBL5	Nonsense_Mutation	SNP	ENST00000330388.2	hg19	CCDS30554.1	.	.	.	.	.	.	.	.	.	.	g	14.87	2.665457	0.47677	.	.	ENSG00000184163	ENST00000330388	.	.	.	3.98	2.98	0.34508	.	0.065332	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-12.7246	8.4044	0.32605	0.0:0.0:0.7665:0.2335	.	.	.	.	X	181	.	ENSP00000329137:Q181X	Q	-	1	0	FAM132A	1168786	1.000000	0.71417	0.979000	0.43373	0.044000	0.14063	1.729000	0.38115	2.252000	0.74401	0.544000	0.68410	CAA	.	.		0.711	FAM132A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004080.4	XM_371208	
CASZ1	54897	hgsc.bcm.edu	37	1	10699170	10699170	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:10699170G>C	ENST00000377022.3	-	21	5426	c.5109C>G	c.(5107-5109)gaC>gaG	p.D1703E	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1703	Asp-rich.|Glu-rich.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		cgtcgtcctcgtcgtcgtcgt	0.731																																					p.D1703E		Atlas-SNP	.											.	CASZ1	150	.	0			c.C5109G						.						6.0	6.0	6.0					1																	10699170		1787	3642	5429	SO:0001583	missense	54897	exon21			GTCCTCGTCGTCG	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.5109C>G	chr1.hg19:g.10699170G>C	ENSP00000366221:p.Asp1703Glu	24.0	0.0		39.0	6.0	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	hg19	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.462549	0.43736	.	.	ENSG00000130940	ENST00000377022	T	0.15952	2.38	2.95	-0.672	0.11377	.	0.130452	0.25302	U	0.031647	T	0.05868	0.0153	N	0.08118	0	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.39078	-0.9631	10	0.21014	T	0.42	-5.0237	3.1393	0.06450	0.1027:0.344:0.3949:0.1584	.	1703	Q86V15	CASZ1_HUMAN	E	1703	ENSP00000366221:D1703E	ENSP00000366221:D1703E	D	-	3	2	CASZ1	10621757	0.995000	0.38212	0.909000	0.35828	0.536000	0.34869	0.566000	0.23593	-0.514000	0.06488	0.195000	0.17529	GAC	.	.		0.731	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
PTCHD2	57540	hgsc.bcm.edu	37	1	11574569	11574569	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:11574569T>C	ENST00000294484.6	+	4	1577	c.1439T>C	c.(1438-1440)cTc>cCc	p.L480P	PTCHD2_ENST00000389575.3_Missense_Mutation_p.L480P	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	480	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GTCTACATCCTCACCTCCTGC	0.577																																					p.L480P		Atlas-SNP	.											.	PTCHD2	193	.	0			c.T1439C						.						110.0	109.0	109.0					1																	11574569		2085	4212	6297	SO:0001583	missense	57540	exon4			ACATCCTCACCTC	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.1439T>C	chr1.hg19:g.11574569T>C	ENSP00000294484:p.Leu480Pro	131.0	0.0		84.0	4.0	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	hg19	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.240377	0.79912	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	D;D	0.96491	-4.03;-4.03	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.97238	0.9097	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97812	1.0251	10	0.66056	D	0.02	-39.7503	14.2637	0.66102	0.0:0.0:0.0:1.0	.	480	Q9P2K9	PTHD2_HUMAN	P	480	ENSP00000294484:L480P;ENSP00000374226:L480P	ENSP00000294484:L480P	L	+	2	0	PTCHD2	11497156	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.628000	0.83189	2.017000	0.59298	0.533000	0.62120	CTC	.	.		0.577	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
FHAD1	114827	hgsc.bcm.edu	37	1	15616080	15616080	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:15616080C>T	ENST00000375998.4	+	3	486	c.486C>T	c.(484-486)tcC>tcT	p.S162S	FHAD1_ENST00000358897.4_Silent_p.S162S|FHAD1_ENST00000375999.3_Silent_p.S162S|FHAD1_ENST00000417793.1_Silent_p.S162S			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	162										skin(1)|stomach(1)	2						TGCCGGCCTCCCACAGGCGGC	0.632																																					p.S162S		Atlas-SNP	.											.	FHAD1	78	.	0			c.C486T						.						63.0	82.0	77.0					1																	15616080		692	1591	2283	SO:0001819	synonymous_variant	114827	exon4			GGCCTCCCACAGG	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.486C>T	chr1.hg19:g.15616080C>T		64.0	0.0		79.0	4.0	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Silent	SNP	ENST00000375998.4	hg19		.	.	.	.	.	.	.	.	.	.	C	0.339	-0.951299	0.02285	.	.	ENSG00000142621	ENST00000433640	.	.	.	3.77	-4.98	0.03019	.	.	.	.	.	T	0.15955	0.0384	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	T	0.24799	-1.0150	4	.	.	.	0.0644	0.4495	0.00499	0.2724:0.2148:0.1343:0.3785	.	.	.	.	S	137	.	.	P	+	1	0	FHAD1	15488667	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.409000	0.07160	-1.130000	0.02914	-0.339000	0.08088	CCA	.	.		0.632	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
SPEN	23013	hgsc.bcm.edu	37	1	16254866	16254866	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:16254866T>C	ENST00000375759.3	+	11	2335	c.2131T>C	c.(2131-2133)Tct>Cct	p.S711P		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	711	Arg-rich.				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)		AAGATTTGAGTCTGACCGGGA	0.483																																					p.S711P		Atlas-SNP	.											.	SPEN	374	.	0			c.T2131C						.						107.0	107.0	107.0					1																	16254866		2203	4300	6503	SO:0001583	missense	23013	exon11			TTTGAGTCTGACC		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.2131T>C	chr1.hg19:g.16254866T>C	ENSP00000364912:p.Ser711Pro	130.0	0.0		113.0	5.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	T	7.257	0.604477	0.14002	.	.	ENSG00000065526	ENST00000375759	T	0.09630	2.96	4.84	2.55	0.30701	.	.	.	.	.	T	0.06962	0.0177	N	0.24115	0.695	0.20074	N	0.999937	B	0.16166	0.016	B	0.10450	0.005	T	0.35968	-0.9767	9	0.62326	D	0.03	-7.7306	3.4928	0.07644	0.2694:0.1582:0.0:0.5724	.	711	Q96T58	MINT_HUMAN	P	711	ENSP00000364912:S711P	ENSP00000364912:S711P	S	+	1	0	SPEN	16127453	0.009000	0.17119	0.768000	0.31515	0.871000	0.50021	0.067000	0.14510	0.367000	0.24454	0.460000	0.39030	TCT	.	.		0.483	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
SPEN	23013	hgsc.bcm.edu	37	1	16255354	16255354	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:16255354A>G	ENST00000375759.3	+	11	2823	c.2619A>G	c.(2617-2619)gaA>gaG	p.E873E		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	873					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)		ACCGCCTGGAACTCATGCCTT	0.453																																					p.E873E		Atlas-SNP	.											.	SPEN	374	.	0			c.A2619G						.						94.0	98.0	97.0					1																	16255354		2203	4300	6503	SO:0001819	synonymous_variant	23013	exon11			CCTGGAACTCATG		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.2619A>G	chr1.hg19:g.16255354A>G		104.0	0.0		91.0	4.0	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	hg19	CCDS164.1																																																																																			.	.		0.453	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
PADI2	11240	hgsc.bcm.edu	37	1	17402249	17402249	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:17402249C>T	ENST00000375486.4	-	12	1443	c.1380G>A	c.(1378-1380)gtG>gtA	p.V460V	PADI2_ENST00000466151.1_5'UTR|PADI2_ENST00000444885.2_Silent_p.V344V	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	460					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	AGTAGAGCTCCACGGGCGCCT	0.602											OREG0013145	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V460V		Atlas-SNP	.											.	PADI2	72	.	0			c.G1380A						.						97.0	95.0	95.0					1																	17402249		2203	4300	6503	SO:0001819	synonymous_variant	11240	exon12			GAGCTCCACGGGC	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.1380G>A	chr1.hg19:g.17402249C>T		132.0	0.0	717	101.0	5.0	NM_007365	Q96DA7|Q9UPN2	Silent	SNP	ENST00000375486.4	hg19	CCDS177.1																																																																																			.	.		0.602	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
KLHDC7A	127707	hgsc.bcm.edu	37	1	18809370	18809370	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:18809370G>A	ENST00000400664.1	+	1	1947	c.1895G>A	c.(1894-1896)cGt>cAt	p.R632H		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	632						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GCCACGGTGCGTGCCAAGGAA	0.706																																					p.R632H		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.G1895A						.						21.0	23.0	22.0					1																	18809370		2202	4297	6499	SO:0001583	missense	127707	exon1			CGGTGCGTGCCAA	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.1895G>A	chr1.hg19:g.18809370G>A	ENSP00000383505:p.Arg632His	47.0	0.0		26.0	13.0	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	hg19	CCDS185.2	.	.	.	.	.	.	.	.	.	.	G	11.64	1.699241	0.30142	.	.	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.65178	-0.14	4.85	4.85	0.62838	Kelch-type beta propeller (1);	0.182827	0.47852	D	0.000206	T	0.38134	0.1029	N	0.14661	0.345	0.21220	N	0.999751	P;P	0.35348	0.496;0.496	B;B	0.14578	0.008;0.011	T	0.41448	-0.9508	10	0.59425	D	0.04	.	10.2342	0.43273	0.0923:0.0:0.9077:0.0	.	569;632	A7E2V3;Q5VTJ3	.;KLD7A_HUMAN	H	632;569	ENSP00000383505:R632H	ENSP00000383505:R632H	R	+	2	0	KLHDC7A	18681957	1.000000	0.71417	0.105000	0.21289	0.145000	0.21501	7.932000	0.87634	2.233000	0.73108	0.561000	0.74099	CGT	.	.		0.706	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
ALDH4A1	8659	hgsc.bcm.edu	37	1	19212052	19212052	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:19212052T>C	ENST00000375341.3	-	5	625	c.368A>G	c.(367-369)gAc>gGc	p.D123G	ALDH4A1_ENST00000454547.1_5'UTR|ALDH4A1_ENST00000538839.1_Missense_Mutation_p.D123G|RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000538309.1_Missense_Mutation_p.D63G|ALDH4A1_ENST00000290597.5_Missense_Mutation_p.D123G|MIR4695_ENST00000577305.1_RNA	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	123					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)			cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGGCCCGGTCTGCAATAGG	0.622																																					p.D123G		Atlas-SNP	.											.	ALDH4A1	72	.	0			c.A368G						.						42.0	38.0	39.0					1																	19212052		2203	4300	6503	SO:0001583	missense	8659	exon5			GCCCGGTCTGCAA	U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	1.5.1.12	"""Aldehyde dehydrogenases"""	406	protein-coding gene	gene with protein product		606811		ALDH4		8621661	Standard	NM_003748		Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.368A>G	chr1.hg19:g.19212052T>C	ENSP00000364490:p.Asp123Gly	64.0	0.0		50.0	4.0	NM_003748	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Missense_Mutation	SNP	ENST00000375341.3	hg19	CCDS188.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.599861	0.87055	.	.	ENSG00000159423	ENST00000290597;ENST00000375341;ENST00000538839;ENST00000538309;ENST00000375335;ENST00000454547;ENST00000375334;ENST00000432718	T;T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04;-1.04	5.41	5.41	0.78517	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.049262	0.85682	D	0.000000	D	0.84147	0.5408	M	0.73372	2.23	0.80722	D	1	P	0.51933	0.949	P	0.55508	0.777	D	0.86015	0.1503	10	0.66056	D	0.02	-44.778	14.2726	0.66159	0.0:0.0:0.0:1.0	.	123	P30038	AL4A1_HUMAN	G	123;123;123;63;107;21;63;107	ENSP00000290597:D123G;ENSP00000364490:D123G;ENSP00000446071:D123G;ENSP00000442988:D63G;ENSP00000393209:D107G	ENSP00000290597:D123G	D	-	2	0	ALDH4A1	19084639	1.000000	0.71417	0.998000	0.56505	0.900000	0.52787	5.678000	0.68153	2.063000	0.61619	0.459000	0.35465	GAC	.	.		0.622	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1		
HSPG2	3339	hgsc.bcm.edu	37	1	22181466	22181466	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:22181466T>C	ENST00000374695.3	-	48	6087	c.6008A>G	c.(6007-6009)gAg>gGg	p.E2003G	HSPG2_ENST00000430507.1_5'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2003	Ig-like C2-type 5.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GTCTGTGCGCTCTGACCGGGC	0.662																																					p.E2003G		Atlas-SNP	.											.	HSPG2	311	.	0			c.A6008G						.						70.0	68.0	69.0					1																	22181466		2203	4300	6503	SO:0001583	missense	3339	exon48			GTGCGCTCTGACC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6008A>G	chr1.hg19:g.22181466T>C	ENSP00000363827:p.Glu2003Gly	161.0	0.0		139.0	6.0	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.049436	0.36181	.	.	ENSG00000142798	ENST00000374695	T	0.68331	-0.32	5.45	5.45	0.79879	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.37530	N	0.002046	T	0.51787	0.1695	N	0.17082	0.46	0.44247	D	0.997098	B	0.28128	0.201	B	0.28385	0.089	T	0.53613	-0.8414	10	0.49607	T	0.09	.	13.4719	0.61287	0.0:0.0:0.0:1.0	.	2003	P98160	PGBM_HUMAN	G	2003	ENSP00000363827:E2003G	ENSP00000363827:E2003G	E	-	2	0	HSPG2	22054053	1.000000	0.71417	0.993000	0.49108	0.042000	0.13812	6.862000	0.75484	2.080000	0.62538	0.402000	0.26972	GAG	.	.		0.662	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
EPHA8	2046	hgsc.bcm.edu	37	1	22927919	22927919	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:22927919T>C	ENST00000166244.3	+	16	2928	c.2856T>C	c.(2854-2856)gcT>gcC	p.A952A		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	952	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.A952A(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		ACCACTTCGCTGCGGGCGGAT	0.701																																					p.A952A		Atlas-SNP	.											EPHA8,NS,carcinoma,0,1	EPHA8	221	.	1	Substitution - coding silent(1)	endometrium(1)	c.T2856C						.						40.0	46.0	44.0					1																	22927919		2203	4296	6499	SO:0001819	synonymous_variant	2046	exon16			CTTCGCTGCGGGC	BC038796	CCDS225.1, CCDS30626.1	1p36.12	2013-02-11	2004-10-28		ENSG00000070886	ENSG00000070886	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3391	protein-coding gene	gene with protein product		176945	"""EphA8"""	EEK		1648701	Standard	NM_001006943		Approved	Hek3	uc001bfx.1	P29322	OTTHUMG00000002892	ENST00000166244.3:c.2856T>C	chr1.hg19:g.22927919T>C		42.0	0.0		36.0	4.0	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	hg19	CCDS225.1																																																																																			.	.		0.701	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526	
RPL11	6135	hgsc.bcm.edu	37	1	24022368	24022368	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:24022368A>G	ENST00000374550.3	+	5	522	c.477A>G	c.(475-477)aaA>aaG	p.K159K	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	159					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)		GAATCAGCAAAGAGGAGGCCA	0.517																																					p.K159K		Atlas-SNP	.											.	RPL11	21	.	0			c.A477G						.						69.0	57.0	61.0					1																	24022368		2201	4299	6500	SO:0001819	synonymous_variant	6135	exon5			CAGCAAAGAGGAG	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.477A>G	chr1.hg19:g.24022368A>G		119.0	0.0		74.0	4.0	NM_000975	P25121|P39026|Q8TDH2|Q9Y674	Silent	SNP	ENST00000374550.3	hg19	CCDS238.1																																																																																			.	.		0.517	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975	
MYOM3	127294	hgsc.bcm.edu	37	1	24406666	24406666	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:24406666C>A	ENST00000374434.3	-	20	2588	c.2426G>T	c.(2425-2427)cGg>cTg	p.R809L	MYOM3_ENST00000329601.7_Missense_Mutation_p.R809L|MYOM3_ENST00000475306.1_5'Flank|RP11-293P20.2_ENST00000439239.2_RNA|RP11-293P20.4_ENST00000429191.1_RNA|MYOM3_ENST00000330966.7_Missense_Mutation_p.R810L	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	809	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		CTCGGATGCCCGTACATCGTA	0.612																																					p.R809L		Atlas-SNP	.											MYOM3,colon,carcinoma,0,1	MYOM3	131	.	0			c.G2426T						.						38.0	44.0	42.0					1																	24406666		2017	4170	6187	SO:0001583	missense	127294	exon20			GATGCCCGTACAT	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.2426G>T	chr1.hg19:g.24406666C>A	ENSP00000363557:p.Arg809Leu	65.0	0.0		49.0	3.0	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	hg19	CCDS41281.1	.	.	.	.	.	.	.	.	.	.	C	7.750	0.703214	0.15172	.	.	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.58652	0.32;0.32;0.32	5.38	2.17	0.27698	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.496761	0.22113	N	0.064454	T	0.53400	0.1794	M	0.65677	2.01	0.09310	N	1	B;P	0.36354	0.148;0.549	B;B	0.37304	0.246;0.217	T	0.43523	-0.9386	10	0.41790	T	0.15	.	9.8516	0.41059	0.0:0.691:0.0:0.309	.	809;809	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	L	809;810;809	ENSP00000363557:R809L;ENSP00000332670:R810L;ENSP00000328415:R809L	ENSP00000328415:R809L	R	-	2	0	MYOM3	24279253	0.002000	0.14202	0.034000	0.17996	0.003000	0.03518	0.052000	0.14163	0.130000	0.18549	0.563000	0.77884	CGG	.	.		0.612	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
IL22RA1	58985	hgsc.bcm.edu	37	1	24460747	24460747	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:24460747T>C	ENST00000270800.1	-	4	523	c.485A>G	c.(484-486)gAc>gGc	p.D162G		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	162	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)			breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		GTAGAACAGGTCATGGAAGAT	0.532																																					p.D162G		Atlas-SNP	.											.	IL22RA1	62	.	0			c.A485G						.						113.0	93.0	100.0					1																	24460747		2203	4300	6503	SO:0001583	missense	58985	exon4			AACAGGTCATGGA	AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"""Interleukins and interleukin receptors"""	13700	protein-coding gene	gene with protein product		605457	"""interleukin 22 receptor"""	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.485A>G	chr1.hg19:g.24460747T>C	ENSP00000270800:p.Asp162Gly	147.0	0.0		85.0	4.0	NM_021258	A8K839|B2R9Y9|Q9HB22	Missense_Mutation	SNP	ENST00000270800.1	hg19	CCDS247.1	.	.	.	.	.	.	.	.	.	.	T	16.90	3.250320	0.59212	.	.	ENSG00000142677	ENST00000270800	T	0.46063	0.88	4.98	4.98	0.66077	Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	0.758712	0.12574	N	0.457035	T	0.49983	0.1589	L	0.32530	0.975	0.22581	N	0.998965	D;P	0.60575	0.988;0.875	D;P	0.63381	0.914;0.79	T	0.36744	-0.9735	10	0.45353	T	0.12	-2.7042	11.0682	0.47987	0.0:0.0:0.0:1.0	.	54;162	B4E2V9;Q8N6P7	.;I22R1_HUMAN	G	162	ENSP00000270800:D162G	ENSP00000270800:D162G	D	-	2	0	IL22RA1	24333334	0.960000	0.32886	0.066000	0.19879	0.854000	0.48673	3.640000	0.54350	1.875000	0.54330	0.459000	0.35465	GAC	.	.		0.532	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1		
IL22RA1	58985	hgsc.bcm.edu	37	1	24463631	24463631	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:24463631A>G	ENST00000270800.1	-	3	383	c.345T>C	c.(343-345)tcT>tcC	p.S115S		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	115	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)			breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		TGTGCTGCAGAGAGCTGAACC	0.627																																					p.S115S		Atlas-SNP	.											.	IL22RA1	62	.	0			c.T345C						.						48.0	45.0	46.0					1																	24463631		2203	4300	6503	SO:0001819	synonymous_variant	58985	exon3			CTGCAGAGAGCTG	AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"""Interleukins and interleukin receptors"""	13700	protein-coding gene	gene with protein product		605457	"""interleukin 22 receptor"""	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.345T>C	chr1.hg19:g.24463631A>G		61.0	0.0		49.0	4.0	NM_021258	A8K839|B2R9Y9|Q9HB22	Silent	SNP	ENST00000270800.1	hg19	CCDS247.1																																																																																			.	.		0.627	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1		
AUNIP	79000	hgsc.bcm.edu	37	1	26162302	26162302	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:26162302A>G	ENST00000374298.3	-	3	310	c.256T>C	c.(256-258)Tct>Cct	p.S86P	AUNIP_ENST00000481602.1_Intron|AUNIP_ENST00000538789.1_Missense_Mutation_p.S86P	NM_024037.1	NP_076942.1	Q9H7T9	AUNIP_HUMAN	aurora kinase A and ninein interacting protein	86					spindle organization (GO:0007051)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)											TCTGTATGAGATGAAACACTC	0.418																																					p.S86P		Atlas-SNP	.											.	AUNIP	1	.	0			c.T256C						.						147.0	139.0	142.0					1																	26162302		2203	4300	6503	SO:0001583	missense	79000	exon3			TATGAGATGAAAC		CCDS266.1, CCDS72731.1	1p36.11	2012-08-07	2012-08-07	2012-08-07	ENSG00000127423	ENSG00000127423			28363	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 135"""	C1orf135		20596670	Standard	NM_001287490		Approved	MGC2603, AIBp	uc001bkw.1	Q9H7T9	OTTHUMG00000007372	ENST00000374298.3:c.256T>C	chr1.hg19:g.26162302A>G	ENSP00000363416:p.Ser86Pro	139.0	0.0		96.0	4.0	NM_024037	C9EI59|Q53F70	Missense_Mutation	SNP	ENST00000374298.3	hg19	CCDS266.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.480097	0.44044	.	.	ENSG00000127423	ENST00000538789;ENST00000374298	T;T	0.60797	0.16;0.16	5.14	2.73	0.32206	.	0.276343	0.26331	N	0.024992	T	0.38799	0.1054	N	0.24115	0.695	0.09310	N	1	B	0.31227	0.314	B	0.34418	0.182	T	0.32161	-0.9917	10	0.72032	D	0.01	-7.3133	3.2163	0.06700	0.6823:0.0:0.1113:0.2065	.	86	Q9H7T9	CA135_HUMAN	P	86	ENSP00000443647:S86P;ENSP00000363416:S86P	ENSP00000363416:S86P	S	-	1	0	C1orf135	26034889	0.064000	0.20934	0.070000	0.20053	0.942000	0.58702	0.159000	0.16442	0.937000	0.37394	0.477000	0.44152	TCT	.	.		0.418	AUNIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019309.2	NM_024037	
NUDC	10726	hgsc.bcm.edu	37	1	27269479	27269479	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:27269479C>A	ENST00000321265.5	+	6	787	c.664C>A	c.(664-666)Ctc>Atc	p.L222I		NM_006600.3	NP_006591.1	Q9Y266	NUDC_HUMAN	nudC nuclear distribution protein	222	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.				cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)				cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;6.1e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.87e-29)|Colorectal(126;5.74e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000281)|STAD - Stomach adenocarcinoma(196;0.000604)|KIRC - Kidney renal clear cell carcinoma(1967;0.000739)|READ - Rectum adenocarcinoma(331;0.0421)		TGATGGGGAGCTCTACAATGA	0.587																																					p.L222I		Atlas-SNP	.											.	NUDC	15	.	0			c.C664A						.						99.0	100.0	99.0					1																	27269479		2203	4300	6503	SO:0001583	missense	10726	exon6			GGGGAGCTCTACA		CCDS292.1	1p35-p34	2013-08-06	2013-08-06		ENSG00000090273	ENSG00000090273			8045	protein-coding gene	gene with protein product		610325	"""nuclear distribution gene C homolog (A. nidulans)"", ""nuclear distribution C homolog (A. nidulans)"""				Standard	NM_006600		Approved	NudC	uc001bng.2	Q9Y266	OTTHUMG00000004226	ENST00000321265.5:c.664C>A	chr1.hg19:g.27269479C>A	ENSP00000319664:p.Leu222Ile	110.0	0.0		72.0	4.0	NM_006600	Q5QP31|Q5QP35|Q9H0N2|Q9Y2B6	Missense_Mutation	SNP	ENST00000321265.5	hg19	CCDS292.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.435768	0.83885	.	.	ENSG00000090273	ENST00000321265	T	0.53857	0.6	5.24	5.24	0.73138	CS-like domain (1);CS domain (1);HSP20-like chaperone (1);	0.000000	0.85682	D	0.000000	T	0.81307	0.4795	H	0.97440	4.005	0.80722	D	1	D;D	0.69078	0.997;0.994	D;D	0.79784	0.993;0.975	D	0.87208	0.2245	9	.	.	.	0.1555	13.2132	0.59836	0.0:0.9235:0.0:0.0765	.	173;222	Q9H2R7;Q9Y266	.;NUDC_HUMAN	I	222	ENSP00000319664:L222I	.	L	+	1	0	NUDC	27142066	0.969000	0.33509	0.994000	0.49952	0.743000	0.42351	2.330000	0.43885	2.473000	0.83533	0.449000	0.29647	CTC	.	.		0.587	NUDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012172.2		
FCN3	8547	hgsc.bcm.edu	37	1	27697419	27697419	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:27697419A>G	ENST00000270879.4	-	6	443	c.438T>C	c.(436-438)tcT>tcC	p.S146S	FCN3_ENST00000354982.2_Silent_p.S135S	NM_003665.2	NP_003656.2	O75636	FCN3_HUMAN	ficolin (collagen/fibrinogen domain containing) 3	146	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	7		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.42e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		AGGAGGACCAAGAGCGGAAGA	0.562																																					p.S146S		Atlas-SNP	.											.	FCN3	30	.	0			c.T438C						.						57.0	63.0	61.0					1																	27697419		2203	4300	6503	SO:0001819	synonymous_variant	8547	exon6			GGACCAAGAGCGG	D88587	CCDS300.1, CCDS301.1	1p36.11	2014-09-17	2013-09-12		ENSG00000142748	ENSG00000142748		"""Fibrinogen C domain containing"""	3625	protein-coding gene	gene with protein product	"""Hakata antigen"""	604973	"""ficolin (collagen/fibrinogen domain-containing) 3 (Hakata antigen)"""			9694814, 10330454	Standard	NM_003665		Approved	FCNH, HAKA1	uc001boa.3	O75636	OTTHUMG00000005722	ENST00000270879.4:c.438T>C	chr1.hg19:g.27697419A>G		118.0	0.0		95.0	5.0	NM_003665	Q6IBJ5|Q8WW86	Silent	SNP	ENST00000270879.4	hg19	CCDS300.1																																																																																			.	.		0.562	FCN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000015667.1		
OPRD1	4985	hgsc.bcm.edu	37	1	29185650	29185650	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:29185650A>G	ENST00000234961.2	+	2	654	c.412A>G	c.(412-414)Acg>Gcg	p.T138A		NM_000911.3	NP_000902.3	P41143	OPRD_HUMAN	opioid receptor, delta 1	138					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adult locomotory behavior (GO:0008344)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|negative regulation of gene expression (GO:0010629)|negative regulation of protein oligomerization (GO:0032460)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein import into nucleus, translocation (GO:0000060)|regulation of calcium ion transport (GO:0051924)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of sensory perception of pain (GO:0051930)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	enkephalin receptor activity (GO:0038046)|opioid receptor activity (GO:0004985)			breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-07)|COAD - Colon adenocarcinoma(152;7.51e-06)|STAD - Stomach adenocarcinoma(196;0.00306)|BRCA - Breast invasive adenocarcinoma(304;0.0241)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)	Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CAGCATCTTCACGCTCACCAT	0.567																																					p.T138A		Atlas-SNP	.											.	OPRD1	36	.	0			c.A412G						.						167.0	135.0	146.0					1																	29185650		2203	4300	6503	SO:0001583	missense	4985	exon2			ATCTTCACGCTCA	U10504	CCDS329.1	1p36.1-p34.3	2012-08-08			ENSG00000116329	ENSG00000116329		"""GPCR / Class A : Opioid receptors"""	8153	protein-coding gene	gene with protein product		165195				8415697	Standard	NM_000911		Approved		uc001brf.1	P41143	OTTHUMG00000003646	ENST00000234961.2:c.412A>G	chr1.hg19:g.29185650A>G	ENSP00000234961:p.Thr138Ala	115.0	0.0		89.0	4.0	NM_000911	B5B0B8	Missense_Mutation	SNP	ENST00000234961.2	hg19	CCDS329.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.207697	0.79240	.	.	ENSG00000116329	ENST00000234961;ENST00000536280	T	0.39229	1.09	4.57	4.57	0.56435	GPCR, rhodopsin-like superfamily (1);	0.059839	0.64402	D	0.000003	T	0.69106	0.3074	H	0.94306	3.52	0.58432	D	0.999999	P	0.51653	0.947	P	0.62740	0.906	T	0.74234	-0.3731	10	0.33141	T	0.24	.	11.9375	0.52882	1.0:0.0:0.0:0.0	.	138	P41143	OPRD_HUMAN	A	138	ENSP00000234961:T138A	ENSP00000234961:T138A	T	+	1	0	OPRD1	29058237	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	9.139000	0.94554	1.924000	0.55735	0.379000	0.24179	ACG	.	.		0.567	OPRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010330.1	NM_000911	
HDAC1	3065	hgsc.bcm.edu	37	1	32797350	32797350	+	Missense_Mutation	SNP	G	G	A	rs375198135		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:32797350G>A	ENST00000373548.3	+	11	1246	c.1162G>A	c.(1162-1164)Gcc>Acc	p.A388T	HDAC1_ENST00000490081.1_3'UTR|HDAC1_ENST00000373541.2_Missense_Mutation_p.A195T	NM_004964.2	NP_004955.2	Q13547	HDAC1_HUMAN	histone deacetylase 1	388					ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|mitotic cell cycle (GO:0000278)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle (GO:0045786)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deacetylation (GO:0006476)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|Sin3 complex (GO:0016580)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	18		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)	TCCTGAGGACGCCATCCCTGA	0.572																																					p.A388T		Atlas-SNP	.											HDAC1,NS,carcinoma,0,1	HDAC1	43	.	0			c.G1162A						.	G	THR/ALA	0,4406		0,0,2203	99.0	93.0	95.0		1162	4.5	1.0	1		95	1,8599	1.2+/-3.3	0,1,4299	no	missense	HDAC1	NM_004964.2	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	388/483	32797350	1,13005	2203	4300	6503	SO:0001583	missense	3065	exon11			GAGGACGCCATCC	D50405	CCDS360.1	1p34	2008-02-05			ENSG00000116478	ENSG00000116478			4852	protein-coding gene	gene with protein product		601241		RPD3L1		8602529	Standard	NM_004964		Approved	HD1, GON-10	uc001bvb.1	Q13547	OTTHUMG00000007529	ENST00000373548.3:c.1162G>A	chr1.hg19:g.32797350G>A	ENSP00000362649:p.Ala388Thr	87.0	0.0		70.0	4.0	NM_004964	Q92534	Missense_Mutation	SNP	ENST00000373548.3	hg19	CCDS360.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.851677	0.51270	0.0	1.16E-4	ENSG00000116478	ENST00000373548;ENST00000373541	T;T	0.74421	-0.84;-0.52	4.52	4.52	0.55395	.	0.101865	0.64402	D	0.000002	T	0.68632	0.3022	L	0.53249	1.67	0.52501	D	0.999952	B	0.13594	0.008	B	0.15870	0.014	T	0.65187	-0.6229	10	0.34782	T	0.22	-5.5647	13.1543	0.59508	0.0:0.0:0.8398:0.1602	.	388	Q13547	HDAC1_HUMAN	T	388;195	ENSP00000362649:A388T;ENSP00000362642:A195T	ENSP00000362642:A195T	A	+	1	0	HDAC1	32569937	1.000000	0.71417	0.984000	0.44739	0.966000	0.64601	5.501000	0.66950	2.447000	0.82792	0.563000	0.77884	GCC	.	.		0.572	HDAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019815.3	NM_004964	
ZMYM4	9202	hgsc.bcm.edu	37	1	35884071	35884071	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:35884071G>T	ENST00000314607.6	+	29	4417	c.4337G>T	c.(4336-4338)cGa>cTa	p.R1446L	ZMYM4_ENST00000373297.2_Missense_Mutation_p.R1357L	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	1446					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R1446Q(2)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AAGAGGAAACGAAATGAAGAT	0.393																																					p.R1446L		Atlas-SNP	.											ZMYM4,rectum,carcinoma,0,2	ZMYM4	143	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4337T						.						121.0	113.0	116.0					1																	35884071		2203	4300	6503	SO:0001583	missense	9202	exon29			GGAAACGAAATGA	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"""Zinc fingers, MYM type"""	13055	protein-coding gene	gene with protein product		613568	"""zinc finger protein 262"""	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.4337G>T	chr1.hg19:g.35884071G>T	ENSP00000322915:p.Arg1446Leu	123.0	0.0		97.0	4.0	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	hg19	CCDS389.1	.	.	.	.	.	.	.	.	.	.	G	33	5.283802	0.95489	.	.	ENSG00000146463	ENST00000314607;ENST00000373297	T;T	0.25250	1.81;1.84	5.84	5.84	0.93424	.	0.315320	0.33959	N	0.004389	T	0.41419	0.1158	L	0.55481	1.735	0.54753	D	0.999982	B	0.30114	0.269	B	0.43658	0.426	T	0.25187	-1.0139	10	0.72032	D	0.01	-7.1968	20.1381	0.98040	0.0:0.0:1.0:0.0	.	1446	Q5VZL5	ZMYM4_HUMAN	L	1446;1357	ENSP00000322915:R1446L;ENSP00000362394:R1357L	ENSP00000322915:R1446L	R	+	2	0	ZMYM4	35656658	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.650000	0.67944	2.763000	0.94921	0.650000	0.86243	CGA	.	.		0.393	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095	
KIAA0319L	79932	hgsc.bcm.edu	37	1	35972224	35972224	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:35972224C>T	ENST00000325722.3	-	3	889	c.655G>A	c.(655-657)Ggc>Agc	p.G219S		NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	219						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TCTGCAGAGCCACTGGTAGTC	0.443																																					p.G219S		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.G655A						.						157.0	145.0	149.0					1																	35972224		2203	4300	6503	SO:0001583	missense	79932	exon3			CAGAGCCACTGGT	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.655G>A	chr1.hg19:g.35972224C>T	ENSP00000318406:p.Gly219Ser	184.0	0.0		123.0	5.0	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Missense_Mutation	SNP	ENST00000325722.3	hg19	CCDS390.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.631|7.631	0.678785|0.678785	0.14841|0.14841	.|.	.|.	ENSG00000142687|ENSG00000142687	ENST00000325722;ENST00000426982;ENST00000440579;ENST00000373258;ENST00000469892|ENST00000431916	T;T;T;T;T|.	0.41400|.	3.36;3.36;2.83;1.57;1.0|.	5.55|5.55	2.49|2.49	0.30216|0.30216	.|.	0.891435|.	0.09683|.	N|.	0.769400|.	T|.	0.18551|.	0.0445|.	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	N|N	1|1	B;B;B|.	0.19583|.	0.037;0.022;0.0|.	B;B;B|.	0.15052|.	0.012;0.008;0.001|.	T|.	0.17289|.	-1.0374|.	10|.	0.02654|.	T|.	1|.	-0.8278|-0.8278	5.0196|5.0196	0.14354|0.14354	0.0:0.6431:0.1729:0.184|0.0:0.6431:0.1729:0.184	.|.	219;219;219|.	B4DYG9;B1AN14;Q8IZA0|.	.;.;K319L_HUMAN|.	S|X	219|82	ENSP00000318406:G219S;ENSP00000395883:G219S;ENSP00000407576:G219S;ENSP00000362355:G219S;ENSP00000419396:G219S|.	ENSP00000318406:G219S|.	G|W	-|-	1|2	0|0	KIAA0319L|KIAA0319L	35744811|35744811	0.076000|0.076000	0.21285|0.21285	0.031000|0.031000	0.17742|0.17742	0.770000|0.770000	0.43624|0.43624	1.052000|1.052000	0.30429|0.30429	1.464000|1.464000	0.47987|0.47987	0.655000|0.655000	0.94253|0.94253	GGC|TGG	.	.		0.443	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874	
RHBDL2	54933	hgsc.bcm.edu	37	1	39381373	39381373	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:39381373A>G	ENST00000289248.2	-	3	1264	c.256T>C	c.(256-258)Ttt>Ctt	p.F86L	RHBDL2_ENST00000372985.3_Missense_Mutation_p.F166L|RHBDL2_ENST00000540558.1_Missense_Mutation_p.F86L|RP5-864K19.4_ENST00000433671.2_RNA|RHBDL2_ENST00000538156.1_Missense_Mutation_p.F153L|RHBDL2_ENST00000372990.1_Missense_Mutation_p.F86L			Q9NX52	RHBL2_HUMAN	rhomboid, veinlet-like 2 (Drosophila)	86						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	8	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			TAGTAAATAAACACTGCCAGC	0.502																																					p.F86L		Atlas-SNP	.											.	RHBDL2	28	.	0			c.T256C						.						105.0	94.0	98.0					1																	39381373		2203	4300	6503	SO:0001583	missense	54933	exon3			AAATAAACACTGC	AK000442	CCDS30680.1	1p35.1	2014-01-28	2001-11-28		ENSG00000158315	ENSG00000158315			16083	protein-coding gene	gene with protein product		608962	"""rhomboid (veinlet, Drosophila)-like 2"""				Standard	NM_017821		Approved	FLJ20435	uc001ccu.1	Q9NX52	OTTHUMG00000000487	ENST00000289248.2:c.256T>C	chr1.hg19:g.39381373A>G	ENSP00000289248:p.Phe86Leu	134.0	0.0		84.0	5.0	NM_017821	B2RNT3|B9EH75|Q6P175|Q8NER8|Q96E02	Missense_Mutation	SNP	ENST00000289248.2	hg19	CCDS30680.1	.	.	.	.	.	.	.	.	.	.	A	35	5.514409	0.96402	.	.	ENSG00000158315	ENST00000372990;ENST00000289248;ENST00000538156;ENST00000372985;ENST00000540558	T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.33933	0.0880	M	0.80332	2.49	0.80722	D	1	D;D;D	0.62365	0.988;0.991;0.991	P;P;P	0.57204	0.755;0.815;0.696	T	0.14615	-1.0466	10	0.54805	T	0.06	-21.9011	14.3335	0.66574	1.0:0.0:0.0:0.0	.	166;153;86	B7Z1Y9;B3KUN4;Q9NX52	.;.;RHBL2_HUMAN	L	86;86;153;166;86	ENSP00000362081:F86L;ENSP00000289248:F86L;ENSP00000439227:F153L;ENSP00000362076:F166L;ENSP00000441097:F86L	ENSP00000289248:F86L	F	-	1	0	RHBDL2	39153960	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	8.543000	0.90651	2.026000	0.59711	0.450000	0.29827	TTT	.	.		0.502	RHBDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001216.1	NM_017821	
BMP8A	353500	hgsc.bcm.edu	37	1	39991422	39991422	+	Silent	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:39991422C>A	ENST00000331593.5	+	7	1507	c.1161C>A	c.(1159-1161)atC>atA	p.I387I	RP11-69E11.4_ENST00000431553.1_RNA|RP11-69E11.4_ENST00000417869.1_RNA|RP11-69E11.4_ENST00000441741.1_RNA|RP11-69E11.4_ENST00000331856.2_RNA|RP11-69E11.4_ENST00000450157.1_RNA|RP11-69E11.4_ENST00000458207.1_RNA|RP11-69E11.4_ENST00000440190.1_RNA	NM_181809.3	NP_861525.2	Q7Z5Y6	BMP8A_HUMAN	bone morphogenetic protein 8a	387					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|diet induced thermogenesis (GO:0002024)|growth (GO:0040007)|negative regulation of insulin secretion (GO:0046676)|ossification (GO:0001503)|regulation of energy homeostasis (GO:2000505)	extracellular space (GO:0005615)				kidney(1)|large_intestine(2)|lung(1)|skin(1)	5	Lung NSC(20;2.08e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;9.69e-19)|Epithelial(16;9.34e-17)|all cancers(16;1.73e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACAACGTCATCCTGCGCAAGC	0.617																																					p.I387I		Atlas-SNP	.											.	BMP8A	24	.	0			c.C1161A						.						172.0	136.0	148.0					1																	39991422		2203	4300	6503	SO:0001819	synonymous_variant	353500	exon7			CGTCATCCTGCGC	AY303954	CCDS437.1	1p35-p32	2014-01-30			ENSG00000183682	ENSG00000183682		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	21650	protein-coding gene	gene with protein product							Standard	NM_181809		Approved		uc001cdi.3	Q7Z5Y6	OTTHUMG00000008394	ENST00000331593.5:c.1161C>A	chr1.hg19:g.39991422C>A		99.0	0.0		85.0	5.0	NM_181809	Q5T3A5	Silent	SNP	ENST00000331593.5	hg19	CCDS437.1																																																																																			.	.		0.617	BMP8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023079.1	NM_181809	
ZFP69	339559	hgsc.bcm.edu	37	1	40961674	40961674	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:40961674T>C	ENST00000372706.1	+	6	2530	c.1524T>C	c.(1522-1524)tcT>tcC	p.S508S	ZFP69_ENST00000372705.3_Silent_p.S508S|RP11-656D10.3_ENST00000450713.1_RNA			Q49AA0	ZFP69_HUMAN	ZFP69 zinc finger protein	508					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										GCTATAACTCTTCACTTAGTC	0.378																																					p.S508S		Atlas-SNP	.											.	.	.	.	0			c.T1524C						.						62.0	64.0	63.0					1																	40961674		2203	4300	6503	SO:0001819	synonymous_variant	339559	exon6			TAACTCTTCACTT	AK122618	CCDS30686.1	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187815	ENSG00000187815		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	24708	protein-coding gene	gene with protein product	"""ZFP69 zinc finger protein A"""		"""zinc finger protein 642"""	ZNF642			Standard	XM_005270808		Approved	ZKSCAN23A, FLJ16030, ZFP69A, ZSCAN54A	uc001cfo.3	Q49AA0	OTTHUMG00000007303	ENST00000372706.1:c.1524T>C	chr1.hg19:g.40961674T>C		123.0	0.0		96.0	4.0	NM_198494	Q5SWM5|Q6ZWK8	Silent	SNP	ENST00000372706.1	hg19	CCDS30686.1																																																																																			.	.		0.378	ZFP69-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019082.1	NM_198494	
SCMH1	22955	hgsc.bcm.edu	37	1	41579042	41579042	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:41579042A>G	ENST00000326197.7	-	7	927	c.628T>C	c.(628-630)Tac>Cac	p.Y210H	SCMH1_ENST00000397171.2_Missense_Mutation_p.Y149H|SCMH1_ENST00000361191.5_Missense_Mutation_p.Y149H|SCMH1_ENST00000372595.1_Missense_Mutation_p.Y149H|SCMH1_ENST00000402904.2_Missense_Mutation_p.Y210H|SCMH1_ENST00000361705.3_Missense_Mutation_p.Y163H|SCMH1_ENST00000397174.2_Missense_Mutation_p.Y190H|SCMH1_ENST00000456518.2_Intron|SCMH1_ENST00000372597.1_Missense_Mutation_p.Y163H|SCMH1_ENST00000372596.1_Missense_Mutation_p.Y149H|SCMH1_ENST00000337495.5_Missense_Mutation_p.Y220H					sex comb on midleg homolog 1 (Drosophila)											breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				CGGCACCAGTAGTCAAAGGCC	0.572																																					p.Y220H		Atlas-SNP	.											.	SCMH1	120	.	0			c.T658C						.						111.0	107.0	109.0					1																	41579042		2203	4300	6503	SO:0001583	missense	22955	exon8			ACCAGTAGTCAAA	AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803		"""Sterile alpha motif (SAM) domain containing"""	19003	protein-coding gene	gene with protein product						10524249	Standard	NM_012236		Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.628T>C	chr1.hg19:g.41579042A>G	ENSP00000318094:p.Tyr210His	88.0	0.0		54.0	4.0	NM_001172219		Missense_Mutation	SNP	ENST00000326197.7	hg19	CCDS30688.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.913512	0.92178	.	.	ENSG00000010803	ENST00000361705;ENST00000402904;ENST00000397174;ENST00000397171;ENST00000361191;ENST00000372597;ENST00000372596;ENST00000337495;ENST00000372595;ENST00000326197	T;T;T;T;T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.62684	0.2448	M	0.88377	2.95	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;0.999;0.998	T	0.69953	-0.5005	10	0.72032	D	0.01	.	15.1834	0.72978	1.0:0.0:0.0:0.0	.	220;163;210	Q96GD3-2;Q96GD3-4;Q96GD3	.;.;SCMH1_HUMAN	H	163;210;190;149;149;163;149;220;149;210	ENSP00000354996:Y163H;ENSP00000386079:Y210H;ENSP00000380359:Y190H;ENSP00000380356:Y149H;ENSP00000354656:Y149H;ENSP00000361678:Y163H;ENSP00000361677:Y149H;ENSP00000337352:Y220H;ENSP00000361676:Y149H;ENSP00000318094:Y210H	ENSP00000318094:Y210H	Y	-	1	0	SCMH1	41351629	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.505000	0.81655	2.266000	0.75297	0.455000	0.32223	TAC	.	.		0.572	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015656.1		
PPIH	10465	hgsc.bcm.edu	37	1	43133074	43133074	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:43133074A>G	ENST00000304979.3	+	9	540	c.518A>G	c.(517-519)cAg>cGg	p.Q173R	PPIH_ENST00000372550.1_Missense_Mutation_p.Q130R|PPIH_ENST00000455203.2_Missense_Mutation_p.Q130R	NM_006347.3	NP_006338.1	O43447	PPIH_HUMAN	peptidylprolyl isomerase H (cyclophilin H)	173	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral genome replication (GO:0045070)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)|U4/U6 x U5 tri-snRNP complex (GO:0046540)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|ribonucleoprotein complex binding (GO:0043021)			endometrium(1)|large_intestine(1)|lung(2)	4	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)			L-Proline(DB00172)	GTGATCTCGCAGTGTGGGGAG	0.478																																					p.Q173R	NSCLC(73;23 1942 10718 46854)	Atlas-SNP	.											.	PPIH	15	.	0			c.A518G						.						175.0	156.0	163.0					1																	43133074		2203	4300	6503	SO:0001583	missense	10465	exon9			TCTCGCAGTGTGG	AF016371	CCDS469.1	1p34.1	2012-06-07	2006-01-12		ENSG00000171960	ENSG00000171960			14651	protein-coding gene	gene with protein product	"""USA-CyP SnuCyp-20"", ""cyclophilin H"", ""U-snRNP-associated cyclophilin SunCyp-20"", ""small nuclear ribonucleoprotein particle-specific cyclophilin H"", ""rotamase H"", ""peptidyl-prolyl cis-trans isomerase H"", ""PPIase h"""	606095	"""peptidyl prolyl isomerase H (cyclophilin H)"""			9404889, 9570313	Standard	NM_006347		Approved	USA-CYP, CYP-20, SnuCyp-20, CYPH, MGC5016	uc001chq.3	O43447	OTTHUMG00000007520	ENST00000304979.3:c.518A>G	chr1.hg19:g.43133074A>G	ENSP00000306614:p.Gln173Arg	86.0	0.0		82.0	4.0	NM_006347	A6NNE7	Missense_Mutation	SNP	ENST00000304979.3	hg19	CCDS469.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.500232	0.64298	.	.	ENSG00000171960	ENST00000304979;ENST00000372550;ENST00000455203	T;T;T	0.40225	1.04;1.36;1.36	5.6	5.6	0.85130	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.167023	0.53938	D	0.000053	T	0.22627	0.0546	N	0.02539	-0.55	0.80722	D	1	B;B	0.17852	0.011;0.024	B;B	0.23150	0.02;0.044	T	0.11397	-1.0589	10	0.87932	D	0	.	13.7456	0.62872	1.0:0.0:0.0:0.0	.	130;173	A6NNE7;O43447	.;PPIH_HUMAN	R	173;130;130	ENSP00000306614:Q173R;ENSP00000361630:Q130R;ENSP00000416361:Q130R	ENSP00000306614:Q173R	Q	+	2	0	PPIH	42905661	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.896000	0.87350	2.125000	0.65367	0.533000	0.62120	CAG	.	.		0.478	PPIH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019778.1	NM_006347	
LEPRE1	64175	hgsc.bcm.edu	37	1	43224582	43224582	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:43224582T>C	ENST00000296388.5	-	4	932	c.881A>G	c.(880-882)aAg>aGg	p.K294R	LEPRE1_ENST00000397054.3_Missense_Mutation_p.K294R|LEPRE1_ENST00000236040.4_Missense_Mutation_p.K294R			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	294					bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TTCAAAGGGCTTCTCTCGACT	0.443																																					p.K294R		Atlas-SNP	.											.	LEPRE1	130	.	0			c.A881G						.						110.0	99.0	103.0					1																	43224582		2203	4300	6503	SO:0001583	missense	64175	exon4			AAGGGCTTCTCTC	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 1"", ""growth suppressor 1"""	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.881A>G	chr1.hg19:g.43224582T>C	ENSP00000296388:p.Lys294Arg	102.0	0.0		70.0	4.0	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	hg19	CCDS472.2	.	.	.	.	.	.	.	.	.	.	T	19.54	3.847584	0.71603	.	.	ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027	T;T;T	0.37058	1.22;1.22;1.22	5.9	5.9	0.94986	.	0.141622	0.64402	D	0.000007	T	0.42268	0.1195	L	0.45137	1.4	0.38896	D	0.95721	D;P;P	0.57899	0.981;0.872;0.932	P;B;P	0.54629	0.757;0.34;0.49	T	0.24154	-1.0168	10	0.13470	T	0.59	-44.1592	14.2838	0.66232	0.0:0.0:0.0:1.0	.	294;159;294	Q32P28-3;B4DNM8;Q32P28	.;.;P3H1_HUMAN	R	294;294;294;159	ENSP00000380245:K294R;ENSP00000236040:K294R;ENSP00000296388:K294R	ENSP00000236040:K294R	K	-	2	0	LEPRE1	42997169	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.952000	0.40343	2.248000	0.74166	0.460000	0.39030	AAG	.	.		0.443	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356	
CCDC24	149473	hgsc.bcm.edu	37	1	44461509	44461509	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:44461509T>C	ENST00000372318.3	+	8	853	c.682T>C	c.(682-684)Tgt>Cgt	p.C228R	SLC6A9_ENST00000372306.3_Intron|CCDC24_ENST00000479055.1_3'UTR|SLC6A9_ENST00000372307.3_Intron	NM_152499.1	NP_689712.1	Q8N4L8	CCD24_HUMAN	coiled-coil domain containing 24	228										endometrium(3)|large_intestine(2)|lung(3)|stomach(1)	9	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				GGGGCCTTCTTGTGTCTCTCC	0.537																																					p.C228R		Atlas-SNP	.											.	CCDC24	22	.	0			c.T682C						.						113.0	114.0	114.0					1																	44461509		2203	4300	6503	SO:0001583	missense	149473	exon8			CCTTCTTGTGTCT		CCDS507.1	1p34.1	2008-02-05			ENSG00000159214	ENSG00000159214			28688	protein-coding gene	gene with protein product						12477932	Standard	NM_152499		Approved	MGC45441	uc001clj.3	Q8N4L8	OTTHUMG00000008299	ENST00000372318.3:c.682T>C	chr1.hg19:g.44461509T>C	ENSP00000361392:p.Cys228Arg	116.0	0.0		86.0	4.0	NM_152499	Q6RWT2	Missense_Mutation	SNP	ENST00000372318.3	hg19	CCDS507.1	.	.	.	.	.	.	.	.	.	.	T	9.357	1.067077	0.20067	.	.	ENSG00000159214	ENST00000372318	.	.	.	5.03	1.11	0.20524	.	1.266720	0.05585	N	0.573587	T	0.34890	0.0913	L	0.54323	1.7	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.10450	0.001;0.005	T	0.22312	-1.0220	9	0.23302	T	0.38	-11.2091	3.2879	0.06939	0.1736:0.2214:0.0:0.605	.	192;228	Q8N4L8-2;Q8N4L8	.;CCD24_HUMAN	R	228	.	ENSP00000361392:C228R	C	+	1	0	CCDC24	44234096	0.000000	0.05858	0.001000	0.08648	0.790000	0.44656	-1.005000	0.03674	0.337000	0.23665	0.421000	0.28195	TGT	.	.		0.537	CCDC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022865.1	NM_152499	
HECTD3	79654	hgsc.bcm.edu	37	1	45469234	45469234	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:45469234T>C	ENST00000372172.4	-	21	2587	c.2516A>G	c.(2515-2517)gAg>gGg	p.E839G	HECTD3_ENST00000486132.1_5'UTR|HECTD3_ENST00000372168.3_Missense_Mutation_p.E449G	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	839	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					GAGCTTCTCCTCGCATACCTT	0.612																																					p.E839G		Atlas-SNP	.											.	HECTD3	158	.	0			c.A2516G						.						84.0	88.0	87.0					1																	45469234		2133	4248	6381	SO:0001583	missense	79654	exon21			TTCTCCTCGCATA	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"""HECT domain containing 3"""			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.2516A>G	chr1.hg19:g.45469234T>C	ENSP00000361245:p.Glu839Gly	146.0	0.0		109.0	5.0	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Missense_Mutation	SNP	ENST00000372172.4	hg19	CCDS41318.1	.	.	.	.	.	.	.	.	.	.	.	19.18	3.777538	0.70107	.	.	ENSG00000126107	ENST00000372172;ENST00000372168	T;T	0.59083	0.29;0.29	5.72	4.59	0.56863	HECT (4);	0.100986	0.64402	D	0.000001	T	0.70954	0.3283	M	0.85859	2.78	0.80722	D	1	B;D	0.56287	0.022;0.975	B;P	0.54060	0.048;0.741	T	0.74372	-0.3687	10	0.56958	D	0.05	.	11.5447	0.50685	0.0:0.0699:0.0:0.9301	.	839;449	Q5T447;Q5T447-2	HECD3_HUMAN;.	G	839;449	ENSP00000361245:E839G;ENSP00000361241:E449G	ENSP00000361241:E449G	E	-	2	0	HECTD3	45241821	1.000000	0.71417	0.998000	0.56505	0.508000	0.34012	7.654000	0.83653	0.994000	0.38892	0.375000	0.23000	GAG	.	.		0.612	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602	
CCDC17	149483	hgsc.bcm.edu	37	1	46086573	46086573	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:46086573A>G	ENST00000528266.1	-	11	1747		c.e11+1		CCDC17_ENST00000343901.2_Splice_Site|CCDC17_ENST00000421127.2_Splice_Site|CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000464739.1_5'Flank			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17											kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					CACCACACTCACCTGAGGAAT	0.592																																					.		Atlas-SNP	.											.	CCDC17	54	.	0			c.1599+2T>C						.						55.0	47.0	50.0					1																	46086573		2203	4300	6503	SO:0001630	splice_region_variant	149483	exon12			ACACTCACCTGAG		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.1599+1T>C	chr1.hg19:g.46086573A>G		118.0	0.0		88.0	4.0	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Splice_Site	SNP	ENST00000528266.1	hg19	CCDS44131.2	.	.	.	.	.	.	.	.	.	.	A	22.5	4.299858	0.81136	.	.	ENSG00000159588	ENST00000421127;ENST00000343901;ENST00000528266	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3473	0.74350	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CCDC17	45859160	1.000000	0.71417	0.995000	0.50966	0.936000	0.57629	6.287000	0.72671	2.263000	0.75096	0.533000	0.62120	.	.	.		0.592	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500	Intron
CMPK1	51727	hgsc.bcm.edu	37	1	47840605	47840605	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:47840605A>G	ENST00000371873.5	+	4	645	c.496A>G	c.(496-498)Agg>Ggg	p.R166G	CMPK1_ENST00000450808.2_Missense_Mutation_p.R117G	NM_001136140.1|NM_016308.2	NP_001129612.1|NP_057392.1			cytidine monophosphate (UMP-CMP) kinase 1, cytosolic											endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|stomach(2)	8						ATGTCTTGAGAGGGGAAAGAG	0.363																																					p.R166G		Atlas-SNP	.											.	CMPK1	13	.	0			c.A496G						.						81.0	79.0	80.0					1																	47840605		2203	4300	6503	SO:0001583	missense	51727	exon4			CTTGAGAGGGGAA	AF070416	CCDS549.1, CCDS44135.1	1p34.1-p33	2008-02-05	2008-01-25	2008-01-25	ENSG00000162368	ENSG00000162368	2.7.4.14		18170	protein-coding gene	gene with protein product	"""UMP-CMP kinase"", ""Cytidine monophosphate kinase"""	191710	"""cytidylate kinase"""	CMPK		10462544	Standard	NM_016308		Approved	UMP-CMPK	uc001cri.3	P30085	OTTHUMG00000007849	ENST00000371873.5:c.496A>G	chr1.hg19:g.47840605A>G	ENSP00000360939:p.Arg166Gly	135.0	0.0		91.0	4.0	NM_016308		Missense_Mutation	SNP	ENST00000371873.5	hg19	CCDS549.1	.	.	.	.	.	.	.	.	.	.	A	18.28	3.588893	0.66105	.	.	ENSG00000162368	ENST00000371873;ENST00000450808	T;T	0.80566	-1.39;-0.55	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.89051	0.6605	M	0.78344	2.41	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.90008	0.4119	10	0.72032	D	0.01	-22.1585	12.4682	0.55771	0.8606:0.1394:0.0:0.0	.	117;166	E9PGI8;B2R6S5	.;.	G	166;117	ENSP00000360939:R166G;ENSP00000398192:R117G	ENSP00000360939:R166G	R	+	1	2	CMPK1	47613192	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.809000	0.47971	2.323000	0.78572	0.528000	0.53228	AGG	.	.		0.363	CMPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021646.2	NM_016308	
FAF1	11124	hgsc.bcm.edu	37	1	50941209	50941209	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:50941209A>G	ENST00000396153.2	-	18	2247	c.1796T>C	c.(1795-1797)gTc>gCc	p.V599A	FAF1_ENST00000545823.1_Missense_Mutation_p.V357A|FAF1_ENST00000371778.4_Missense_Mutation_p.V599A	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	599	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.				apoptotic process (GO:0006915)|cell death (GO:0008219)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein complex assembly (GO:0031334)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of cell adhesion (GO:0030155)|regulation of protein catabolic process (GO:0042176)|regulation of protein kinase activity (GO:0045859)	CD95 death-inducing signaling complex (GO:0031265)|Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	heat shock protein binding (GO:0031072)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		AAAATCAAAGACAATCTGGAG	0.498																																					p.V599A		Atlas-SNP	.											.	FAF1	64	.	0			c.T1796C						.						98.0	100.0	99.0					1																	50941209		2203	4300	6503	SO:0001583	missense	11124	exon18			TCAAAGACAATCT	AF132938	CCDS554.1	1p32.3	2012-09-20			ENSG00000185104	ENSG00000185104		"""UBX domain containing"""	3578	protein-coding gene	gene with protein product	"""TNFRSF6-associated factor 1"", ""UBX domain protein 3A"""	604460				10462485	Standard	NM_007051		Approved	CGI-03, hFAF1, HFAF1s, UBXD12, UBXN3A	uc001cse.1	Q9UNN5	OTTHUMG00000007930	ENST00000396153.2:c.1796T>C	chr1.hg19:g.50941209A>G	ENSP00000379457:p.Val599Ala	115.0	0.0		97.0	4.0	NM_007051	Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Missense_Mutation	SNP	ENST00000396153.2	hg19	CCDS554.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.877865	0.91664	.	.	ENSG00000185104	ENST00000396153;ENST00000371778;ENST00000545823;ENST00000371780;ENST00000543607	.	.	.	5.51	5.51	0.81932	UBX (3);	0.124659	0.53938	D	0.000057	T	0.69531	0.3121	M	0.75085	2.285	0.52099	D	0.999944	P;P	0.38280	0.583;0.625	B;B	0.43701	0.428;0.185	T	0.74097	-0.3775	9	0.87932	D	0	-3.8747	15.6291	0.76888	1.0:0.0:0.0:0.0	.	357;599	B4DEJ6;Q9UNN5	.;FAF1_HUMAN	A	599;599;357;439;447	.	ENSP00000360843:V599A	V	-	2	0	FAF1	50713797	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.890000	0.92477	2.083000	0.62718	0.533000	0.62120	GTC	.	.		0.498	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1	NM_007051	
CYB5RL	606495	hgsc.bcm.edu	37	1	54640392	54640392	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:54640392T>C	ENST00000534324.1	-	6	847	c.848A>G	c.(847-849)aAg>aGg	p.K283R	CYB5RL_ENST00000537208.1_Missense_Mutation_p.K215R|CYB5RL_ENST00000401046.3_Missense_Mutation_p.K135R|CYB5RL_ENST00000542737.1_Missense_Mutation_p.K283R|RP11-446E24.4_ENST00000311841.7_Intron|CYB5RL_ENST00000287899.8_Missense_Mutation_p.K215R|RP11-446E24.4_ENST00000525949.1_5'Flank|AL357673.1_ENST00000536061.1_5'Flank|CYB5RL_ENST00000419823.2_Missense_Mutation_p.K283R			Q6IPT4	NB5R5_HUMAN	cytochrome b5 reductase-like	283							cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|urinary_tract(1)	8						TGCGAATGGCTTTCTCCGACA	0.542																																					p.K283R		Atlas-SNP	.											.	CYB5RL	17	.	0			c.A848G						.						42.0	44.0	43.0					1																	54640392		1948	4167	6115	SO:0001583	missense	606495	exon8			AATGGCTTTCTCC		CCDS44151.1	1p32.3	2011-04-08			ENSG00000215883	ENSG00000215883			32220	protein-coding gene	gene with protein product						12477932	Standard	NM_001031672		Approved	LOC606495	uc009vzo.3	Q6IPT4	OTTHUMG00000008082	ENST00000534324.1:c.848A>G	chr1.hg19:g.54640392T>C	ENSP00000434343:p.Lys283Arg	62.0	0.0		41.0	4.0	NM_001031672	B7ZBS4|Q8NF25	Missense_Mutation	SNP	ENST00000534324.1	hg19	CCDS44151.1	.	.	.	.	.	.	.	.	.	.	T	11.67	1.707564	0.30322	.	.	ENSG00000215883	ENST00000419823;ENST00000401046;ENST00000534324;ENST00000287899;ENST00000542737;ENST00000537208	D;D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.15;-2.18;-2.15	5.14	2.79	0.32731	Oxidoreductase FAD/NAD(P)-binding (1);	0.176073	0.26446	N	0.024325	T	0.80204	0.4580	L	0.39397	1.21	0.32899	D	0.512984	B;B	0.15141	0.012;0.003	B;B	0.17433	0.018;0.006	T	0.76440	-0.2958	10	0.49607	T	0.09	-24.5527	8.26	0.31779	0.0:0.1568:0.0:0.8432	.	283;135	Q6IPT4;Q6IPT4-3	NB5R5_HUMAN;.	R	283;135;283;215;283;215	ENSP00000409075:K283R;ENSP00000383825:K135R;ENSP00000434343:K283R;ENSP00000287899:K215R;ENSP00000438151:K283R;ENSP00000443797:K215R	ENSP00000287899:K215R	K	-	2	0	CYB5RL	54412980	1.000000	0.71417	1.000000	0.80357	0.633000	0.38033	0.780000	0.26760	0.411000	0.25702	0.454000	0.30748	AAG	.	.		0.542	CYB5RL-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388318.1	NM_001031672	
MROH7	374977	hgsc.bcm.edu	37	1	55139780	55139780	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:55139780T>C	ENST00000421030.2	+	10	2177	c.1892T>C	c.(1891-1893)cTg>cCg	p.L631P	MROH7_ENST00000454855.2_Missense_Mutation_p.L149P|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.L631P|MROH7_ENST00000409996.1_Missense_Mutation_p.L199P|MROH7_ENST00000545244.1_Missense_Mutation_p.L199P|MROH7_ENST00000395690.2_Missense_Mutation_p.L631P|MROH7_ENST00000339553.5_Missense_Mutation_p.L631P	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	631						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											TGTGAGGCTCTGGACGGCATC	0.527																																					p.L631P		Atlas-SNP	.											.	.	.	.	0			c.T1892C						.						119.0	125.0	123.0					1																	55139780		1964	4169	6133	SO:0001583	missense	374977	exon10			AGGCTCTGGACGG	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"""maestro heat-like repeat containing"""	24802	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 175"", ""HEAT repeat containing 8"""	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.1892T>C	chr1.hg19:g.55139780T>C	ENSP00000396622:p.Leu631Pro	172.0	0.0		147.0	6.0	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	hg19	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	T	15.76	2.927839	0.52759	.	.	ENSG00000184313	ENST00000421030;ENST00000545244;ENST00000414867;ENST00000339553;ENST00000409996;ENST00000454855;ENST00000395690	T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01	4.73	4.73	0.59995	.	0.172732	0.27008	N	0.021392	T	0.55689	0.1936	M	0.66939	2.045	0.80722	D	1	D;D;D	0.55385	0.971;0.958;0.958	P;P;P	0.58454	0.839;0.804;0.66	T	0.59123	-0.7513	10	0.62326	D	0.03	-10.9028	10.763	0.46277	0.0:0.0:0.0:1.0	.	631;631;199	F8W8P2;Q68CQ1;F5H7R4	.;HEAT8_HUMAN;.	P	631;199;660;631;199;149;631	ENSP00000396622:L631P;ENSP00000442333:L199P;ENSP00000343211:L631P;ENSP00000387048:L199P;ENSP00000401130:L149P;ENSP00000379044:L631P	ENSP00000343211:L631P	L	+	2	0	HEATR8	54912368	1.000000	0.71417	0.998000	0.56505	0.763000	0.43281	3.667000	0.54547	1.809000	0.52856	0.450000	0.29827	CTG	.	.		0.527	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
BSND	7809	hgsc.bcm.edu	37	1	55473990	55473990	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:55473990A>G	ENST00000371265.4	+	4	906	c.652A>G	c.(652-654)Agg>Ggg	p.R218G		NM_057176.2	NP_476517.1	Q8WZ55	BSND_HUMAN	barttin CLCNK-type chloride channel accessory beta subunit	218					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride channel activity (GO:0005254)|chloride channel regulator activity (GO:0017081)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17						TCCACATGACAGGGAGGAAGC	0.607																																					p.R218G	Ovarian(191;1657 2078 22894 42033 48899)	Atlas-SNP	.											.	BSND	36	.	0			c.A652G						.						47.0	47.0	47.0					1																	55473990		2203	4300	6503	SO:0001583	missense	7809	exon4			CATGACAGGGAGG	AY034632	CCDS602.1	1p32.3	2014-06-17	2014-06-17		ENSG00000162399	ENSG00000162399			16512	protein-coding gene	gene with protein product		606412	"""deafness, autosomal recessive 73"", ""Bartter syndrome, infantile, with sensorineural deafness (Barttin)"""	DFNB73		11687798, 11734858, 19646679	Standard	NM_057176		Approved	BART	uc001cye.3	Q8WZ55	OTTHUMG00000008112	ENST00000371265.4:c.652A>G	chr1.hg19:g.55473990A>G	ENSP00000360312:p.Arg218Gly	99.0	0.0		90.0	4.0	NM_057176	Q6NT28	Missense_Mutation	SNP	ENST00000371265.4	hg19	CCDS602.1	.	.	.	.	.	.	.	.	.	.	A	7.719	0.696747	0.15106	.	.	ENSG00000162399	ENST00000371265	T	0.63096	-0.02	4.74	-1.15	0.09709	.	1.224520	0.05600	N	0.576207	T	0.33323	0.0859	N	0.02736	-0.51	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20140	-1.0284	10	0.09338	T	0.73	-2.6923	8.9829	0.35977	0.6993:0.0:0.3007:0.0	.	218	Q8WZ55	BSND_HUMAN	G	218	ENSP00000360312:R218G	ENSP00000360312:R218G	R	+	1	2	BSND	55246578	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.089000	0.11180	-0.067000	0.12976	-1.223000	0.01593	AGG	.	.		0.607	BSND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022213.4	NM_057176	
KANK4	163782	hgsc.bcm.edu	37	1	62739084	62739084	+	Silent	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:62739084C>A	ENST00000371153.4	-	3	2070	c.1692G>T	c.(1690-1692)gtG>gtT	p.V564V	KANK4_ENST00000354381.3_Intron|KANK4_ENST00000371150.1_5'Flank	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	564						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						GGATCTTCTTCACATACTGCC	0.622																																					p.V564V		Atlas-SNP	.											.	KANK4	135	.	0			c.G1692T						.						57.0	53.0	54.0					1																	62739084		2203	4300	6503	SO:0001819	synonymous_variant	163782	exon3			CTTCTTCACATAC	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	27263	protein-coding gene	gene with protein product		614612	"""ankyrin repeat domain 38"""	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.1692G>T	chr1.hg19:g.62739084C>A		251.0	0.0		151.0	22.0	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Silent	SNP	ENST00000371153.4	hg19	CCDS620.1																																																																																			.	.		0.622	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712	
USP1	7398	hgsc.bcm.edu	37	1	62910512	62910512	+	Missense_Mutation	SNP	G	G	A	rs372316949	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:62910512G>A	ENST00000339950.4	+	6	1476	c.661G>A	c.(661-663)Gaa>Aaa	p.E221K	USP1_ENST00000371146.1_Missense_Mutation_p.E221K	NM_003368.4	NP_003359.3	O94782	UBP1_HUMAN	ubiquitin specific peptidase 1	221	USP.				DNA repair (GO:0006281)|monoubiquitinated protein deubiquitination (GO:0035520)|protein deubiquitination (GO:0016579)|regulation of DNA repair (GO:0006282)|response to UV (GO:0009411)|skeletal system development (GO:0001501)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	19		all_neural(321;0.0281)		BRCA - Breast invasive adenocarcinoma(111;8.01e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00245)|OV - Ovarian serous cystadenocarcinoma(397;0.0535)		CCTAAAAAAAGAAGAAGTAAA	0.353																																					p.E221K	Ovarian(122;1846 2315 3982 19504)	Atlas-SNP	.											.	USP1	51	.	0			c.G661A						.						69.0	76.0	74.0					1																	62910512		2202	4299	6501	SO:0001583	missense	7398	exon6			AAAAAAGAAGAAG		CCDS621.1	1p31.3	2008-05-14	2005-08-08		ENSG00000162607	ENSG00000162607		"""Ubiquitin-specific peptidases"""	12607	protein-coding gene	gene with protein product		603478	"""ubiquitin specific protease 1"""			12838346	Standard	NM_003368		Approved		uc001dak.2	O94782	OTTHUMG00000008972	ENST00000339950.4:c.661G>A	chr1.hg19:g.62910512G>A	ENSP00000343526:p.Glu221Lys	171.0	0.0		125.0	13.0	NM_001017415	A0PJ95|D3DQ57|Q05BX7|Q59H66|Q9UFR0|Q9UNJ3	Missense_Mutation	SNP	ENST00000339950.4	hg19	CCDS621.1	.	.	.	.	.	.	.	.	.	.	G	32	5.177196	0.94846	.	.	ENSG00000162607	ENST00000371146;ENST00000339950	T;T	0.20463	2.07;2.07	5.43	5.43	0.79202	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.048213	0.85682	D	0.000000	T	0.31702	0.0805	N	0.17379	0.485	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.06092	-1.0846	10	0.23891	T	0.37	-17.8517	19.4366	0.94798	0.0:0.0:1.0:0.0	.	221	O94782	UBP1_HUMAN	K	221	ENSP00000360188:E221K;ENSP00000343526:E221K	ENSP00000343526:E221K	E	+	1	0	USP1	62683100	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.068000	0.93961	2.815000	0.96918	0.650000	0.86243	GAA	.	.		0.353	USP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024881.1	NM_001017415	
DOCK7	85440	hgsc.bcm.edu	37	1	62995054	62995054	+	Silent	SNP	T	T	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:62995054T>G	ENST00000340370.5	-	29	3599	c.3582A>C	c.(3580-3582)tcA>tcC	p.S1194S	DOCK7_ENST00000251157.5_Silent_p.S1225S	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1225					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						ACCGCGGGTCTGAGTCGTGAC	0.403																																					p.S1225S		Atlas-SNP	.											.	DOCK7	184	.	0			c.A3675C						.						109.0	103.0	105.0					1																	62995054		2203	4300	6503	SO:0001819	synonymous_variant	85440	exon30			CGGGTCTGAGTCG		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.3582A>C	chr1.hg19:g.62995054T>G		161.0	0.0		119.0	12.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	hg19	CCDS30734.1																																																																																			.	.		0.403	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
JAK1	3716	hgsc.bcm.edu	37	1	65307245	65307245	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:65307245G>A	ENST00000342505.4	-	18	2691	c.2443C>T	c.(2443-2445)Cca>Tca	p.P815S	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	815	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TTACATGATGGTGTCACTGGC	0.493			Mis		ALL																																p.P815S		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.C2443T						.						121.0	115.0	117.0					1																	65307245		1967	4155	6122	SO:0001583	missense	3716	exon18			ATGATGGTGTCAC	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.2443C>T	chr1.hg19:g.65307245G>A	ENSP00000343204:p.Pro815Ser	177.0	0.0		147.0	45.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.519567	0.85495	.	.	ENSG00000162434	ENST00000342505	D	0.86230	-2.09	4.61	4.61	0.57282	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.93177	0.7827	M	0.83953	2.67	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	D	0.93553	0.6888	9	0.62326	D	0.03	-2.2034	17.9931	0.89175	0.0:0.0:1.0:0.0	.	815	P23458	JAK1_HUMAN	S	815	ENSP00000343204:P815S	ENSP00000343204:P815S	P	-	1	0	JAK1	65079833	1.000000	0.71417	0.698000	0.30274	0.738000	0.42128	9.146000	0.94640	2.550000	0.86006	0.557000	0.71058	CCA	.	.		0.493	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
JAK1	3716	hgsc.bcm.edu	37	1	65335078	65335078	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:65335078T>C	ENST00000342505.4	-	6	811	c.563A>G	c.(562-564)gAg>gGg	p.E188G		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	188	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	CCCTAGACACTCGTTCTCAAT	0.512			Mis		ALL																																p.E188G		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.A563G						.						145.0	139.0	141.0					1																	65335078		2023	4191	6214	SO:0001583	missense	3716	exon6			AGACACTCGTTCT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.563A>G	chr1.hg19:g.65335078T>C	ENSP00000343204:p.Glu188Gly	149.0	0.0		87.0	4.0	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.726912	0.89390	.	.	ENSG00000162434	ENST00000342505	T	0.72615	-0.67	5.33	5.33	0.75918	FERM central domain (1);Band 4.1 domain (1);FERM domain (1);	.	.	.	.	D	0.82829	0.5122	M	0.85859	2.78	0.58432	D	0.999998	D	0.76494	0.999	D	0.80764	0.994	D	0.86274	0.1663	9	0.87932	D	0	.	15.6084	0.76692	0.0:0.0:0.0:1.0	.	188	P23458	JAK1_HUMAN	G	188	ENSP00000343204:E188G	ENSP00000343204:E188G	E	-	2	0	JAK1	65107666	1.000000	0.71417	0.999000	0.59377	0.767000	0.43475	7.676000	0.84012	2.152000	0.67230	0.533000	0.62120	GAG	.	.		0.512	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
ERICH3	127254	hgsc.bcm.edu	37	1	75037860	75037860	+	Silent	SNP	T	T	C	rs10539747	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:75037860T>C	ENST00000326665.5	-	14	3752	c.3534A>G	c.(3532-3534)ggA>ggG	p.G1178G	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1178	Glu-rich.							p.G1178G(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						GTCTTTCCCCTCCTCCTTCTT	0.493																																					p.G1178G		Atlas-SNP	.											C1orf173,NS,carcinoma,0,1	C1orf173	380	.	1	Substitution - coding silent(1)	lung(1)	c.A3534G						.						124.0	117.0	120.0					1																	75037860		2203	4297	6500	SO:0001819	synonymous_variant	127254	exon14			TTCCCCTCCTCCT																												ENST00000326665.5:c.3534A>G	chr1.hg19:g.75037860T>C		199.0	0.0		146.0	6.0	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Silent	SNP	ENST00000326665.5	hg19	CCDS30755.1																																																																																			.	.		0.493	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
ELTD1	64123	hgsc.bcm.edu	37	1	79385900	79385900	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:79385900A>G	ENST00000370742.3	-	10	1492	c.1429T>C	c.(1429-1431)Ttt>Ctt	p.F477L		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	477					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		CCAACAAGAAAAACAAGTTCA	0.328																																					p.F477L		Atlas-SNP	.											.	ELTD1	143	.	0			c.T1429C						.						87.0	82.0	83.0					1																	79385900		1823	4069	5892	SO:0001583	missense	64123	exon10			CAAGAAAAACAAG	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"""-"", ""GPCR / Class B : Orphans"""	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1429T>C	chr1.hg19:g.79385900A>G	ENSP00000359778:p.Phe477Leu	91.0	0.0		75.0	4.0	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	hg19	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631991	0.87660	.	.	ENSG00000162618	ENST00000370742	T	0.44482	0.92	5.01	5.01	0.66863	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.55433	0.1920	M	0.74467	2.265	0.80722	D	1	D	0.71674	0.998	D	0.73380	0.98	T	0.58951	-0.7545	9	.	.	.	.	15.0178	0.71600	1.0:0.0:0.0:0.0	.	477	Q9HBW9	ELTD1_HUMAN	L	477	ENSP00000359778:F477L	.	F	-	1	0	ELTD1	79158488	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.255000	0.95524	2.002000	0.58637	0.533000	0.62120	TTT	.	.		0.328	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
ALG14	199857	hgsc.bcm.edu	37	1	95448692	95448692	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:95448692A>G	ENST00000370205.5	-	4	637	c.591T>C	c.(589-591)gtT>gtC	p.V197V		NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	197					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	6		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		CCGGCCACTGAACAATGAAGT	0.403																																					p.V197V		Atlas-SNP	.											.	ALG14	13	.	0			c.T591C						.						108.0	100.0	103.0					1																	95448692		2203	4300	6503	SO:0001819	synonymous_variant	199857	exon4			CCACTGAACAATG		CCDS752.1	1p21.3	2013-02-21	2013-02-21		ENSG00000172339	ENSG00000172339			28287	protein-coding gene	gene with protein product		612866	"""asparagine-linked glycosylation 14 homolog (yeast)"", ""asparagine-linked glycosylation 14 homolog (S. cerevisiae)"""			15615718	Standard	NM_144988		Approved	MGC19780	uc001dra.2	Q96F25	OTTHUMG00000010781	ENST00000370205.5:c.591T>C	chr1.hg19:g.95448692A>G		162.0	0.0		100.0	4.0	NM_144988	A8K030	Silent	SNP	ENST00000370205.5	hg19	CCDS752.1																																																																																			.	.		0.403	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029699.2	NM_144988	
AKNAD1	254268	hgsc.bcm.edu	37	1	109394791	109394791	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:109394791G>A	ENST00000370001.3	-	2	764	c.496C>T	c.(496-498)Cca>Tca	p.P166S	AKNAD1_ENST00000357393.4_Intron|AKNAD1_ENST00000369994.1_Missense_Mutation_p.P166S|AKNAD1_ENST00000369995.3_Missense_Mutation_p.P166S	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	166						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						GTGAGTTCTGGGGTTTGTTCT	0.408																																					p.P166S		Atlas-SNP	.											.	AKNAD1	83	.	0			c.C496T						.						59.0	61.0	60.0					1																	109394791		2203	4299	6502	SO:0001583	missense	254268	exon2			GTTCTGGGGTTTG	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 62"""	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.496C>T	chr1.hg19:g.109394791G>A	ENSP00000359018:p.Pro166Ser	412.0	0.0		294.0	14.0	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	hg19	CCDS791.2	.	.	.	.	.	.	.	.	.	.	G	6.761	0.509331	0.12883	.	.	ENSG00000162641	ENST00000370001;ENST00000369994;ENST00000369995	T;T;T	0.07800	3.18;3.18;3.16	5.77	-2.1	0.07210	.	0.664334	0.14926	N	0.290352	T	0.01454	0.0047	L	0.29908	0.895	0.09310	N	0.999993	B	0.20052	0.041	B	0.14578	0.011	T	0.45234	-0.9275	10	0.30854	T	0.27	0.1785	5.138	0.14945	0.4742:0.0:0.3244:0.2014	.	166	Q5T1N1	AKND1_HUMAN	S	166	ENSP00000359018:P166S;ENSP00000359011:P166S;ENSP00000359012:P166S	ENSP00000359011:P166S	P	-	1	0	AKNAD1	109196314	0.000000	0.05858	0.834000	0.33040	0.604000	0.37047	-0.130000	0.10498	-0.199000	0.10317	-0.302000	0.09304	CCA	.	.		0.408	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
KIAA1324	57535	hgsc.bcm.edu	37	1	109716107	109716107	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:109716107T>C	ENST00000369939.3	+	6	891	c.708T>C	c.(706-708)aaT>aaC	p.N236N	KIAA1324_ENST00000529753.1_Silent_p.N236N	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	236					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)		TGGAGCTAAATCGAGGCAATA	0.438																																					p.N236N		Atlas-SNP	.											.	KIAA1324	77	.	0			c.T708C						.						186.0	167.0	174.0					1																	109716107		2203	4300	6503	SO:0001819	synonymous_variant	57535	exon6			GCTAAATCGAGGC	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.708T>C	chr1.hg19:g.109716107T>C		107.0	0.0		91.0	4.0	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Silent	SNP	ENST00000369939.3	hg19	CCDS794.1																																																																																			.	.		0.438	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775	
CELSR2	1952	hgsc.bcm.edu	37	1	109805547	109805547	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:109805547A>G	ENST00000271332.3	+	7	4725	c.4664A>G	c.(4663-4665)cAc>cGc	p.H1555R		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1555	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		GACAGCCGGCACATAGACATG	0.652																																					p.H1555R	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.A4664G						.						46.0	44.0	45.0					1																	109805547		2203	4300	6503	SO:0001583	missense	1952	exon7			GCCGGCACATAGA	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.4664A>G	chr1.hg19:g.109805547A>G	ENSP00000271332:p.His1555Arg	111.0	0.0		94.0	4.0	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	A	8.398	0.841304	0.16891	.	.	ENSG00000143126	ENST00000271332	T	0.79352	-1.26	4.74	2.48	0.30137	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	T	0.29491	0.0735	N	0.03324	-0.35	0.40419	D	0.97982	B	0.02656	0.0	B	0.01281	0.0	T	0.14420	-1.0473	9	0.18276	T	0.48	.	4.8587	0.13571	0.5012:0.2806:0.2182:0.0	.	1555	Q9HCU4	CELR2_HUMAN	R	1555	ENSP00000271332:H1555R	ENSP00000271332:H1555R	H	+	2	0	CELSR2	109607070	0.000000	0.05858	0.948000	0.38648	0.953000	0.61014	0.364000	0.20325	0.962000	0.38057	0.459000	0.35465	CAC	.	.		0.652	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
RSBN1	54665	hgsc.bcm.edu	37	1	114309729	114309729	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:114309729C>T	ENST00000261441.5	-	6	1990	c.1927G>A	c.(1927-1929)Gtt>Att	p.V643I	RSBN1_ENST00000369581.2_5'UTR	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	643						nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACCTGGGAAACTGGAGGTTCA	0.333																																					p.V643I		Atlas-SNP	.											.	RSBN1	71	.	0			c.G1927A						.						81.0	78.0	79.0					1																	114309729		2203	4300	6503	SO:0001583	missense	54665	exon6			GGGAAACTGGAGG	AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019			25642	protein-coding gene	gene with protein product		615858				12477932	Standard	NM_018364		Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.1927G>A	chr1.hg19:g.114309729C>T	ENSP00000261441:p.Val643Ile	137.0	0.0		90.0	4.0	NM_018364	A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	Missense_Mutation	SNP	ENST00000261441.5	hg19	CCDS862.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.934912	0.52866	.	.	ENSG00000081019	ENST00000261441	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.38825	0.1055	L	0.28274	0.84	0.58432	D	0.999999	P	0.45715	0.865	B	0.44278	0.445	T	0.15065	-1.0450	9	0.17832	T	0.49	-10.0189	20.2566	0.98424	0.0:1.0:0.0:0.0	.	643	Q5VWQ0	RSBN1_HUMAN	I	643	.	ENSP00000261441:V643I	V	-	1	0	RSBN1	114111252	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.875000	0.56108	2.793000	0.96121	0.561000	0.74099	GTT	.	.		0.333	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033022.2	NM_018364	
CD101	9398	hgsc.bcm.edu	37	1	117552527	117552527	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:117552527A>G	ENST00000256652.4	+	2	157	c.99A>G	c.(97-99)agA>agG	p.R33R	CD101_ENST00000369470.1_Silent_p.R33R	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	33	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CACTGTTTAGAGCTGAAGGTT	0.468																																					p.R33R		Atlas-SNP	.											.	CD101	95	.	0			c.A99G						.						95.0	90.0	91.0					1																	117552527		2203	4300	6503	SO:0001819	synonymous_variant	9398	exon2			GTTTAGAGCTGAA	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.99A>G	chr1.hg19:g.117552527A>G		113.0	0.0		84.0	4.0	NM_001256109	Q15856	Silent	SNP	ENST00000256652.4	hg19	CCDS891.1																																																																																			.	.		0.468	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
SPAG17	200162	hgsc.bcm.edu	37	1	118727720	118727720	+	Missense_Mutation	SNP	A	A	G	rs139383446	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:118727720A>G	ENST00000336338.5	-	1	126	c.61T>C	c.(61-63)Tcg>Ccg	p.S21P		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	21						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GCTATGAGCGAGGGTTCCCAT	0.577																																					p.S21P		Atlas-SNP	.											.	SPAG17	263	.	0			c.T61C						.						204.0	195.0	198.0					1																	118727720		2203	4300	6503	SO:0001583	missense	200162	exon1			TGAGCGAGGGTTC		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.61T>C	chr1.hg19:g.118727720A>G	ENSP00000337804:p.Ser21Pro	152.0	0.0		97.0	4.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.824982	0.71143	.	.	ENSG00000155761	ENST00000336338	T	0.20463	2.07	4.99	3.83	0.44106	.	0.699229	0.12534	N	0.460503	T	0.14657	0.0354	L	0.40543	1.245	0.20975	N	0.999813	D	0.58268	0.982	P	0.54924	0.764	T	0.07770	-1.0755	10	0.56958	D	0.05	.	8.8277	0.35065	0.8103:0.1897:0.0:0.0	.	21	Q6Q759	SPG17_HUMAN	P	21	ENSP00000337804:S21P	ENSP00000337804:S21P	S	-	1	0	SPAG17	118529243	0.041000	0.20044	0.713000	0.30519	0.951000	0.60555	0.253000	0.18296	0.991000	0.38814	0.454000	0.30748	TCG	.	A|0.999;C|0.001		0.577	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
HMGCS2	3158	hgsc.bcm.edu	37	1	120295968	120295968	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:120295968A>G	ENST00000369406.3	-	7	1278	c.1229T>C	c.(1228-1230)tTc>tCc	p.F410S	HMGCS2_ENST00000544913.2_Missense_Mutation_p.F368S|HMGCS2_ENST00000476640.1_5'Flank	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	410					cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|ketone body biosynthetic process (GO:0046951)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxymethylglutaryl-CoA synthase activity (GO:0004421)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		GCCATAAGAGAAGGCACCAAT	0.478																																					p.F410S		Atlas-SNP	.											.	HMGCS2	58	.	0			c.T1229C						.						66.0	66.0	66.0					1																	120295968		2203	4300	6503	SO:0001583	missense	3158	exon7			TAAGAGAAGGCAC	BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"""3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"""			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.1229T>C	chr1.hg19:g.120295968A>G	ENSP00000358414:p.Phe410Ser	144.0	0.0		97.0	4.0	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Missense_Mutation	SNP	ENST00000369406.3	hg19	CCDS905.1	.	.	.	.	.	.	.	.	.	.	A	19.40	3.821288	0.71028	.	.	ENSG00000134240	ENST00000369406;ENST00000544913	D;D	0.84298	-1.83;-1.83	5.39	4.24	0.50183	Hydroxymethylglutaryl-coenzyme A synthase C-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.080767	0.53938	D	0.000050	D	0.91205	0.7229	M	0.89534	3.04	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92212	0.5777	10	0.87932	D	0	-28.5483	10.7945	0.46453	0.8577:0.0:0.0:0.1423	.	368;410	B7Z8R3;P54868	.;HMCS2_HUMAN	S	410;368	ENSP00000358414:F410S;ENSP00000439495:F368S	ENSP00000358414:F410S	F	-	2	0	HMGCS2	120097491	1.000000	0.71417	1.000000	0.80357	0.674000	0.39518	6.684000	0.74538	0.945000	0.37605	0.379000	0.24179	TTC	.	.		0.478	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518	
NBPF10	100132406	hgsc.bcm.edu	37	1	145367777	145367777	+	Missense_Mutation	SNP	G	G	T	rs200743139		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:145367777G>T	ENST00000342960.5	+	83	10408	c.10373G>T	c.(10372-10374)aGg>aTg	p.R3458M	NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000369338.1_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	755						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		gaaagaagaaggggaagaaaa	0.428																																					p.R3458M		Atlas-SNP	.											NBPF10,NS,carcinoma,0,1	NBPF10	221	.	0			c.G10373T						.																																			SO:0001583	missense	100132406	exon83			GAAGAAGGGGAAG	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.10373G>T	chr1.hg19:g.145367777G>T	ENSP00000345684:p.Arg3458Met	8.0	2.0		13.0	6.0	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	hg19	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	10.39	1.335798	0.24253	.	.	ENSG00000163386	ENST00000369339;ENST00000342960	T	0.05258	3.47	.	.	.	.	.	.	.	.	T	0.03651	0.0104	L	0.51422	1.61	0.09310	N	1	.	.	.	.	.	.	T	0.38351	-0.9665	4	0.87932	D	0	.	.	.	.	.	.	.	.	M	578;3458	ENSP00000345684:R3458M	ENSP00000345684:R3458M	R	+	2	0	NBPF10	144079134	.	.	.	.	.	.	.	.	.	.	.	.	AGG	.	.		0.428	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
TDRKH	11022	hgsc.bcm.edu	37	1	151751633	151751633	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:151751633T>C	ENST00000368822.1	-	5	1140	c.507A>G	c.(505-507)ctA>ctG	p.L169L	TDRKH_ENST00000368823.1_Silent_p.L165L|TDRKH_ENST00000368827.6_Silent_p.L169L|TDRKH_ENST00000368825.3_Silent_p.L124L|TDRKH_ENST00000440583.2_5'UTR|TDRKH_ENST00000368824.3_Silent_p.L169L|TDRKH_ENST00000484421.1_5'UTR|TDRKH_ENST00000458431.2_Silent_p.L169L			Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing	169	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	mitochondrion (GO:0005739)|pi-body (GO:0071546)|piP-body (GO:0071547)	RNA binding (GO:0003723)			breast(5)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			GTCTTGATAGTAGTAATGTCC	0.413																																					p.L169L		Atlas-SNP	.											.	TDRKH	45	.	0			c.A507G						.						187.0	175.0	178.0					1																	151751633		1878	4108	5986	SO:0001819	synonymous_variant	11022	exon5			TGATAGTAGTAAT	AF227192	CCDS41394.1, CCDS41395.1	1q21	2013-01-23	2003-11-07		ENSG00000182134	ENSG00000182134		"""Tudor domain containing"""	11713	protein-coding gene	gene with protein product		609501	"""tudor and KH domain containing"""			10767542	Standard	NM_001083964		Approved	TDRD2	uc001eza.4	Q9Y2W6	OTTHUMG00000013062	ENST00000368822.1:c.507A>G	chr1.hg19:g.151751633T>C		399.0	0.0		506.0	76.0	NM_001083965	D3DV24|Q5SZR3|Q5SZR5|Q8N582|Q9NYV5	Silent	SNP	ENST00000368822.1	hg19	CCDS41394.1																																																																																			.	.		0.413	TDRKH-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000036648.2	NM_006862	
UBE2Q1	55585	hgsc.bcm.edu	37	1	154524627	154524627	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:154524627A>G	ENST00000292211.4	-	8	987	c.908T>C	c.(907-909)cTc>cCc	p.L303P	UBE2Q1_ENST00000497453.1_5'Flank|UBE2Q1-AS1_ENST00000441613.1_RNA	NM_017582.6	NP_060052.3	Q7Z7E8	UB2Q1_HUMAN	ubiquitin-conjugating enzyme E2Q family member 1	303					embryo implantation (GO:0007566)|fertilization (GO:0009566)|mating behavior (GO:0007617)|prolactin secretion (GO:0070459)|protein ubiquitination (GO:0016567)|reproductive system development (GO:0061458)|suckling behavior (GO:0001967)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	16	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			GAGGATCTGGAGATCGTTGTG	0.493																																					p.L303P		Atlas-SNP	.											.	UBE2Q1	35	.	0			c.T908C						.						91.0	98.0	96.0					1																	154524627		2203	4300	6503	SO:0001583	missense	55585	exon8			ATCTGGAGATCGT	AJ243666	CCDS1069.1	1q22	2008-05-02	2008-05-02	2005-08-05	ENSG00000160714	ENSG00000160714		"""Ubiquitin-conjugating enzymes E2"""	15698	protein-coding gene	gene with protein product			"""ubiquitin-conjugating enzyme E2Q (putative)"""	UBE2Q			Standard	NM_017582		Approved	PRO3094, NICE-5	uc001fff.1	Q7Z7E8	OTTHUMG00000037265	ENST00000292211.4:c.908T>C	chr1.hg19:g.154524627A>G	ENSP00000292211:p.Leu303Pro	104.0	0.0		150.0	6.0	NM_017582	B4DF92|Q3B841|Q5I0X2|Q6IS04|Q6P7P2|Q96MV4|Q9BVX5|Q9UGL6	Missense_Mutation	SNP	ENST00000292211.4	hg19	CCDS1069.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.518519	0.85495	.	.	ENSG00000160714	ENST00000292211	.	.	.	5.02	5.02	0.67125	Ubiquitin-conjugating enzyme, E2 (1);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.64402	D	0.000001	T	0.76535	0.4001	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81417	-0.0942	9	0.87932	D	0	-9.7885	13.7173	0.62705	1.0:0.0:0.0:0.0	.	303	Q7Z7E8	UB2Q1_HUMAN	P	303	.	ENSP00000292211:L303P	L	-	2	0	UBE2Q1	152791251	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.669000	0.91163	2.121000	0.65114	0.459000	0.35465	CTC	.	.		0.493	UBE2Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090704.1	NM_017582	
GPATCH4	54865	hgsc.bcm.edu	37	1	156565051	156565051	+	Missense_Mutation	SNP	G	G	C	rs75463812		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:156565051G>C	ENST00000438976.2	-	8	1112	c.1082C>G	c.(1081-1083)aCt>aGt	p.T361S	GPATCH4_ENST00000368232.4_Missense_Mutation_p.T356S|GPATCH4_ENST00000497287.1_5'Flank			Q5T3I0	GPTC4_HUMAN	G patch domain containing 4	356							poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(3)|stomach(1)	17	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCACCTAAAAGTTTCCTCACC	0.507																																					p.T361S		Atlas-SNP	.											.	GPATCH4	34	.	0			c.C1082G						.						191.0	191.0	191.0					1																	156565051		2203	4300	6503	SO:0001583	missense	54865	exon8			CTAAAAGTTTCCT	BC056904	CCDS1146.1, CCDS44245.1	1q22	2013-01-28		2006-12-13	ENSG00000160818	ENSG00000160818		"""G patch domain containing"""	25982	protein-coding gene	gene with protein product				GPATC4		12477932	Standard	NM_015590		Approved	FLJ20249, DKFZP434F1735	uc001fpl.3	Q5T3I0	OTTHUMG00000033203	ENST00000438976.2:c.1082C>G	chr1.hg19:g.156565051G>C	ENSP00000396441:p.Thr361Ser	543.0	0.0		692.0	29.0	NM_015590	Q5T3I1|Q6ZUE7|Q8IWG8|Q9NXH4	Missense_Mutation	SNP	ENST00000438976.2	hg19	CCDS44245.1	.	.	.	.	.	.	.	.	.	.	G	8.543	0.873684	0.17322	.	.	ENSG00000160818	ENST00000368232;ENST00000368229;ENST00000438976	.	.	.	3.86	1.91	0.25777	.	0.922459	0.08880	N	0.880267	T	0.12178	0.0296	L	0.29908	0.895	0.09310	N	0.999997	B;B	0.22003	0.063;0.063	B;B	0.19666	0.026;0.026	T	0.33394	-0.9870	9	0.25106	T	0.35	-9.1235	8.1478	0.31121	0.0929:0.1607:0.7465:0.0	.	361;356	E9PAV9;Q5T3I0	.;GPTC4_HUMAN	S	356;356;361	.	ENSP00000357212:T356S	T	-	2	0	GPATCH4	154831675	0.003000	0.15002	0.000000	0.03702	0.036000	0.12997	1.263000	0.33004	0.555000	0.29079	0.557000	0.71058	ACT	.	C|1.000;|0.000		0.507	GPATCH4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386947.1	NM_017725	
CASQ1	844	hgsc.bcm.edu	37	1	160160793	160160793	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:160160793A>G	ENST00000368078.3	+	1	448	c.252A>G	c.(250-252)caA>caG	p.Q84Q	CASQ1_ENST00000368079.3_Silent_p.Q78Q			P31415	CASQ1_HUMAN	calsequestrin 1 (fast-twitch, skeletal muscle)	84					endoplasmic reticulum organization (GO:0007029)|ion transmembrane transport (GO:0034220)|protein polymerization (GO:0051258)|regulation of sequestering of calcium ion (GO:0051282)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to heat (GO:0009408)|response to organic substance (GO:0010033)|sarcomere organization (GO:0045214)|skeletal muscle tissue development (GO:0007519)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna lumen (GO:0014804)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	21	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CACAAAGACAATTTGAGATGG	0.522																																					p.Q84Q		Atlas-SNP	.											.	CASQ1	55	.	0			c.A252G						.						73.0	71.0	72.0					1																	160160793		2203	4300	6503	SO:0001819	synonymous_variant	844	exon1			AAGACAATTTGAG	S73775	CCDS1198.1, CCDS1198.2	1q21	2011-10-19			ENSG00000143318	ENSG00000143318		"""Protein disulfide isomerases"""	1512	protein-coding gene	gene with protein product	"""calsequestrin 1, fast-twitch, skeletal muscle"", ""calmitine"""	114250		CASQ		8406504, 2321095	Standard	NM_001231		Approved	PDIB1	uc010pja.2	P31415	OTTHUMG00000031607	ENST00000368078.3:c.252A>G	chr1.hg19:g.160160793A>G		88.0	0.0		109.0	5.0	NM_001231	B1AKZ2|B2R863|Q8TBW7	Silent	SNP	ENST00000368078.3	hg19	CCDS1198.2	.	.	.	.	.	.	.	.	.	.	A	8.410	0.843930	0.16963	.	.	ENSG00000143318	ENST00000441151	.	.	.	4.21	-4.72	0.03269	.	.	.	.	.	T	0.56411	0.1983	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68827	-0.5306	5	0.59425	D	0.04	.	13.1934	0.59723	0.3557:0.0:0.6443:0.0	.	.	.	.	S	34	.	ENSP00000387681:N34S	N	+	2	0	CASQ1	158427417	0.104000	0.21937	0.776000	0.31678	0.994000	0.84299	-0.497000	0.06428	-0.923000	0.03785	0.369000	0.22263	AAT	.	.		0.522	CASQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077412.1	NM_001231	
ARHGAP30	257106	hgsc.bcm.edu	37	1	161019075	161019075	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:161019075T>C	ENST00000368013.3	-	12	2056	c.1736A>G	c.(1735-1737)gAg>gGg	p.E579G	ARHGAP30_ENST00000368016.3_Missense_Mutation_p.E579G|ARHGAP30_ENST00000368015.1_Missense_Mutation_p.E402G	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	579					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			AAACTGTGCCTCATCCAGAGA	0.592																																					p.E579G		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.A1736G						.						88.0	95.0	92.0					1																	161019075		2203	4300	6503	SO:0001583	missense	257106	exon12			TGTGCCTCATCCA	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.1736A>G	chr1.hg19:g.161019075T>C	ENSP00000356992:p.Glu579Gly	68.0	0.0		108.0	5.0	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	hg19	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	T	18.54	3.645527	0.67358	.	.	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368017;ENST00000368015	T;T;T	0.39997	2.65;2.55;1.05	5.18	5.18	0.71444	.	0.259165	0.27451	N	0.019310	T	0.42585	0.1209	M	0.65975	2.015	0.34804	D	0.737002	P;D	0.55605	0.877;0.972	B;P	0.53912	0.417;0.737	T	0.48854	-0.8998	10	0.44086	T	0.13	.	12.9925	0.58627	0.0:0.0:0.0:1.0	.	579;579	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	G	579;579;431;402	ENSP00000356995:E579G;ENSP00000356992:E579G;ENSP00000356994:E402G	ENSP00000356992:E579G	E	-	2	0	ARHGAP30	159285699	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	3.796000	0.55507	1.961000	0.56991	0.454000	0.30748	GAG	.	.		0.592	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
NOS1AP	9722	hgsc.bcm.edu	37	1	162335312	162335312	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:162335312T>C	ENST00000361897.5	+	9	1460	c.1058T>C	c.(1057-1059)gTc>gCc	p.V353A	NOS1AP_ENST00000530878.1_Missense_Mutation_p.V348A|RP11-565P22.6_ENST00000431696.1_Missense_Mutation_p.V39A|NOS1AP_ENST00000493151.1_Missense_Mutation_p.V58A	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	353					regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			TCCCTGCTGGTCAAGCAGGTG	0.607																																					p.V353A		Atlas-SNP	.											.	NOS1AP	139	.	0			c.T1058C						.						59.0	52.0	54.0					1																	162335312		2203	4300	6503	SO:0001583	missense	9722	exon9			TGCTGGTCAAGCA	AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"""C-terminal PDZ domain ligand of neuronal nitric oxide synthase"""	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.1058T>C	chr1.hg19:g.162335312T>C	ENSP00000355133:p.Val353Ala	68.0	0.0		85.0	4.0	NM_014697	B7ZLF5|O43564|Q3T551|Q5VU95	Missense_Mutation	SNP	ENST00000361897.5	hg19	CCDS1237.1	.	.	.	.	.	.	.	.	.	.	T	32	5.189634	0.94923	.	.	ENSG00000198929;ENSG00000198929;ENSG00000198929;ENSG00000198929;ENSG00000254706	ENST00000530878;ENST00000361897;ENST00000464284;ENST00000493151;ENST00000431696	D;D	0.84442	-1.85;-1.85	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.89455	0.6720	M	0.66297	2.02	.	.	.	D;D;D	0.76494	0.999;0.991;0.991	D;P;P	0.80764	0.994;0.639;0.787	D	0.90663	0.4592	9	0.59425	D	0.04	.	14.766	0.69640	0.0:0.0:0.0:1.0	.	58;348;353	Q3T551;B7ZLF5;O75052	.;.;CAPON_HUMAN	A	348;353;9;58;39	ENSP00000431586:V348A;ENSP00000355133:V353A	ENSP00000355133:V353A	V	+	2	0	NOS1AP;RP11-565P22.6	160601936	1.000000	0.71417	0.996000	0.52242	0.999000	0.98932	7.522000	0.81844	2.162000	0.67917	0.533000	0.62120	GTC	.	.		0.607	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697	
F5	2153	hgsc.bcm.edu	37	1	169510014	169510014	+	Silent	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:169510014G>A	ENST00000367797.3	-	13	4515	c.4314C>T	c.(4312-4314)ctC>ctT	p.L1438L	F5_ENST00000367796.3_Silent_p.L1443L	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1438	35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.				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)	TGTCTGGAGAGAGAGTCACCT	0.507																																					p.L1438L		Atlas-SNP	.											.	F5	301	.	0			c.C4314T						.						70.0	74.0	73.0					1																	169510014		2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			TGGAGAGAGAGTC	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.4314C>T	chr1.hg19:g.169510014G>A		161.0	0.0		215.0	9.0	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	hg19	CCDS1281.1																																																																																			.	.		0.507	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
TNR	7143	hgsc.bcm.edu	37	1	175375825	175375825	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:175375825A>G	ENST00000367674.2	-	3	734	c.26T>C	c.(25-27)gTt>gCt	p.V9A	TNR_ENST00000263525.2_Missense_Mutation_p.V9A			Q92752	TENR_HUMAN	tenascin R	9					associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					GTTCTTCAGAACCACTGTTTC	0.537																																					p.V9A		Atlas-SNP	.											.	TNR	399	.	0			c.T26C						.						141.0	129.0	133.0					1																	175375825		2203	4300	6503	SO:0001583	missense	7143	exon3			TTCAGAACCACTG	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.26T>C	chr1.hg19:g.175375825A>G	ENSP00000356646:p.Val9Ala	122.0	0.0		171.0	7.0	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	hg19	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	A	6.929	0.541114	0.13250	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.26223	1.75;1.75	5.56	3.25	0.37280	.	0.617832	0.16137	N	0.227903	T	0.12305	0.0299	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.005;0.0	B;B	0.09377	0.004;0.0	T	0.31916	-0.9926	10	0.12430	T	0.62	.	7.2581	0.26187	0.7401:0.0:0.2599:0.0	.	9;9	B4DIX8;Q92752	.;TENR_HUMAN	A	9	ENSP00000356646:V9A;ENSP00000263525:V9A	ENSP00000263525:V9A	V	-	2	0	TNR	173642448	0.271000	0.24162	0.526000	0.27913	0.990000	0.78478	1.234000	0.32660	0.927000	0.37143	0.459000	0.35465	GTT	.	.		0.537	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
NFASC	23114	hgsc.bcm.edu	37	1	204937944	204937944	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:204937944A>G	ENST00000401399.1	+	9	1036	c.837A>G	c.(835-837)gcA>gcG	p.A279A	NFASC_ENST00000367172.4_Silent_p.A279A|NFASC_ENST00000339876.6_Silent_p.A279A|NFASC_ENST00000367170.4_Silent_p.A279A|NFASC_ENST00000404076.1_Silent_p.A273A|NFASC_ENST00000367171.4_Silent_p.A279A|NFASC_ENST00000404907.1_Silent_p.A290A|NFASC_ENST00000360049.4_Silent_p.A290A|NFASC_ENST00000513543.1_Silent_p.A290A|NFASC_ENST00000367169.4_Silent_p.A279A|NFASC_ENST00000539706.1_Silent_p.A290A|NFASC_ENST00000403080.1_Silent_p.A279A|NFASC_ENST00000338515.6_Silent_p.A279A|NFASC_ENST00000338586.6_Silent_p.A279A			O94856	NFASC_HUMAN	neurofascin	279	Ig-like C2-type 3.				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)			CAGACATCGCATGGTACAAGA	0.512																																					p.A290A		Atlas-SNP	.											.	NFASC	396	.	0			c.A870G						.						69.0	62.0	64.0					1																	204937944		2203	4300	6503	SO:0001819	synonymous_variant	23114	exon10			CATCGCATGGTAC	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.837A>G	chr1.hg19:g.204937944A>G		87.0	0.0		100.0	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	Silent	SNP	ENST00000401399.1	hg19	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	A	9.552	1.116264	0.20795	.	.	ENSG00000163531	ENST00000367173	.	.	.	5.5	-11.0	0.00169	.	.	.	.	.	T	0.60366	0.2263	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.77448	-0.2584	4	.	.	.	.	16.347	0.83138	0.1114:0.3135:0.5751:0.0	.	.	.	.	R	249	.	.	H	+	2	0	NFASC	203204567	0.002000	0.14202	0.061000	0.19648	0.995000	0.86356	-1.564000	0.02152	-3.633000	0.00129	-0.297000	0.09499	CAT	.	.		0.512	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
LAMB3	3914	hgsc.bcm.edu	37	1	209788716	209788716	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:209788716A>G	ENST00000356082.4	-	23	3553	c.3419T>C	c.(3418-3420)aTc>aCc	p.I1140T	LAMB3_ENST00000391911.1_Missense_Mutation_p.I1140T|LAMB3_ENST00000367030.3_Missense_Mutation_p.I1140T	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	1140	Domain I.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		GCGCAGCATGATGGCCTGGCT	0.592																																					p.I1140T		Atlas-SNP	.											.	LAMB3	136	.	0			c.T3419C						.						101.0	84.0	90.0					1																	209788716		2203	4300	6503	SO:0001583	missense	3914	exon23			AGCATGATGGCCT	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.3419T>C	chr1.hg19:g.209788716A>G	ENSP00000348384:p.Ile1140Thr	75.0	0.0		98.0	4.0	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	hg19	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.147286	0.77888	.	.	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.36699	1.24;1.24;1.24	5.42	5.42	0.78866	.	0.222334	0.37715	N	0.001961	T	0.40222	0.1108	L	0.32530	0.975	0.32949	D	0.519421	D	0.57257	0.979	P	0.52554	0.702	T	0.56068	-0.8040	10	0.72032	D	0.01	.	13.6932	0.62559	1.0:0.0:0.0:0.0	.	1140	Q13751	LAMB3_HUMAN	T	1140	ENSP00000375778:I1140T;ENSP00000348384:I1140T;ENSP00000355997:I1140T	ENSP00000348384:I1140T	I	-	2	0	LAMB3	207855339	0.998000	0.40836	0.954000	0.39281	0.860000	0.49131	4.485000	0.60279	2.062000	0.61559	0.374000	0.22700	ATC	.	.		0.592	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
LAMB3	3914	hgsc.bcm.edu	37	1	209799289	209799289	+	Silent	SNP	G	G	A	rs376183751		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:209799289G>A	ENST00000356082.4	-	14	1814	c.1680C>T	c.(1678-1680)acC>acT	p.T560T	LAMB3_ENST00000391911.1_Silent_p.T560T|LAMB3_ENST00000367030.3_Silent_p.T560T|MIR4260_ENST00000583107.1_RNA	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	560	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		AGCGGGGCCCGGTCAAGCCAG	0.647																																					p.T560T		Atlas-SNP	.											LAMB3,bladder,carcinoma,0,1	LAMB3	136	.	0			c.C1680T						.	G	,,	1,4405		0,1,2202	25.0	28.0	27.0		1680,1680,1680	-10.0	0.0	1		27	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	0,1,6500	AA,AG,GG		0.0,0.0227,0.0077	,,	560/1173,560/1173,560/1173	209799289	1,13001	2203	4298	6501	SO:0001819	synonymous_variant	3914	exon14			GGGCCCGGTCAAG	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.1680C>T	chr1.hg19:g.209799289G>A		30.0	0.0		77.0	4.0	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	hg19	CCDS1487.1																																																																																			.	.		0.647	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
RPS6KC1	26750	hgsc.bcm.edu	37	1	213415488	213415488	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:213415488A>G	ENST00000366960.3	+	11	2819	c.2669A>G	c.(2668-2670)gAt>gGt	p.D890G	RPS6KC1_ENST00000366959.3_Missense_Mutation_p.D878G|RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543354.1_Missense_Mutation_p.D593G|RPS6KC1_ENST00000543470.1_Missense_Mutation_p.D678G	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	890	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GAGGACCTTGATAAAAAATTA	0.428																																					p.D890G		Atlas-SNP	.											.	RPS6KC1	114	.	0			c.A2669G						.						86.0	91.0	89.0					1																	213415488		2203	4300	6503	SO:0001583	missense	26750	exon11			ACCTTGATAAAAA	AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"""ribosomal protein S6 kinase, 52kD, polypeptide 1"""			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.2669A>G	chr1.hg19:g.213415488A>G	ENSP00000355927:p.Asp890Gly	132.0	0.0		124.0	5.0	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	hg19	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	A	17.06	3.291679	0.59976	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	5.91	4.78	0.61160	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.047787	0.85682	N	0.000000	T	0.69557	0.3124	L	0.35723	1.085	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.69691	-0.5077	10	0.51188	T	0.08	-47.1616	12.0664	0.53590	0.933:0.0:0.067:0.0	.	678;890;878	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	G	678;890;878;593	ENSP00000442306:D678G;ENSP00000355927:D890G;ENSP00000355926:D878G;ENSP00000439282:D593G	ENSP00000355926:D878G	D	+	2	0	RPS6KC1	211482111	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.495000	0.90481	1.049000	0.40321	0.533000	0.62120	GAT	.	.		0.428	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424	
DNAH14	127602	hgsc.bcm.edu	37	1	225328438	225328438	+	Intron	SNP	G	G	T	rs138066581|rs202118490|rs569277296	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:225328438G>T	ENST00000445597.2	+	17	3051				DNAH14_ENST00000430092.1_Missense_Mutation_p.R1391I|DNAH14_ENST00000439375.2_Missense_Mutation_p.R1391I			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TATAGAGAGAGATATATATAT	0.244													t|||	18	0.00359425	0.0	0.0	5008	,	,		13995	0.0169		0.0	False		,,,				2504	0.001				p.R1391I		Atlas-SNP	.											.	DNAH14	300	.	0			c.G4172T						.						9.0	7.0	7.0					1																	225328438		688	1552	2240	SO:0001627	intron_variant	127602	exon27			GAGAGAGATATAT	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.3052-32G>T	chr1.hg19:g.225328438G>T		21.0	0.0		28.0	13.0	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	hg19		.	.	.	.	.	.	.	.	.	.	g	4.743	0.138195	0.09083	.	.	ENSG00000185842	ENST00000430092;ENST00000439375	T;T	0.33216	1.42;1.42	5.46	0.51	0.16983	.	.	.	.	.	T	0.23014	0.0556	L	0.43923	1.385	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21861	-1.0233	9	0.39692	T	0.17	.	6.4194	0.21736	0.0:0.227:0.1318:0.6412	.	1391	Q0VDD8-4	.	I	1391	ENSP00000414402:R1391I;ENSP00000392061:R1391I	ENSP00000414402:R1391I	R	+	2	0	DNAH14	223395061	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.134000	0.15932	-0.174000	0.10743	-2.900000	0.00093	AGA	.	.		0.244	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232650005	232650005	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:232650005C>A	ENST00000366630.1	-	2	1439	c.1081G>T	c.(1081-1083)Gca>Tca	p.A361S	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.A361S			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	361					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GCTGCAGATGCCCCAGTGGTT	0.488																																					p.A361S		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.G1081T						.						101.0	103.0	103.0					1																	232650005		1952	4136	6088	SO:0001583	missense	57568	exon1			CAGATGCCCCAGT	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.1081G>T	chr1.hg19:g.232650005C>A	ENSP00000355589:p.Ala361Ser	61.0	0.0		70.0	48.0	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.694733	0.88830	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	D;D	0.91577	-2.87;-2.87	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.95472	0.8529	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95411	0.8498	10	0.72032	D	0.01	-26.4199	19.3561	0.94414	0.0:1.0:0.0:0.0	.	361	Q9P2F8	SI1L2_HUMAN	S	361	ENSP00000355589:A361S;ENSP00000262861:A361S	ENSP00000262861:A361S	A	-	1	0	SIPA1L2	230716628	1.000000	0.71417	0.938000	0.37757	0.992000	0.81027	7.651000	0.83577	2.810000	0.96702	0.650000	0.86243	GCA	.	.		0.488	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
SH3BP5L	80851	hgsc.bcm.edu	37	1	249106273	249106273	+	Silent	SNP	C	C	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr1:249106273C>G	ENST00000366472.5	-	7	2237	c.1008G>C	c.(1006-1008)ctG>ctC	p.L336L	SH3BP5L_ENST00000411742.2_Silent_p.L304L|SH3BP5L_ENST00000475978.1_5'UTR	NM_030645.1	NP_085148.1	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	336										endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			TGCGCAGGCTCAGCAGACTCA	0.692																																					p.L336L		Atlas-SNP	.											.	SH3BP5L	47	.	0			c.G1008C						.						21.0	27.0	25.0					1																	249106273		2198	4296	6494	SO:0001819	synonymous_variant	80851	exon7			CAGGCTCAGCAGA	AB051507	CCDS31126.1	1q44	2008-02-05			ENSG00000175137	ENSG00000175137			29360	protein-coding gene	gene with protein product							Standard	NM_030645		Approved	KIAA1720	uc001iew.1	Q7L8J4	OTTHUMG00000040389	ENST00000366472.5:c.1008G>C	chr1.hg19:g.249106273C>G		63.0	0.0		83.0	12.0	NM_030645	B4DQ94|Q96FI5|Q9BQH8|Q9C0E3	Silent	SNP	ENST00000366472.5	hg19	CCDS31126.1																																																																																			.	.		0.692	SH3BP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097140.1	NM_030645	
PXDN	7837	hgsc.bcm.edu	37	2	1664712	1664712	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:1664712T>C	ENST00000252804.4	-	14	1828	c.1778A>G	c.(1777-1779)gAg>gGg	p.E593G		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	593	Ig-like C2-type 4.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GGCCACACACTCATAGCGACC	0.537																																					p.E593G		Atlas-SNP	.											.	PXDN	255	.	0			c.A1778G						.						97.0	102.0	100.0					2																	1664712		2055	4191	6246	SO:0001583	missense	7837	exon14			ACACACTCATAGC	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1778A>G	chr2.hg19:g.1664712T>C	ENSP00000252804:p.Glu593Gly	78.0	0.0		75.0	4.0	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	hg19	CCDS46221.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.65|17.65	3.442826|3.442826	0.63067|0.63067	.|.	.|.	ENSG00000130508|ENSG00000130508	ENST00000252804|ENST00000433670	T|.	0.77620|.	-1.11|.	5.05|5.05	5.05|5.05	0.67936|0.67936	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.063286|.	0.64402|.	N|.	0.000007|.	T|T	0.53110|0.53110	0.1776|0.1776	N|N	0.25380|0.25380	0.74|0.74	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.997|.	D;D|.	0.79108|.	0.991;0.992|.	T|T	0.50162|0.50162	-0.8860|-0.8860	10|5	0.87932|.	D|.	0|.	-46.6424|-46.6424	15.0638|15.0638	0.71977|0.71977	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	593;593|.	Q92626-2;Q92626|.	.;PXDN_HUMAN|.	G|G	593|589	ENSP00000252804:E593G|.	ENSP00000252804:E593G|.	E|S	-|-	2|1	0|0	PXDN|PXDN	1643719|1643719	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.027000|0.027000	0.11550|0.11550	7.908000|7.908000	0.87438|0.87438	2.028000|2.028000	0.59812|0.59812	0.482000|0.482000	0.46254|0.46254	GAG|AGT	.	.		0.537	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
ASAP2	8853	hgsc.bcm.edu	37	2	9531316	9531316	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:9531316A>G	ENST00000281419.3	+	23	2849	c.2509A>G	c.(2509-2511)Aca>Gca	p.T837A	ASAP2_ENST00000491413.1_Intron|ASAP2_ENST00000315273.4_Intron	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	837	Pro-rich.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						TCTTCGCGTGACATCTACCAG	0.572																																					p.T837A		Atlas-SNP	.											.	ASAP2	91	.	0			c.A2509G						.						154.0	157.0	156.0					2																	9531316		2203	4300	6503	SO:0001583	missense	8853	exon23			CGCGTGACATCTA	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	2721	protein-coding gene	gene with protein product	"""centaurin, beta 3"""	603817	"""development and differentiation enhancing factor 2"""	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2509A>G	chr2.hg19:g.9531316A>G	ENSP00000281419:p.Thr837Ala	113.0	0.0		99.0	4.0	NM_003887	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	hg19	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.222354	0.58560	.	.	ENSG00000151693	ENST00000281419	T	0.56941	0.43	4.36	3.2	0.36748	.	0.646852	0.13487	N	0.384258	T	0.29389	0.0732	N	0.08118	0	0.80722	D	1	P	0.36027	0.533	B	0.34536	0.185	T	0.03060	-1.1077	10	0.21014	T	0.42	.	9.8219	0.40887	0.918:0.0:0.082:0.0	.	837	O43150	ASAP2_HUMAN	A	837	ENSP00000281419:T837A	ENSP00000281419:T837A	T	+	1	0	ASAP2	9448767	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.921000	0.56454	0.838000	0.34948	0.254000	0.18369	ACA	.	.		0.572	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887	
KLF11	8462	hgsc.bcm.edu	37	2	10188645	10188645	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:10188645A>G	ENST00000305883.1	+	3	1343	c.1181A>G	c.(1180-1182)tAt>tGt	p.Y394C	KLF11_ENST00000540845.1_Missense_Mutation_p.Y377C|KLF11_ENST00000535335.1_Missense_Mutation_p.Y377C	NM_003597.4	NP_003588.1	O14901	KLF11_HUMAN	Kruppel-like factor 11	394					apoptotic process (GO:0006915)|cellular response to peptide (GO:1901653)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.133)|OV - Ovarian serous cystadenocarcinoma(76;0.228)		AGGAGGAACTATGTATGCAGC	0.552											OREG0014425	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y394C	Melanoma(56;431 1507 23687 50789)	Atlas-SNP	.											.	KLF11	45	.	0			c.A1181G						.						93.0	93.0	93.0					2																	10188645		2203	4300	6503	SO:0001583	missense	8462	exon3			GGAACTATGTATG	AF028008	CCDS1668.1, CCDS54333.1	2p25	2013-01-08	2004-11-29	2004-12-01	ENSG00000172059	ENSG00000172059		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	11811	protein-coding gene	gene with protein product		603301	"""TGFB inducible early growth response 2"""	TIEG2		9748269, 11087666	Standard	NM_001177716		Approved	Tieg3, MODY7	uc002raf.1	O14901	OTTHUMG00000119004	ENST00000305883.1:c.1181A>G	chr2.hg19:g.10188645A>G	ENSP00000307023:p.Tyr394Cys	81.0	0.0	662	78.0	4.0	NM_003597	B4DZE7|Q9EPF4	Missense_Mutation	SNP	ENST00000305883.1	hg19	CCDS1668.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.492158	0.64074	.	.	ENSG00000172059	ENST00000305883;ENST00000540845;ENST00000535335	T;T;T	0.18960	2.18;2.18;2.18	5.51	5.51	0.81932	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.51550	0.1681	M	0.85197	2.74	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.57573	-0.7788	9	.	.	.	.	15.6141	0.76750	1.0:0.0:0.0:0.0	.	394	O14901	KLF11_HUMAN	C	394;377;377	ENSP00000307023:Y394C;ENSP00000444690:Y377C;ENSP00000442722:Y377C	.	Y	+	2	0	KLF11	10106096	1.000000	0.71417	0.529000	0.27951	0.495000	0.33615	9.291000	0.96070	2.094000	0.63399	0.172000	0.16884	TAT	.	.		0.552	KLF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000239202.3	NM_003597	
PDIA6	10130	hgsc.bcm.edu	37	2	10925108	10925108	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:10925108A>G	ENST00000272227.3	-	12	1353	c.1206T>C	c.(1204-1206)gcT>gcC	p.A402A	PDIA6_ENST00000404371.2_Silent_p.A454A|PDIA6_ENST00000381611.4_Silent_p.A407A|ATP6V1C2_ENST00000381661.3_3'UTR|PDIA6_ENST00000540494.1_Silent_p.A399A|PDIA6_ENST00000404824.2_Silent_p.A450A	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	402					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		TGGTAGGGAAAGCCCCGCCTC	0.572																																					p.A402A	GBM(73;509 1219 34219 41343 41551)	Atlas-SNP	.											.	PDIA6	31	.	0			c.T1206C						.						34.0	30.0	31.0					2																	10925108		2201	4296	6497	SO:0001819	synonymous_variant	10130	exon12			AGGGAAAGCCCCG	BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	5.3.4.1	"""Protein disulfide isomerases"""	30168	protein-coding gene	gene with protein product	"""protein disulfide isomerase-related protein"""	611099	"""thioredoxin domain containing 7 (protein disulfide isomerase)"", ""protein disulfide isomerase-associated 6"""	TXNDC7		7590364, 12204115	Standard	XM_005246145		Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000272227.3:c.1206T>C	chr2.hg19:g.10925108A>G		88.0	0.0		79.0	4.0	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000272227.3	hg19	CCDS1675.1																																																																																			.	.		0.572	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742	
GREB1	9687	hgsc.bcm.edu	37	2	11772120	11772120	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:11772120A>G	ENST00000381486.2	+	27	4997	c.4697A>G	c.(4696-4698)gAc>gGc	p.D1566G	GREB1_ENST00000234142.5_Missense_Mutation_p.D1566G|GREB1_ENST00000396123.1_Missense_Mutation_p.D564G	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1566						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)		CACGCAATGGACGGTGCCAGC	0.478																																					p.D1566G	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.A4697G						.						97.0	96.0	97.0					2																	11772120		1984	4149	6133	SO:0001583	missense	9687	exon27			CAATGGACGGTGC		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.4697A>G	chr2.hg19:g.11772120A>G	ENSP00000370896:p.Asp1566Gly	187.0	0.0		146.0	6.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	A	19.59	3.855327	0.71719	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.50001	0.76;0.76;0.76	5.48	5.48	0.80851	.	0.046725	0.85682	D	0.000000	T	0.49253	0.1546	M	0.61703	1.905	0.80722	D	1	P	0.36110	0.537	B	0.36959	0.237	T	0.53920	-0.8370	10	0.59425	D	0.04	-30.0742	15.552	0.76161	1.0:0.0:0.0:0.0	.	1566	Q4ZG55	GREB1_HUMAN	G	1566;1566;564	ENSP00000370896:D1566G;ENSP00000234142:D1566G;ENSP00000379429:D564G	ENSP00000234142:D1566G	D	+	2	0	GREB1	11689571	1.000000	0.71417	0.919000	0.36401	0.442000	0.32017	8.837000	0.92110	2.079000	0.62486	0.455000	0.32223	GAC	.	.		0.478	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
DDX1	1653	hgsc.bcm.edu	37	2	15746378	15746378	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:15746378A>G	ENST00000381341.2	+	13	1196	c.807A>G	c.(805-807)tcA>tcG	p.S269S	DDX1_ENST00000233084.3_Silent_p.S269S			Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 1	269	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Necessary for interaction with HNRNPK.|Necessary for interaction with RELA.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|multicellular organismal development (GO:0007275)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translational initiation (GO:0006446)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	cleavage body (GO:0071920)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|tRNA-splicing ligase complex (GO:0072669)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA/RNA helicase activity (GO:0033677)|double-stranded RNA binding (GO:0003725)|exonuclease activity (GO:0004527)|nuclease activity (GO:0004518)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|transcription cofactor activity (GO:0003712)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(13)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		TTGTCAAATCACAGCACTCAG	0.393																																					p.S269S		Atlas-SNP	.											.	DDX1	70	.	0			c.A807G						.						64.0	59.0	61.0					2																	15746378		2203	4300	6503	SO:0001819	synonymous_variant	1653	exon12			CAAATCACAGCAC	X70649	CCDS1686.1	2p24	2012-02-23	2012-02-23		ENSG00000079785	ENSG00000079785		"""DEAD-boxes"""	2734	protein-coding gene	gene with protein product		601257	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 1"""			1552844, 19058135	Standard	NM_004939		Approved	DBP-RB	uc002rce.4	Q92499	OTTHUMG00000090593	ENST00000381341.2:c.807A>G	chr2.hg19:g.15746378A>G		158.0	0.0		149.0	6.0	NM_004939	B4DME8|B4DPN6	Silent	SNP	ENST00000381341.2	hg19	CCDS1686.1																																																																																			.	.		0.393	DDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207141.2	NM_004939	
SMC6	79677	hgsc.bcm.edu	37	2	17922879	17922879	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:17922879T>C	ENST00000448223.2	-	4	507	c.238A>G	c.(238-240)Agt>Ggt	p.S80G	SMC6_ENST00000402989.1_Splice_Site_p.S80G|SMC6_ENST00000351948.4_Splice_Site_p.S80G|SMC6_ENST00000381272.4_Splice_Site_p.S80G	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	80					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AAACACTTACTTCCATTGTTG	0.323																																					p.S80G		Atlas-SNP	.											.	SMC6	102	.	0			c.A238G						.						127.0	127.0	127.0					2																	17922879		2203	4300	6503	SO:0001630	splice_region_variant	79677	exon4			ACTTACTTCCATT	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"""Structural maintenance of chromosomes proteins"""	20466	protein-coding gene	gene with protein product		609387	"""SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"""	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.238+1A>G	chr2.hg19:g.17922879T>C		79.0	0.0		60.0	4.0	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	hg19	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	T	33	5.246391	0.95305	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.79845	-1.31;-1.31;1.99;-1.31;1.99	5.89	5.89	0.94794	RecF/RecN/SMC (1);	0.114600	0.85682	D	0.000000	D	0.88858	0.6551	M	0.75615	2.305	0.80722	D	1	P;D;P	0.58268	0.939;0.982;0.883	P;D;P	0.70227	0.783;0.968;0.835	D	0.88900	0.3352	9	.	.	.	.	15.2952	0.73898	0.0:0.0:0.0:1.0	.	80;80;80	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	G	80	ENSP00000404092:S80G;ENSP00000323439:S80G;ENSP00000370672:S80G;ENSP00000384539:S80G;ENSP00000408644:S80G	.	S	-	1	0	SMC6	17786360	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.622000	0.83099	2.246000	0.74042	0.533000	0.62120	AGT	.	.		0.323	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624	Missense_Mutation
ASXL2	55252	hgsc.bcm.edu	37	2	25965337	25965337	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:25965337C>G	ENST00000435504.4	-	13	4162	c.3869G>C	c.(3868-3870)aGt>aCt	p.S1290T	ASXL2_ENST00000336112.4_Missense_Mutation_p.S1262T|ASXL2_ENST00000272341.4_Missense_Mutation_p.S773T|ASXL2_ENST00000404843.1_Missense_Mutation_p.S773T			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	1290					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AACAGTAGAACTGAAAAGCTC	0.542																																					p.S1290T		Atlas-SNP	.											.	ASXL2	217	.	0			c.G3869C						.						38.0	40.0	39.0					2																	25965337		1944	4128	6072	SO:0001583	missense	55252	exon12			GTAGAACTGAAAA			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"""additional sex combs like 2 (Drosophila)"""			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.3869G>C	chr2.hg19:g.25965337C>G	ENSP00000391447:p.Ser1290Thr	187.0	0.0		138.0	10.0	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	hg19		.	.	.	.	.	.	.	.	.	.	T	11.82	1.752668	0.31046	.	.	ENSG00000143970	ENST00000435504;ENST00000336112;ENST00000404843;ENST00000272341	T;T;T;T	0.18960	2.2;2.2;2.18;2.18	4.79	-9.57	0.00562	.	1.174300	0.05956	N	0.639799	T	0.13628	0.0330	N	0.19112	0.55	0.09310	N	1	P;B	0.46220	0.874;0.094	B;B	0.44163	0.443;0.026	T	0.30650	-0.9971	10	0.20046	T	0.44	1.5602	14.0348	0.64638	0.0778:0.7438:0.0785:0.1	.	773;1290	Q76L83-2;Q76L83	.;ASXL2_HUMAN	T	1290;1262;773;773	ENSP00000391447:S1290T;ENSP00000337250:S1262T;ENSP00000383920:S773T;ENSP00000272341:S773T	ENSP00000272341:S773T	S	-	2	0	ASXL2	25818841	0.000000	0.05858	0.000000	0.03702	0.935000	0.57460	-2.133000	0.01308	-3.216000	0.00213	-0.254000	0.11334	AGT	.	.		0.542	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263	
CGREF1	10669	hgsc.bcm.edu	37	2	27325406	27325406	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:27325406T>C	ENST00000260595.5	-	3	426	c.134A>G	c.(133-135)cAg>cGg	p.Q45R	CGREF1_ENST00000404694.3_Missense_Mutation_p.Q167R|CGREF1_ENST00000402550.1_Missense_Mutation_p.Q45R|CGREF1_ENST00000452318.2_5'UTR|CGREF1_ENST00000312734.4_Missense_Mutation_p.Q45R|CGREF1_ENST00000402394.1_Missense_Mutation_p.Q45R|CGREF1_ENST00000405600.1_Missense_Mutation_p.Q45R			Q99674	CGRE1_HUMAN	cell growth regulator with EF-hand domain 1	45					cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			kidney(1)|lung(4)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAGCTGCTCCTGGCCTGGCTG	0.642																																					p.Q45R		Atlas-SNP	.											.	CGREF1	31	.	0			c.A134G						.						52.0	57.0	56.0					2																	27325406		2203	4300	6503	SO:0001583	missense	10669	exon3			TGCTCCTGGCCTG	BC034764	CCDS33162.1, CCDS33162.2, CCDS54339.1	2p23.3	2013-01-10			ENSG00000138028	ENSG00000138028		"""EF-hand domain containing"""	16962	protein-coding gene	gene with protein product		606137				8968090	Standard	NM_006569		Approved	CGR11	uc002riq.3	Q99674	OTTHUMG00000152009	ENST00000260595.5:c.134A>G	chr2.hg19:g.27325406T>C	ENSP00000260595:p.Gln45Arg	68.0	0.0		74.0	4.0	NM_001166239	A6NHV7|B4DXY8|B5MCB7|B5MCC9|B5MCP5|E7EU99|Q8N4B7	Missense_Mutation	SNP	ENST00000260595.5	hg19		.	.	.	.	.	.	.	.	.	.	T	2.145	-0.395939	0.04899	.	.	ENSG00000138028	ENST00000402550;ENST00000402394;ENST00000405600;ENST00000389521;ENST00000312734;ENST00000404694;ENST00000260595	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.27	-10.5	0.00291	.	1.639240	0.03276	N	0.185498	T	0.15435	0.0372	N	0.24115	0.695	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.07102	-1.0790	10	0.14252	T	0.57	-15.0524	8.452	0.32877	0.0771:0.1376:0.5791:0.2063	.	167;45;45	B5MCC9;B5MCP5;Q99674	.;.;CGRE1_HUMAN	R	45;45;45;45;45;167;45	ENSP00000385452:Q45R;ENSP00000386113:Q45R;ENSP00000324025:Q45R;ENSP00000385574:Q167R;ENSP00000260595:Q45R	ENSP00000260595:Q45R	Q	-	2	0	CGREF1	27178910	0.001000	0.12720	0.001000	0.08648	0.021000	0.10359	-0.448000	0.06820	-2.171000	0.00775	-3.722000	0.00023	CAG	.	.		0.642	CGREF1-201	KNOWN	basic	protein_coding	protein_coding		NM_006569	
CAD	790	hgsc.bcm.edu	37	2	27458485	27458485	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:27458485T>C	ENST00000403525.1	+	24	4006	c.3862T>C	c.(3862-3864)Ttc>Ctc	p.F1288L	CAD_ENST00000264705.4_Missense_Mutation_p.F1351L			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACAGCTGACTTCTACACTGA	0.542																																					p.F1351L		Atlas-SNP	.											.	CAD	199	.	0			c.T4051C						.						61.0	59.0	60.0					2																	27458485		2203	4300	6503	SO:0001583	missense	790	exon25			GCTGACTTCTACA	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.3862T>C	chr2.hg19:g.27458485T>C	ENSP00000384510:p.Phe1288Leu	107.0	0.0		112.0	6.0	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	hg19		.	.	.	.	.	.	.	.	.	.	T	34	5.361358	0.95877	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	T;T	0.81078	-1.45;-1.45	4.82	4.82	0.62117	Methylglyoxal synthase-like domain (4);	0.043580	0.85682	D	0.000000	D	0.89577	0.6755	M	0.82517	2.595	0.80722	D	1	D;D	0.69078	0.968;0.997	P;D	0.77004	0.885;0.989	D	0.91146	0.4949	10	0.87932	D	0	-2.118	13.529	0.61611	0.0:0.0:0.0:1.0	.	1288;1351	F8VPD4;P27708	.;PYR1_HUMAN	L	1351;1288	ENSP00000264705:F1351L;ENSP00000384510:F1288L	ENSP00000264705:F1351L	F	+	1	0	CAD	27311989	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.268000	0.78473	1.941000	0.56285	0.459000	0.35465	TTC	.	.		0.542	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		
C2orf16	84226	hgsc.bcm.edu	37	2	27802654	27802654	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:27802654T>C	ENST00000408964.2	+	1	3266	c.3215T>C	c.(3214-3216)cTt>cCt	p.L1072P	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1072						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CCAAATTATCTTTCCCAGGCC	0.443																																					p.L1072P		Atlas-SNP	.											.	C2orf16	357	.	0			c.T3215C						.						121.0	121.0	121.0					2																	27802654		1913	4135	6048	SO:0001583	missense	84226	exon1			ATTATCTTTCCCA	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.3215T>C	chr2.hg19:g.27802654T>C	ENSP00000386190:p.Leu1072Pro	142.0	0.0		108.0	5.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	hg19	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	T	8.403	0.842421	0.16963	.	.	ENSG00000221843	ENST00000408964	T	0.15139	2.45	5.12	1.46	0.22682	.	.	.	.	.	T	0.12390	0.0301	L	0.29908	0.895	0.09310	N	0.999994	B	0.19073	0.033	B	0.22601	0.04	T	0.29305	-1.0016	9	0.87932	D	0	.	6.168	0.20400	0.0:0.3087:0.0:0.6912	.	1072	Q68DN1	CB016_HUMAN	P	1072	ENSP00000386190:L1072P	ENSP00000386190:L1072P	L	+	2	0	C2orf16	27656158	0.003000	0.15002	0.006000	0.13384	0.010000	0.07245	1.089000	0.30890	0.290000	0.22444	0.260000	0.18958	CTT	.	.		0.443	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
C2orf16	84226	hgsc.bcm.edu	37	2	27803186	27803186	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:27803186A>G	ENST00000408964.2	+	1	3798	c.3747A>G	c.(3745-3747)agA>agG	p.R1249R	RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000416005.2_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000379717.1_5'Flank|ZNF512_ENST00000355467.4_5'Flank|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1249						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CAAAAACTAGAGCACCTGGGC	0.473																																					p.R1249R		Atlas-SNP	.											.	C2orf16	357	.	0			c.A3747G						.						109.0	108.0	108.0					2																	27803186		1867	4116	5983	SO:0001819	synonymous_variant	84226	exon1			AACTAGAGCACCT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.3747A>G	chr2.hg19:g.27803186A>G		161.0	0.0		116.0	5.0	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	hg19	CCDS42666.1																																																																																			.	.		0.473	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
CCDC121	79635	hgsc.bcm.edu	37	2	27851424	27851424	+	Intron	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:27851424G>A	ENST00000324364.3	-	1	63				GPN1_ENST00000503738.1_5'Flank|CCDC121_ENST00000394775.3_Silent_p.P69P|GPN1_ENST00000458167.2_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|GPN1_ENST00000610189.1_5'Flank|GPN1_ENST00000407583.3_5'Flank|GPN1_ENST00000424214.1_5'Flank|GPN1_ENST00000515877.1_5'UTR|GPN1_ENST00000264718.3_5'Flank|ZNF512_ENST00000556601.1_Intron	NM_024584.4	NP_078860.2	Q6ZUS5	CC121_HUMAN	coiled-coil domain containing 121											breast(1)|endometrium(3)|large_intestine(2)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(172;0.155)					GGTGCTCAAAGGGTCTCGGTG	0.582																																					p.P69P		Atlas-SNP	.											.	CCDC121	43	.	0			c.C207T						.						41.0	39.0	40.0					2																	27851424		692	1591	2283	SO:0001627	intron_variant	79635	exon1			CTCAAAGGGTCTC	AK125354	CCDS1759.1, CCDS46247.1	2p23.2	2008-02-05			ENSG00000176714	ENSG00000176714			25833	protein-coding gene	gene with protein product							Standard	NM_024584		Approved	FLJ43364, FLJ13646	uc002rld.3	Q6ZUS5	OTTHUMG00000128427	ENST00000324364.3:c.117+392C>T	chr2.hg19:g.27851424G>A		153.0	0.0		123.0	5.0	NM_001142683	B3KW66|J3KQZ8|Q9H8G6	Silent	SNP	ENST00000324364.3	hg19	CCDS1759.1																																																																																			.	.		0.582	CCDC121-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250215.1	NM_024584	
RBKS	64080	hgsc.bcm.edu	37	2	28004570	28004570	+	Missense_Mutation	SNP	G	G	T	rs200310841		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:28004570G>T	ENST00000302188.3	-	8	1633	c.881C>A	c.(880-882)tCc>tAc	p.S294Y	AC110084.1_ENST00000601759.1_Intron	NM_022128.1	NP_071411.1	Q9H477	RBSK_HUMAN	ribokinase	294					D-ribose catabolic process (GO:0019303)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ribokinase activity (GO:0004747)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7	Acute lymphoblastic leukemia(172;0.155)					AATGAAATTGGATCTGTTGAG	0.458																																					p.S294Y		Atlas-SNP	.											.	RBKS	23	.	0			c.C881A						.						132.0	129.0	130.0					2																	28004570		2203	4300	6503	SO:0001583	missense	64080	exon8			AAATTGGATCTGT	BC017425	CCDS1762.1	2p23.3	2008-02-05			ENSG00000171174	ENSG00000171174	2.7.1.15		30325	protein-coding gene	gene with protein product		611132				8382990	Standard	NM_022128		Approved	DKFZp686G13268, RBSK	uc002rlo.1	Q9H477	OTTHUMG00000097833	ENST00000302188.3:c.881C>A	chr2.hg19:g.28004570G>T	ENSP00000306817:p.Ser294Tyr	146.0	0.0		83.0	4.0	NM_022128	A9UK04|B4DV96	Missense_Mutation	SNP	ENST00000302188.3	hg19	CCDS1762.1	.	.	.	.	.	.	.	.	.	.	G	19.49	3.837587	0.71373	.	.	ENSG00000171174	ENST00000302188	T	0.77877	-1.13	5.66	5.66	0.87406	Carbohydrate/purine kinase (1);	0.158108	0.56097	D	0.000025	D	0.87497	0.6192	M	0.75615	2.305	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.88509	0.3088	10	0.87932	D	0	-8.4338	16.4964	0.84246	0.0:0.197:0.803:0.0	.	294	Q9H477	RBSK_HUMAN	Y	294	ENSP00000306817:S294Y	ENSP00000306817:S294Y	S	-	2	0	RBKS	27858074	1.000000	0.71417	0.999000	0.59377	0.730000	0.41778	5.343000	0.65976	2.656000	0.90262	0.655000	0.94253	TCC	.	.		0.458	RBKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215118.1	NM_022128	
XDH	7498	hgsc.bcm.edu	37	2	31604573	31604573	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:31604573A>G	ENST00000379416.3	-	12	1106	c.1058T>C	c.(1057-1059)aTc>aCc	p.I353T	XDH_ENST00000491727.1_5'Flank	NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	353	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	GCTGGCAGTGATGATGTTCCC	0.587																																					p.I353T	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.T1058C						.						93.0	86.0	88.0					2																	31604573		2203	4300	6503	SO:0001583	missense	7498	exon12			GCAGTGATGATGT	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.1058T>C	chr2.hg19:g.31604573A>G	ENSP00000368727:p.Ile353Thr	105.0	0.0		92.0	4.0	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	hg19	CCDS1775.1	.	.	.	.	.	.	.	.	.	.	A	17.62	3.433643	0.62955	.	.	ENSG00000158125	ENST00000379416	T	0.22134	1.97	5.96	5.96	0.96718	FAD-binding, type 2 (2);CO dehydrogenase flavoprotein-like, FAD-binding, subdomain 2 (1);Xanthine dehydrogenase, small subunit (1);Molybdopterin dehydrogenase, FAD-binding (1);	0.039194	0.85682	D	0.000000	T	0.31295	0.0792	M	0.76170	2.325	0.58432	D	0.999998	B	0.22983	0.078	B	0.30029	0.11	T	0.06162	-1.0842	10	0.56958	D	0.05	.	15.2697	0.73689	1.0:0.0:0.0:0.0	.	353	P47989	XDH_HUMAN	T	353	ENSP00000368727:I353T	ENSP00000368727:I353T	I	-	2	0	XDH	31458077	1.000000	0.71417	0.986000	0.45419	0.910000	0.53928	8.632000	0.90995	2.282000	0.76494	0.450000	0.29827	ATC	.	.		0.587	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
SLC30A6	55676	hgsc.bcm.edu	37	2	32399138	32399138	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:32399138A>G	ENST00000282587.5	+	3	134	c.97A>G	c.(97-99)Aag>Gag	p.K33E	SLC30A6_ENST00000406369.1_Intron|SLC30A6_ENST00000357055.3_5'UTR|SLC30A6_ENST00000379343.2_Missense_Mutation_p.K33E|SLC30A6_ENST00000435660.1_Missense_Mutation_p.K33E|SLC30A6_ENST00000538303.1_Missense_Mutation_p.K4E	NM_017964.3	NP_060434.2	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter), member 6	33					cellular protein metabolic process (GO:0044267)|Golgi to endosome transport (GO:0006895)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(4)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					ACAGTCCTGGAAGATACTGCT	0.348																																					p.K33E		Atlas-SNP	.											.	SLC30A6	37	.	0			c.A97G						.						198.0	187.0	191.0					2																	32399138		2203	4300	6503	SO:0001583	missense	55676	exon3			TCCTGGAAGATAC	AK055663	CCDS1780.1, CCDS54341.1, CCDS54342.1, CCDS54343.1	2p22.3	2013-05-22			ENSG00000152683	ENSG00000152683		"""Solute carriers"""	19305	protein-coding gene	gene with protein product		611148					Standard	NM_017964		Approved	FLJ31101, ZNT6	uc002rof.2	Q6NXT4	OTTHUMG00000128456	ENST00000282587.5:c.97A>G	chr2.hg19:g.32399138A>G	ENSP00000282587:p.Lys33Glu	367.0	0.0		271.0	103.0	NM_001193513	A5YM45|B7Z901|Q8N5C9|Q96NC3	Missense_Mutation	SNP	ENST00000282587.5	hg19	CCDS1780.1	.	.	.	.	.	.	.	.	.	.	A	16.75	3.210719	0.58343	.	.	ENSG00000152683	ENST00000379343;ENST00000440718;ENST00000282587;ENST00000435660;ENST00000538303	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.09	5.09	0.68999	.	0.105147	0.64402	D	0.000005	T	0.49915	0.1585	L	0.27053	0.805	0.80722	D	1	B;B;B;B	0.24882	0.007;0.113;0.036;0.017	B;B;B;B	0.22601	0.011;0.04;0.037;0.011	T	0.49570	-0.8926	10	0.49607	T	0.09	-4.316	13.8575	0.63537	1.0:0.0:0.0:0.0	.	4;33;33;33	B7Z901;Q6NXT4-3;Q6NXT4-2;Q6NXT4	.;.;.;ZNT6_HUMAN	E	33;4;33;33;4	ENSP00000393946:K4E;ENSP00000282587:K33E;ENSP00000399005:K33E;ENSP00000440678:K4E	ENSP00000282587:K33E	K	+	1	0	SLC30A6	32252642	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.237000	0.78164	1.909000	0.55274	0.460000	0.39030	AAG	.	.		0.348	SLC30A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250254.2		
STRN	6801	hgsc.bcm.edu	37	2	37094974	37094974	+	Nonsense_Mutation	SNP	A	A	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:37094974A>T	ENST00000263918.4	-	12	1538	c.1530T>A	c.(1528-1530)taT>taA	p.Y510*	STRN_ENST00000379213.2_Nonsense_Mutation_p.Y461*|RNU6-577P_ENST00000516947.1_RNA	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	510					dendrite development (GO:0016358)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|tight junction assembly (GO:0070830)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|estrogen receptor binding (GO:0030331)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)	p.Y510*(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33		Ovarian(717;0.0129)|all_hematologic(82;0.21)				CTCTGAATGTATAGATAGGTT	0.299																																					p.Y510X		Atlas-SNP	.											STRN,extremity,malignant_melanoma,0,1	STRN	71	.	1	Substitution - Nonsense(1)	skin(1)	c.T1530A						.						102.0	107.0	105.0					2																	37094974		2203	4292	6495	SO:0001587	stop_gained	6801	exon12			GAATGTATAGATA	AJ223814	CCDS1784.1	2p22.2	2013-01-10	2001-11-28		ENSG00000115808	ENSG00000115808		"""WD repeat domain containing"""	11424	protein-coding gene	gene with protein product		614765	"""striatin, calmodulin-binding protein"""			9693043, 8769426	Standard	NM_003162		Approved	SG2NA	uc002rpn.3	O43815	OTTHUMG00000100959	ENST00000263918.4:c.1530T>A	chr2.hg19:g.37094974A>T	ENSP00000263918:p.Tyr510*	91.0	0.0		65.0	3.0	NM_003162	Q3KP65|Q53TQ8|Q9NP38	Nonsense_Mutation	SNP	ENST00000263918.4	hg19	CCDS1784.1	.	.	.	.	.	.	.	.	.	.	A	37	6.265639	0.97426	.	.	ENSG00000115808	ENST00000263918;ENST00000538092;ENST00000379213	.	.	.	5.29	1.53	0.23141	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.7655	8.3881	0.32512	0.7046:0.0:0.2954:0.0	.	.	.	.	X	510;485;461	.	ENSP00000263918:Y510X	Y	-	3	2	STRN	36948478	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	2.401000	0.44513	0.020000	0.15106	-0.250000	0.11733	TAT	.	.		0.299	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1		
NRXN1	9378	hgsc.bcm.edu	37	2	51254792	51254792	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:51254792T>C	ENST00000406316.2	-	2	2096	c.620A>G	c.(619-621)gAg>gGg	p.E207G	NRXN1_ENST00000405472.3_Missense_Mutation_p.E207G|NRXN1_ENST00000401669.2_Missense_Mutation_p.E207G|NRXN1_ENST00000406859.3_Missense_Mutation_p.E207G|NRXN1_ENST00000405581.1_Missense_Mutation_p.E207G|NRXN1_ENST00000402717.3_Missense_Mutation_p.E207G|NRXN1_ENST00000404971.1_Missense_Mutation_p.E207G	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	207	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GTTGGGCGGCTCATCGTCCAG	0.697																																					p.E207G		Atlas-SNP	.											.	NRXN1	1118	.	0			c.A620G						.						18.0	23.0	21.0					2																	51254792		2050	4175	6225	SO:0001583	missense	9378	exon2			GGCGGCTCATCGT	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.620A>G	chr2.hg19:g.51254792T>C	ENSP00000384311:p.Glu207Gly	119.0	0.0		114.0	5.0	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.976948	0.74360	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859;ENST00000405581	T;T;T;T;T;T;T	0.71461	0.12;0.11;-0.57;-0.46;-0.17;-0.03;3.32	5.5	5.5	0.81552	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.835445	0.09637	U	0.775557	D	0.82783	0.5112	M	0.65975	2.015	0.42561	D	0.993145	B;D;B	0.67145	0.0;0.996;0.001	B;D;B	0.66497	0.002;0.944;0.002	T	0.76515	-0.2931	10	0.36615	T	0.2	.	15.6222	0.76816	0.0:0.0:0.0:1.0	.	207;207;207	Q9ULB1-3;F8WB18;Q9ULB1	.;.;NRX1A_HUMAN	G	207	ENSP00000385142:E207G;ENSP00000384311:E207G;ENSP00000434015:E207G;ENSP00000385017:E207G;ENSP00000385434:E207G;ENSP00000385681:E207G;ENSP00000385310:E207G	ENSP00000385017:E207G	E	-	2	0	NRXN1	51108296	0.995000	0.38212	1.000000	0.80357	0.895000	0.52256	4.129000	0.57957	2.087000	0.62958	0.460000	0.39030	GAG	.	.		0.697	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
SPTBN1	6711	hgsc.bcm.edu	37	2	54753654	54753654	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:54753654G>T	ENST00000356805.4	+	2	380	c.99G>T	c.(97-99)gaG>gaT	p.E33D	AC092839.3_ENST00000433475.1_RNA	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	33	Actin-binding.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GGGACAATGAGAACAGCTCTG	0.537																																					p.E33D		Atlas-SNP	.											.	SPTBN1	378	.	0			c.G99T						.						147.0	132.0	137.0					2																	54753654		2203	4300	6503	SO:0001583	missense	6711	exon2			CAATGAGAACAGC		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.99G>T	chr2.hg19:g.54753654G>T	ENSP00000349259:p.Glu33Asp	103.0	0.0		95.0	4.0	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	G	5.135	0.210554	0.09757	.	.	ENSG00000115306	ENST00000356805;ENST00000389980	T;T	0.60040	0.22;0.22	5.77	2.5	0.30297	Calponin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.22666	0.0547	N	0.01410	-0.885	0.80722	D	1	B	0.13594	0.008	B	0.15052	0.012	T	0.31024	-0.9958	10	0.02654	T	1	.	10.8349	0.46681	0.1992:0.1114:0.6894:0.0	.	33	Q01082	SPTB2_HUMAN	D	33	ENSP00000349259:E33D;ENSP00000374630:E33D	ENSP00000349259:E33D	E	+	3	2	SPTBN1	54607158	1.000000	0.71417	0.988000	0.46212	0.961000	0.63080	2.133000	0.42093	0.340000	0.23745	-0.813000	0.03139	GAG	.	.		0.537	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
EHBP1	23301	hgsc.bcm.edu	37	2	63086387	63086387	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:63086387G>A	ENST00000263991.5	+	9	1305	c.823G>A	c.(823-825)Gct>Act	p.A275T	EHBP1_ENST00000405015.3_Missense_Mutation_p.A240T|EHBP1_ENST00000431489.1_Missense_Mutation_p.A240T|EHBP1_ENST00000354487.3_Missense_Mutation_p.A240T|EHBP1_ENST00000405289.1_Missense_Mutation_p.A240T|AC007098.1_ENST00000452397.1_RNA	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	275						cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			TGATCCTGATGCTGCAGAATT	0.353																																					p.A275T		Atlas-SNP	.											.	EHBP1	127	.	0			c.G823A						.						123.0	119.0	121.0					2																	63086387		2203	4300	6503	SO:0001583	missense	23301	exon9			CCTGATGCTGCAG	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.823G>A	chr2.hg19:g.63086387G>A	ENSP00000263991:p.Ala275Thr	128.0	0.0		80.0	4.0	NM_015252	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	hg19	CCDS1872.1	.	.	.	.	.	.	.	.	.	.	G	8.982	0.975558	0.18736	.	.	ENSG00000115504	ENST00000405015;ENST00000405482;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T;T;T;T;T;T	0.72835	-0.69;0.99;-0.69;-0.69;-0.69;-0.69	4.88	4.0	0.46444	.	0.255372	0.32002	N	0.006723	T	0.49047	0.1534	N	0.14661	0.345	0.19300	N	0.999977	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.24977	-1.0145	10	0.14656	T	0.56	.	9.9057	0.41375	0.2194:0.0:0.7806:0.0	.	240;240;275	Q8NDI1-2;Q8NDI1-3;Q8NDI1	.;.;EHBP1_HUMAN	T	240;240;240;275;240;240	ENSP00000384143:A240T;ENSP00000384829:A240T;ENSP00000403783:A240T;ENSP00000263991:A275T;ENSP00000346482:A240T;ENSP00000385524:A240T	ENSP00000263991:A275T	A	+	1	0	EHBP1	62939891	1.000000	0.71417	0.992000	0.48379	0.719000	0.41307	2.158000	0.42329	1.061000	0.40601	0.591000	0.81541	GCT	.	.		0.353	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252	
SERTAD2	9792	hgsc.bcm.edu	37	2	64863856	64863856	+	Silent	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:64863856G>A	ENST00000313349.3	-	2	447	c.150C>T	c.(148-150)aaC>aaT	p.N50N	SERTAD2_ENST00000476805.2_5'UTR	NM_014755.2	NP_055570.1	Q14140	SRTD2_HUMAN	SERTA domain containing 2	50	SERTA. {ECO:0000255|PROSITE- ProRule:PRU00396}.				negative regulation of cell growth (GO:0030308)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|skin(1)	12						GGGGCCTGTGGTTATAGAGTT	0.493																																					p.N50N		Atlas-SNP	.											.	SERTAD2	32	.	0			c.C150T						.						136.0	141.0	139.0					2																	64863856		2203	4300	6503	SO:0001819	synonymous_variant	9792	exon2			CCTGTGGTTATAG	D50917	CCDS33210.1	2p15	2007-05-01			ENSG00000179833	ENSG00000179833			30784	protein-coding gene	gene with protein product	"""transcriptional regulator interacting with the PHS-bromodomain 2"""					8590280, 11331592	Standard	NM_014755		Approved	TRIP-Br2, KIAA0127, Sei-2	uc002sde.2	Q14140	OTTHUMG00000152678	ENST00000313349.3:c.150C>T	chr2.hg19:g.64863856G>A		237.0	0.0		220.0	21.0	NM_014755	Q53TS2	Silent	SNP	ENST00000313349.3	hg19	CCDS33210.1																																																																																			.	.		0.493	SERTAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327322.2	NM_014755	
AAK1	22848	hgsc.bcm.edu	37	2	69741753	69741753	+	Silent	SNP	C	C	T	rs66931661|rs3832159	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:69741753C>T	ENST00000409085.4	-	13	2002	c.1626G>A	c.(1624-1626)caG>caA	p.Q542Q	AAK1_ENST00000406297.3_Silent_p.Q542Q|RN7SL604P_ENST00000492589.2_RNA|AAK1_ENST00000409068.1_Silent_p.Q542Q	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	542	Gln-rich.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						gttgctgttgctgttgttgtt	0.552																																					p.Q542Q		Atlas-SNP	.											.	AAK1	121	.	0			c.G1626A						.						33.0	35.0	34.0					2																	69741753		2192	4296	6488	SO:0001819	synonymous_variant	22848	exon13			CTGTTGCTGTTGT	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1626G>A	chr2.hg19:g.69741753C>T		147.0	0.0		134.0	14.0	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	hg19	CCDS1893.2																																																																																			.	.		0.552	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
VAX2	25806	hgsc.bcm.edu	37	2	71148294	71148294	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:71148294C>T	ENST00000234392.2	+	2	346	c.314C>T	c.(313-315)aCa>aTa	p.T105I		NM_012476.2	NP_036608.1	Q9UIW0	VAX2_HUMAN	ventral anterior homeobox 2	105					axonogenesis (GO:0007409)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic eye morphogenesis (GO:0048048)|forebrain development (GO:0030900)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	7						CCCAAGCGGACACGTACATCC	0.612																																					p.T105I		Atlas-SNP	.											.	VAX2	27	.	0			c.C314T						.						49.0	45.0	46.0					2																	71148294		2203	4300	6503	SO:0001583	missense	25806	exon2			AGCGGACACGTAC	Y17791	CCDS1911.1	2p13.3	2011-06-20			ENSG00000116035	ENSG00000116035		"""Homeoboxes / ANTP class : NKL subclass"""	12661	protein-coding gene	gene with protein product		604295				10485894	Standard	NM_012476		Approved	DRES93	uc002shh.3	Q9UIW0	OTTHUMG00000129714	ENST00000234392.2:c.314C>T	chr2.hg19:g.71148294C>T	ENSP00000234392:p.Thr105Ile	144.0	0.0		95.0	4.0	NM_012476	Q53Y33	Missense_Mutation	SNP	ENST00000234392.2	hg19	CCDS1911.1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.769813	0.69992	.	.	ENSG00000116035	ENST00000234392	D	0.96396	-4.0	5.43	4.55	0.56014	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.90796	0.7110	N	0.05199	-0.095	0.80722	D	1	P	0.36647	0.563	B	0.37989	0.262	D	0.91278	0.5049	10	0.72032	D	0.01	-21.0553	14.1912	0.65639	0.0:0.8496:0.1504:0.0	.	105	Q9UIW0	VAX2_HUMAN	I	105	ENSP00000234392:T105I	ENSP00000234392:T105I	T	+	2	0	VAX2	71001802	1.000000	0.71417	0.987000	0.45799	0.790000	0.44656	5.724000	0.68500	1.283000	0.44513	0.655000	0.94253	ACA	.	.		0.612	VAX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251923.1		
KDM3A	55818	hgsc.bcm.edu	37	2	86705806	86705806	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:86705806A>G	ENST00000409556.1	+	16	2629	c.2264A>G	c.(2263-2265)aAc>aGc	p.N755S	KDM3A_ENST00000312912.5_Missense_Mutation_p.N755S|KDM3A_ENST00000409064.1_Missense_Mutation_p.N755S|KDM3A_ENST00000542128.1_Missense_Mutation_p.N703S			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	755					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						CCTTGTTCAAACAGGCAATTC	0.383																																					p.N755S	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.A2264G						.						111.0	100.0	104.0					2																	86705806		2203	4300	6503	SO:0001583	missense	55818	exon15			GTTCAAACAGGCA	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"""Chromatin-modifying enzymes / K-demethylases"""	20815	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 2A"""	611512	"""jumonji domain containing 1"", ""jumonji domain containing 1A"""	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.2264A>G	chr2.hg19:g.86705806A>G	ENSP00000386660:p.Asn755Ser	132.0	0.0		87.0	4.0	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	hg19	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	A	12.00	1.805795	0.31961	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.58797	0.31;0.31;0.31;0.31	5.73	3.29	0.37713	.	0.132172	0.51477	D	0.000096	T	0.41282	0.1152	L	0.28192	0.835	0.37720	D	0.92488	B;B	0.25312	0.123;0.017	B;B	0.29862	0.108;0.013	T	0.30416	-0.9979	10	0.23891	T	0.37	.	8.1164	0.30946	0.7946:0.1344:0.071:0.0	.	703;755	F5H070;Q9Y4C1	.;KDM3A_HUMAN	S	755;755;755;755;703	ENSP00000386660:N755S;ENSP00000323659:N755S;ENSP00000386516:N755S;ENSP00000438324:N703S	ENSP00000323659:N755S	N	+	2	0	KDM3A	86559317	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.339000	0.52135	0.971000	0.38288	0.533000	0.62120	AAC	.	.		0.383	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	
PROM2	150696	hgsc.bcm.edu	37	2	95940507	95940507	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:95940507A>G	ENST00000317620.9	+	1	307	c.174A>G	c.(172-174)ggA>ggG	p.G58G	PROM2_ENST00000542147.1_Silent_p.G58G|PROM2_ENST00000403131.2_Silent_p.G58G|PROM2_ENST00000317668.4_Silent_p.G58G|PROM2_ENST00000463580.1_3'UTR	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	58					negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						GTGCGCCAGGACTCCTGGACT	0.662																																					p.G58G		Atlas-SNP	.											.	PROM2	78	.	0			c.A174G						.						82.0	91.0	88.0					2																	95940507		2203	4300	6503	SO:0001819	synonymous_variant	150696	exon1			GCCAGGACTCCTG	AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.174A>G	chr2.hg19:g.95940507A>G		99.0	0.0		78.0	4.0	NM_001165977	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Silent	SNP	ENST00000317620.9	hg19	CCDS2012.1																																																																																			.	.		0.662	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707	
SNRNP200	23020	hgsc.bcm.edu	37	2	96965077	96965077	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:96965077A>G	ENST00000323853.5	-	6	796	c.719T>C	c.(718-720)cTc>cCc	p.L240P	SNRNP200_ENST00000349783.5_Missense_Mutation_p.L240P	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	240					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						ATTAGCCGAGAGGGTGCAGCG	0.493																																					p.L240P		Atlas-SNP	.											.	SNRNP200	195	.	0			c.T719C						.						256.0	230.0	239.0					2																	96965077		2203	4300	6503	SO:0001583	missense	23020	exon6			GCCGAGAGGGTGC	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 200 KD"""	601664	"""activating signal cointegrator 1 complex subunit 3-like 1"", ""retinitis pigmentosa 33 (autosomal dominant)"""	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.719T>C	chr2.hg19:g.96965077A>G	ENSP00000317123:p.Leu240Pro	119.0	0.0		100.0	5.0	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	hg19	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.440609	0.43326	.	.	ENSG00000144028	ENST00000323853;ENST00000349783	T;T	0.49720	0.77;0.77	5.07	5.07	0.68467	.	0.066905	0.64402	D	0.000016	T	0.48874	0.1524	M	0.74647	2.275	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.46638	-0.9177	10	0.35671	T	0.21	-14.5291	13.9456	0.64082	1.0:0.0:0.0:0.0	.	240	O75643	U520_HUMAN	P	240	ENSP00000317123:L240P;ENSP00000326937:L240P	ENSP00000317123:L240P	L	-	2	0	SNRNP200	96328804	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	8.641000	0.91032	2.125000	0.65367	0.454000	0.30748	CTC	.	.		0.493	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014	
ARID5A	10865	hgsc.bcm.edu	37	2	97216921	97216921	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:97216921A>G	ENST00000357485.3	+	7	734	c.656A>G	c.(655-657)cAg>cGg	p.Q219R	ARID5A_ENST00000454558.2_Missense_Mutation_p.Q151R	NM_212481.1	NP_997646.1	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A (MRF1-like)	219					chondrocyte differentiation (GO:0002062)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|skin(1)|urinary_tract(2)	14						ACAGAACAGCAGGGCCTGGCC	0.587																																					p.Q219R		Atlas-SNP	.											.	ARID5A	31	.	0			c.A656G						.						59.0	66.0	64.0					2																	97216921		2203	4300	6503	SO:0001583	missense	10865	exon7			AACAGCAGGGCCT	M62324	CCDS33251.1	2p11.1	2013-02-07			ENSG00000196843	ENSG00000196843		"""-"""	17361	protein-coding gene	gene with protein product	"""modulator recognition factor 1"""	611583				8649988	Standard	NM_212481		Approved	MRF-1, RP11-363D14	uc002swe.3	Q03989	OTTHUMG00000155229	ENST00000357485.3:c.656A>G	chr2.hg19:g.97216921A>G	ENSP00000350078:p.Gln219Arg	122.0	0.0		93.0	4.0	NM_212481	Q6NX37	Missense_Mutation	SNP	ENST00000357485.3	hg19	CCDS33251.1	.	.	.	.	.	.	.	.	.	.	A	2.975	-0.211513	0.06140	.	.	ENSG00000196843	ENST00000357485;ENST00000359765;ENST00000454558	T	0.63580	-0.05	4.63	-3.23	0.05109	.	0.544000	0.13830	N	0.359795	T	0.21631	0.0521	N	0.02011	-0.69	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.23084	-1.0198	10	0.09843	T	0.71	-0.0151	0.5205	0.00611	0.2832:0.3139:0.1421:0.2608	.	219;151;219	A6NM59;C9J1Q0;Q03989	.;.;ARI5A_HUMAN	R	219;219;151	ENSP00000350078:Q219R	ENSP00000350078:Q219R	Q	+	2	0	ARID5A	96580648	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	0.185000	0.16958	-0.496000	0.06650	-0.527000	0.04329	CAG	.	.		0.587	ARID5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338888.2	NM_212481	
CLASP1	23332	hgsc.bcm.edu	37	2	122205082	122205082	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:122205082A>G	ENST00000263710.4	-	19	2132	c.1743T>C	c.(1741-1743)gcT>gcC	p.A581A	CLASP1_ENST00000541377.1_Splice_Site_p.A581A|CLASP1_ENST00000409078.3_Splice_Site_p.A581A|CLASP1_ENST00000541859.1_Splice_Site_p.A350A|CLASP1_ENST00000455322.2_Splice_Site_p.A581A|CLASP1_ENST00000397587.3_Splice_Site_p.A581A|CLASP1_ENST00000545861.1_Splice_Site_p.A349A	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	581	Ser-rich.				axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					TAACTGTAGAAGCTTTAGTGA	0.383																																					p.A581A		Atlas-SNP	.											.	CLASP1	135	.	0			c.T1743C						.						33.0	33.0	33.0					2																	122205082		1838	4024	5862	SO:0001630	splice_region_variant	23332	exon19			TGTAGAAGCTTTA	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"""multiple asters 1"""	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.1742-1T>C	chr2.hg19:g.122205082A>G		109.0	0.0		83.0	4.0	NM_001207051	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Silent	SNP	ENST00000263710.4	hg19																																																																																				.	.		0.383	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282	Silent
CNTNAP5	129684	hgsc.bcm.edu	37	2	125367485	125367485	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:125367485T>C	ENST00000431078.1	+	12	2225	c.1861T>C	c.(1861-1863)Tgc>Cgc	p.C621R		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	621	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		CCAGGTGTACTGCAATATCAC	0.532																																					p.C621R		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.T1861C						.						64.0	64.0	64.0					2																	125367485		1877	4113	5990	SO:0001583	missense	129684	exon12			GTGTACTGCAATA	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.1861T>C	chr2.hg19:g.125367485T>C	ENSP00000399013:p.Cys621Arg	71.0	0.0		42.0	4.0	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	T	18.38	3.612381	0.66672	.	.	ENSG00000155052	ENST00000431078	T	0.39997	1.05	5.66	5.66	0.87406	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (2);	0.000000	0.56097	D	0.000039	T	0.74741	0.3756	H	0.95114	3.625	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.82914	-0.0221	10	0.87932	D	0	.	15.0047	0.71501	0.0:0.0:0.0:1.0	.	621	Q8WYK1	CNTP5_HUMAN	R	621	ENSP00000399013:C621R	ENSP00000399013:C621R	C	+	1	0	CNTNAP5	125083955	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	7.264000	0.78432	2.279000	0.76181	0.533000	0.62120	TGC	.	.		0.532	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
GPR148	344561	hgsc.bcm.edu	37	2	131486858	131486858	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:131486858C>T	ENST00000309926.4	+	1	216	c.134C>T	c.(133-135)cCc>cTc	p.P45L		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	45				CMPQAASNTSLGLGDLRVPSSMLYWLFLPSSLLAAA -> S S (in Ref. 2; AAP34196). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(15)|skin(3)|upper_aerodigestive_tract(1)	27	Colorectal(110;0.1)					CTCAGGGTGCCCAGCTCCATG	0.622																																					p.P45L		Atlas-SNP	.											.	GPR148	54	.	0			c.C134T						.						78.0	70.0	73.0					2																	131486858		2203	4300	6503	SO:0001583	missense	344561	exon1			GGGTGCCCAGCTC	AY255532	CCDS2163.1	2q21.2	2012-08-21			ENSG00000173302	ENSG00000173302		"""GPCR / Class A : Orphans"""	23623	protein-coding gene	gene with protein product						12679517	Standard	NM_207364		Approved	PGR6	uc002trv.2	Q8TDV2	OTTHUMG00000131655	ENST00000309926.4:c.134C>T	chr2.hg19:g.131486858C>T	ENSP00000308908:p.Pro45Leu	103.0	0.0		93.0	4.0	NM_207364	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	hg19	CCDS2163.1	.	.	.	.	.	.	.	.	.	.	.	11.74	1.730211	0.30684	.	.	ENSG00000173302	ENST00000309926	T	0.35605	1.3	2.55	2.55	0.30701	.	0.939982	0.08667	U	0.911494	T	0.21631	0.0521	N	0.08118	0	0.09310	N	1	D	0.60160	0.987	P	0.46362	0.514	T	0.01767	-1.1278	10	0.08381	T	0.77	-11.1141	11.2415	0.48972	0.0:1.0:0.0:0.0	.	45	Q8TDV2	GP148_HUMAN	L	45	ENSP00000308908:P45L	ENSP00000308908:P45L	P	+	2	0	GPR148	131203328	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	0.641000	0.24720	1.379000	0.46325	0.462000	0.41574	CCC	.	.		0.622	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092	
THSD7B	80731	hgsc.bcm.edu	37	2	138373887	138373887	+	Splice_Site	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:138373887G>A	ENST00000409968.1	+	18	3743		c.e18+1		THSD7B_ENST00000413152.2_Splice_Site|THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000272643.3_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)		AATCTAACAGGTACAGTTAAA	0.413																																					.		Atlas-SNP	.											.	THSD7B	506	.	0			c.3477+1G>A						.						171.0	177.0	175.0					2																	138373887		2018	4178	6196	SO:0001630	splice_region_variant	80731	exon17			TAACAGGTACAGT			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.3565+1G>A	chr2.hg19:g.138373887G>A		103.0	0.0		98.0	4.0	NM_001080427		Splice_Site	SNP	ENST00000409968.1	hg19		.	.	.	.	.	.	.	.	.	.	G	24.2	4.505367	0.85282	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	.	.	.	5.2	5.2	0.72013	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.6547	0.88174	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	THSD7B	138090357	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	8.389000	0.90172	2.703000	0.92315	0.650000	0.86243	.	.	.		0.413	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9	Intron
LRP1B	53353	hgsc.bcm.edu	37	2	141707824	141707824	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:141707824T>C	ENST00000389484.3	-	20	4087	c.3116A>G	c.(3115-3117)cAg>cGg	p.Q1039R		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1039	LDL-receptor class A 7. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ACAATTGATCTGGGCTTCATC	0.373										TSP Lung(27;0.18)																											p.Q1039R	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A3116G						.						50.0	41.0	44.0					2																	141707824		2203	4300	6503	SO:0001583	missense	53353	exon20			TTGATCTGGGCTT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.3116A>G	chr2.hg19:g.141707824T>C	ENSP00000374135:p.Gln1039Arg	133.0	0.0		124.0	5.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	7.997	0.754496	0.15778	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.95205	-2.25;-3.64	5.53	4.31	0.51392	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.301645	0.30244	U	0.010063	D	0.88869	0.6554	L	0.38175	1.15	0.09310	N	1	B;B	0.15719	0.001;0.014	B;B	0.15052	0.006;0.012	T	0.74902	-0.3506	10	0.19147	T	0.46	.	8.2266	0.31572	0.0:0.0714:0.1343:0.7943	.	222;1039	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	R	1039;977;184	ENSP00000374135:Q1039R;ENSP00000413239:Q184R	ENSP00000374135:Q1039R	Q	-	2	0	LRP1B	141424294	0.990000	0.36364	0.230000	0.23976	0.808000	0.45660	1.950000	0.40323	2.112000	0.64535	0.460000	0.39030	CAG	.	.		0.373	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
ZEB2	9839	hgsc.bcm.edu	37	2	145162558	145162558	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:145162558T>C	ENST00000558170.2	-	5	1621	c.437A>G	c.(436-438)gAa>gGa	p.E146G	ZEB2_ENST00000539609.3_Missense_Mutation_p.E122G|ZEB2_ENST00000409487.3_Missense_Mutation_p.E146G|ZEB2_ENST00000303660.4_Missense_Mutation_p.E146G	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	146					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		GGCAAAGTATTCCTCAAAATC	0.453																																					p.E146G	Melanoma(33;1235 1264 5755 16332)	Atlas-SNP	.											.	ZEB2	218	.	0			c.A437G						.						91.0	81.0	84.0					2																	145162558		2203	4300	6503	SO:0001583	missense	9839	exon5			AAGTATTCCTCAA	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	14881	protein-coding gene	gene with protein product	"""SMAD interacting protein 1"""	605802	"""zinc finger homeobox 1b"""	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.437A>G	chr2.hg19:g.145162558T>C	ENSP00000454157:p.Glu146Gly	95.0	0.0		95.0	4.0	NM_014795	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	hg19	CCDS2186.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.93|15.93	2.979008|2.979008	0.53827|0.53827	.|.	.|.	ENSG00000169554|ENSG00000169554	ENST00000392860;ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902;ENST00000392861|ENST00000431672;ENST00000440875	D;T;T;T;T|.	0.81579|.	-1.51;-1.05;-1.05;-1.05;-1.05|.	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	0.143203|.	0.64402|.	D|.	0.000005|.	T|T	0.59783|0.59783	0.2219|0.2219	L|L	0.36672|0.36672	1.1|1.1	0.58432|0.58432	D|D	0.999998|0.999998	P;B;B;B|.	0.43352|.	0.804;0.435;0.231;0.231|.	B;B;B;B|.	0.37144|.	0.242;0.078;0.054;0.054|.	T|T	0.55503|0.55503	-0.8131|-0.8131	10|5	0.66056|.	D|.	0.02|.	-12.5066|-12.5066	16.5655|16.5655	0.84588|0.84588	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	122;11;145;146|.	F5H814;Q53TD9;A0JP08;O60315|.	.;.;.;ZEB2_HUMAN|.	G|D	141;122;146;146;146;146|112;133	ENSP00000443792:E122G;ENSP00000302501:E146G;ENSP00000386854:E146G;ENSP00000395496:E146G;ENSP00000376601:E146G|.	ENSP00000302501:E146G|.	E|N	-|-	2|1	0|0	ZEB2|ZEB2	144879028|144879028	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	8.040000|8.040000	0.89188|0.89188	2.302000|2.302000	0.77476|0.77476	0.533000|0.533000	0.62120|0.62120	GAA|AAT	.	.		0.453	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795	
RIF1	55183	hgsc.bcm.edu	37	2	152316610	152316610	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:152316610G>A	ENST00000243326.5	+	25	3535	c.3052G>A	c.(3052-3054)Gaa>Aaa	p.E1018K	RIF1_ENST00000428287.2_Missense_Mutation_p.E1018K|RIF1_ENST00000444746.2_Missense_Mutation_p.E1018K|RIF1_ENST00000430328.2_Missense_Mutation_p.E1018K|RIF1_ENST00000453091.2_Missense_Mutation_p.E1018K			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		GAATAAAAAAGAAAATATGAA	0.269																																					p.E1018K		Atlas-SNP	.											.	RIF1	244	.	0			c.G3052A						.						24.0	27.0	26.0					2																	152316610		2177	4275	6452	SO:0001583	missense	55183	exon26			AAAAAAGAAAATA	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.3052G>A	chr2.hg19:g.152316610G>A	ENSP00000243326:p.Glu1018Lys	137.0	0.0		186.0	21.0	NM_018151	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	hg19	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.431952	0.25813	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.78	4.89	0.63831	.	0.723385	0.13884	N	0.356121	T	0.17831	0.0428	N	0.17474	0.49	0.80722	D	1	B;B	0.12630	0.004;0.006	B;B	0.17098	0.004;0.017	T	0.03306	-1.1050	10	0.07644	T	0.81	-6.1798	10.7453	0.46177	0.1529:0.0:0.8471:0.0	.	1018;1018	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	K	1018	ENSP00000390181:E1018K;ENSP00000414615:E1018K;ENSP00000415691:E1018K;ENSP00000243326:E1018K;ENSP00000416123:E1018K	ENSP00000243326:E1018K	E	+	1	0	RIF1	152024856	1.000000	0.71417	0.658000	0.29665	0.302000	0.27658	2.337000	0.43947	1.416000	0.47057	0.555000	0.69702	GAA	.	.		0.269	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		
ACVR1	90	hgsc.bcm.edu	37	2	158636913	158636913	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:158636913T>C	ENST00000263640.3	-	4	696	c.267A>G	c.(265-267)caA>caG	p.Q89Q	ACVR1_ENST00000409283.2_Silent_p.Q89Q|ACVR1_ENST00000487456.1_5'UTR|ACVR1_ENST00000410057.2_Silent_p.Q89Q|ACVR1_ENST00000434821.1_Silent_p.Q89Q	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	89					activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	ACTCCACGGCTTGGCCAGGGG	0.547																																					p.Q89Q		Atlas-SNP	.											.	ACVR1	52	.	0			c.A267G						.						64.0	67.0	66.0					2																	158636913		2203	4300	6503	SO:0001819	synonymous_variant	90	exon4			CACGGCTTGGCCA		CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.267A>G	chr2.hg19:g.158636913T>C		102.0	0.0		86.0	4.0	NM_001105		Silent	SNP	ENST00000263640.3	hg19	CCDS2206.1																																																																																			.	.		0.547	ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105	
FIGN	55137	hgsc.bcm.edu	37	2	164467712	164467712	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:164467712A>G	ENST00000333129.3	-	3	944	c.630T>C	c.(628-630)caT>caC	p.H210H	FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	210	Pro-rich.				mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)			breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						AAGGAGACGGATGAGGTGAAG	0.542																																					p.H210H		Atlas-SNP	.											.	FIGN	106	.	0			c.T630C						.						73.0	81.0	79.0					2																	164467712		2059	4203	6262	SO:0001819	synonymous_variant	55137	exon3			AGACGGATGAGGT	AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"""ATPases / AAA-type"""	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.630T>C	chr2.hg19:g.164467712A>G		198.0	0.0		167.0	7.0	NM_018086	B3KWM0|Q9H6M5|Q9NVZ9	Silent	SNP	ENST00000333129.3	hg19	CCDS2221.2																																																																																			.	.		0.542	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086	
SP3	6670	hgsc.bcm.edu	37	2	174820457	174820457	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:174820457T>C	ENST00000310015.6	-	4	1313	c.783A>G	c.(781-783)ccA>ccG	p.P261P	SP3_ENST00000418194.2_Silent_p.P193P|SP3_ENST00000455789.2_Silent_p.P208P|SP3_ENST00000483084.1_5'Flank	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	261					B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)		EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			TAATATTTCCTGGCAGACCAA	0.468																																					p.P261P		Atlas-SNP	.											.	SP3	82	.	0			c.A783G						.						90.0	88.0	89.0					2																	174820457		2203	4300	6503	SO:0001819	synonymous_variant	6670	exon4			ATTTCCTGGCAGA	M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.783A>G	chr2.hg19:g.174820457T>C		90.0	0.0		71.0	4.0	NM_003111	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Silent	SNP	ENST00000310015.6	hg19	CCDS2254.1	.	.	.	.	.	.	.	.	.	.	T	4.001	-0.002544	0.07819	.	.	ENSG00000172845	ENST00000416195	.	.	.	5.95	4.8	0.61643	.	.	.	.	.	T	0.57770	0.2076	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55192	-0.8179	4	.	.	.	.	7.0973	0.25317	0.1308:0.0688:0.0:0.8004	.	.	.	.	R	218	.	.	Q	-	2	0	SP3	174528703	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.068000	0.41471	1.079000	0.41038	-0.371000	0.07208	CAG	.	.		0.468	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111	
PDE11A	50940	hgsc.bcm.edu	37	2	178494173	178494173	+	Missense_Mutation	SNP	G	G	A	rs397723704|rs3830637	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:178494173G>A	ENST00000286063.6	-	20	3081	c.2764C>T	c.(2764-2766)Cct>Tct	p.P922S	PDE11A_ENST00000450799.2_Missense_Mutation_p.P113S|PDE11A_ENST00000409504.1_Missense_Mutation_p.P564S|PDE11A_ENST00000449286.2_Missense_Mutation_p.P564S|PDE11A_ENST00000358450.4_Missense_Mutation_p.P672S|PDE11A_ENST00000389683.3_Missense_Mutation_p.P478S	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	922					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	ACACTGGCAGGGGAGGATGAG	0.502									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.P922S		Atlas-SNP	.											.	PDE11A	283	.	0			c.C2764T						.						236.0	179.0	198.0					2																	178494173		2203	4300	6503	SO:0001583	missense	50940	exon20	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	TGGCAGGGGAGGA	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"""Phosphodiesterases"""	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2764C>T	chr2.hg19:g.178494173G>A	ENSP00000286063:p.Pro922Ser	268.0	0.0		254.0	13.0	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	hg19	CCDS33334.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.28|11.28	1.592474|1.592474	0.28357|0.28357	.|.	.|.	ENSG00000128655|ENSG00000128655	ENST00000436700|ENST00000286063;ENST00000358450;ENST00000450799;ENST00000409504;ENST00000389683;ENST00000449286	.|T;T;T;T;T;T	.|0.70749	.|-0.17;0.06;-0.1;-0.06;-0.51;-0.06	5.62|5.62	-0.681|-0.681	0.11342|0.11342	.|.	3.486060|3.486060	0.00890|0.00890	N|N	0.002221|0.002221	T|T	0.49915|0.49915	0.1585|0.1585	N|N	0.14661|0.14661	0.345|0.345	0.20196|0.20196	N|N	0.99993|0.99993	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.28235|0.28235	-1.0050|-1.0050	6|10	.|0.36615	.|T	.|0.2	.|.	0.627|0.627	0.00788|0.00788	0.3361:0.1255:0.2887:0.2497|0.3361:0.1255:0.2887:0.2497	.|.	.|672;922	.|Q9HCR9-2;Q9HCR9	.|.;PDE11_HUMAN	L|S	124|922;672;113;564;478;564	.|ENSP00000286063:P922S;ENSP00000351232:P672S;ENSP00000387964:P113S;ENSP00000386539:P564S;ENSP00000374333:P478S;ENSP00000390599:P564S	.|ENSP00000286063:P922S	P|P	-|-	2|1	0|0	PDE11A|PDE11A	178202419|178202419	0.452000|0.452000	0.25713|0.25713	0.002000|0.002000	0.10522|0.10522	0.053000|0.053000	0.15095|0.15095	0.290000|0.290000	0.18975|0.18975	-0.018000|-0.018000	0.14079|0.14079	-0.293000|-0.293000	0.09583|0.09583	CCC|CCT	.	.		0.502	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		
TTN	7273	hgsc.bcm.edu	37	2	179667053	179667053	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:179667053T>C	ENST00000591111.1	-	3	331	c.107A>G	c.(106-108)gAg>gGg	p.E36G	TTN_ENST00000342175.6_Missense_Mutation_p.E36G|TTN_ENST00000360870.5_Missense_Mutation_p.E36G|TTN_ENST00000589042.1_Missense_Mutation_p.E36G|TTN_ENST00000342992.6_Missense_Mutation_p.E36G|TTN_ENST00000460472.2_Missense_Mutation_p.E36G|TTN_ENST00000359218.5_Missense_Mutation_p.E36G			Q8WZ42	TITIN_HUMAN	titin	32647	Ig-like 1.				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)			CCAGCTCACCTCAGGAACTGG	0.527																																					p.E36G		Atlas-SNP	.											.	TTN	18412	.	0			c.A107G						.						68.0	57.0	61.0					2																	179667053		2203	4300	6503	SO:0001583	missense	7273	exon3			CTCACCTCAGGAA	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.107A>G	chr2.hg19:g.179667053T>C	ENSP00000465570:p.Glu36Gly	146.0	0.0		120.0	5.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.85	2.955924	0.53293	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870;ENST00000412264	T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39	5.74	5.74	0.90152	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.83727	0.5317	M	0.84433	2.695	0.44142	D	0.996938	D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0	D;D;D;D;D	0.87578	0.997;0.997;0.997;0.997;0.998	D	0.86523	0.1817	9	0.87932	D	0	.	16.0351	0.80621	0.0:0.0:0.0:1.0	.	36;36;36;36;36	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	G	36;36;36;36;36;36;51	ENSP00000343764:E36G;ENSP00000434586:E36G;ENSP00000340554:E36G;ENSP00000352154:E36G;ENSP00000354117:E36G	ENSP00000340554:E36G	E	-	2	0	TTN	179375298	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.846000	0.86887	2.186000	0.69663	0.533000	0.62120	GAG	.	.		0.527	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RFTN2	130132	hgsc.bcm.edu	37	2	198480674	198480674	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:198480674A>G	ENST00000295049.4	-	7	1616	c.1080T>C	c.(1078-1080)ccT>ccC	p.P360P		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	360					dsRNA transport (GO:0033227)|response to exogenous dsRNA (GO:0043330)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(13)|urinary_tract(3)	30						TGTGCAGCAGAGGGCCATAAT	0.428																																					p.P360P		Atlas-SNP	.											.	RFTN2	68	.	0			c.T1080C						.						90.0	73.0	79.0					2																	198480674		2198	4287	6485	SO:0001819	synonymous_variant	130132	exon7			CAGCAGAGGGCCA	AK055136	CCDS2323.1	2q33.1	2008-02-05	2006-09-28	2006-09-28	ENSG00000162944	ENSG00000162944			26402	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 11"""	C2orf11			Standard	NM_144629		Approved	FLJ30574, Raftlin-2	uc002uuo.4	Q52LD8	OTTHUMG00000132746	ENST00000295049.4:c.1080T>C	chr2.hg19:g.198480674A>G		108.0	0.0		98.0	4.0	NM_144629	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Silent	SNP	ENST00000295049.4	hg19	CCDS2323.1																																																																																			.	.		0.428	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629	
FASTKD2	22868	hgsc.bcm.edu	37	2	207652780	207652780	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:207652780T>C	ENST00000236980.6	+	9	2062	c.1714T>C	c.(1714-1716)Tca>Cca	p.S572P	FASTKD2_ENST00000403094.3_Missense_Mutation_p.S572P|FASTKD2_ENST00000402774.3_Missense_Mutation_p.S572P	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	572					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		GCTGCCATCGTCACATACAAA	0.488																																					p.S572P		Atlas-SNP	.											.	FASTKD2	49	.	0			c.T1714C						.						69.0	65.0	67.0					2																	207652780		2203	4300	6503	SO:0001583	missense	22868	exon9			CCATCGTCACATA	BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"""KIAA0971"""	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.1714T>C	chr2.hg19:g.207652780T>C	ENSP00000236980:p.Ser572Pro	95.0	0.0		66.0	4.0	NM_001136193	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	hg19	CCDS2371.1	.	.	.	.	.	.	.	.	.	.	t	10.54	1.379882	0.24944	.	.	ENSG00000118246	ENST00000236980;ENST00000402774;ENST00000403094	T;T;T	0.49720	0.77;0.77;0.77	5.44	-2.93	0.05598	FAST kinase-like protein, subdomain 2 (1);	0.775465	0.12555	N	0.458720	T	0.33381	0.0861	L	0.47716	1.5	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.14023	0.004;0.01	T	0.21759	-1.0236	10	0.27785	T	0.31	-1.8665	6.5505	0.22431	0.0:0.3775:0.1415:0.481	.	572;572	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	P	572	ENSP00000236980:S572P;ENSP00000385990:S572P;ENSP00000384929:S572P	ENSP00000236980:S572P	S	+	1	0	FASTKD2	207361025	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.607000	0.02070	-0.686000	0.05170	-0.261000	0.10672	TCA	.	.		0.488	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929	
MAP2	4133	hgsc.bcm.edu	37	2	210558428	210558428	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:210558428A>G	ENST00000360351.4	+	7	2040	c.1534A>G	c.(1534-1536)Atg>Gtg	p.M512V	MAP2_ENST00000392194.1_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000447185.1_Missense_Mutation_p.M508V|MAP2_ENST00000361559.4_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	512					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AGATTCAGCCATGACCTCTAA	0.418																																					p.M512V	Pancreas(27;423 979 28787 29963)	Atlas-SNP	.											.	MAP2	372	.	0			c.A1534G						.						78.0	78.0	78.0					2																	210558428		2203	4300	6503	SO:0001583	missense	4133	exon7			TCAGCCATGACCT		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.1534A>G	chr2.hg19:g.210558428A>G	ENSP00000353508:p.Met512Val	107.0	0.0		76.0	4.0	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	hg19	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	A	0.057	-1.233648	0.01505	.	.	ENSG00000078018	ENST00000360351;ENST00000447185	T;T	0.20463	2.07;2.07	5.62	-4.44	0.03557	MAP2/Tau projection (1);	0.750110	0.12834	N	0.435344	T	0.14056	0.0340	L	0.44542	1.39	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.31420	-0.9944	10	0.21014	T	0.42	-0.5443	10.0179	0.42024	0.1806:0.3516:0.4678:0.0	.	508;512	P11137-3;P11137	.;MAP2_HUMAN	V	512;508	ENSP00000353508:M512V;ENSP00000392164:M508V	ENSP00000353508:M512V	M	+	1	0	MAP2	210266673	0.000000	0.05858	0.000000	0.03702	0.344000	0.29017	-0.549000	0.06041	-0.828000	0.04273	-0.280000	0.10049	ATG	.	.		0.418	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538	
RQCD1	9125	hgsc.bcm.edu	37	2	219447748	219447748	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:219447748T>C	ENST00000273064.6	+	3	634	c.259T>C	c.(259-261)Tct>Cct	p.S87P	RQCD1_ENST00000295701.5_Missense_Mutation_p.S87P|RQCD1_ENST00000509807.2_Missense_Mutation_p.S87P|RQCD1_ENST00000542068.1_Missense_Mutation_p.S87P	NM_005444.2	NP_005435.1	Q92600	RCD1_HUMAN	RCD1 required for cell differentiation1 homolog (S. pombe)	87					cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of ligand-dependent nuclear receptor transcription coactivator activity (GO:2000327)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)	15		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000192)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCACACCAGTCTAACAGAGT	0.388																																					p.S87P		Atlas-SNP	.											.	RQCD1	32	.	0			c.T259C						.						149.0	132.0	138.0					2																	219447748		2203	4300	6503	SO:0001583	missense	9125	exon3			CACCAGTCTAACA	D87957	CCDS33379.1, CCDS63123.1	2q35	2010-04-23	2001-11-28		ENSG00000144580	ENSG00000144580			10445	protein-coding gene	gene with protein product	"""cancer/testis antigen 129"""	612054	"""rcd1 (required for cell differentiation, S.pombe) homolog 1"""			9447985	Standard	NM_001271634		Approved	RCD1, RCD1+, CNOT9, CT129	uc010zki.3	Q92600	OTTHUMG00000154750	ENST00000273064.6:c.259T>C	chr2.hg19:g.219447748T>C	ENSP00000273064:p.Ser87Pro	130.0	0.0		95.0	4.0	NM_001271634	B2RPI0|B5MDQ4|B7Z1E5|Q96IX4	Missense_Mutation	SNP	ENST00000273064.6	hg19	CCDS33379.1	.	.	.	.	.	.	.	.	.	.	T	32	5.105907	0.94292	.	.	ENSG00000144580	ENST00000273064;ENST00000509807;ENST00000542068;ENST00000295701	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	6.08	6.08	0.98989	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77961	0.4209	H	0.94658	3.565	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.993;0.993	D	0.84395	0.0557	10	0.87932	D	0	0.3815	16.6438	0.85155	0.0:0.0:0.0:1.0	.	87;87;87	B7Z1E5;Q92600;B5MDQ4	.;RCD1_HUMAN;.	P	87	ENSP00000273064:S87P;ENSP00000441357:S87P;ENSP00000443687:S87P;ENSP00000295701:S87P	ENSP00000273064:S87P	S	+	1	0	RQCD1	219155992	1.000000	0.71417	0.929000	0.37066	0.986000	0.74619	8.040000	0.89188	2.333000	0.79357	0.533000	0.62120	TCT	.	.		0.388	RQCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336920.1	NM_005444	
OBSL1	23363	hgsc.bcm.edu	37	2	220432976	220432976	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:220432976T>C	ENST00000404537.1	-	2	1139	c.1083A>G	c.(1081-1083)gaA>gaG	p.E361E	OBSL1_ENST00000491370.1_5'Flank|OBSL1_ENST00000289656.3_5'UTR|OBSL1_ENST00000265318.4_Silent_p.E361E|OBSL1_ENST00000603926.1_Silent_p.E361E|OBSL1_ENST00000373873.4_Silent_p.E361E|OBSL1_ENST00000373876.1_Silent_p.E361E	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	361	Ig-like 4.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		GTACTTTACATTCCAGCACGG	0.647											OREG0003988	type=REGULATORY REGION|Gene=OBSL1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.E361E		Atlas-SNP	.											OBSL1_ENST00000404537,NS,carcinoma,0,1	OBSL1	120	.	0			c.A1083G						.						26.0	31.0	29.0					2																	220432976		1969	4138	6107	SO:0001819	synonymous_variant	23363	exon2			TTTACATTCCAGC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.1083A>G	chr2.hg19:g.220432976T>C		88.0	1.0	2266	40.0	2.0	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	hg19	CCDS46520.1																																																																																			.	.		0.647	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
STK11IP	114790	hgsc.bcm.edu	37	2	220470738	220470738	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:220470738A>G	ENST00000456909.1	+	9	896	c.806A>G	c.(805-807)cAc>cGc	p.H269R	STK11IP_ENST00000459692.1_3'UTR|STK11IP_ENST00000295641.10_Missense_Mutation_p.H280R			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	280					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTGGAAGGACACCGGGAGCTG	0.602											OREG0003992	type=REGULATORY REGION|Gene=STK11IP|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.H280R		Atlas-SNP	.											.	STK11IP	152	.	0			c.A839G						.						24.0	30.0	28.0					2																	220470738		2157	4270	6427	SO:0001583	missense	114790	exon9			AAGGACACCGGGA	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"""LKB1 interacting protein"""	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.806A>G	chr2.hg19:g.220470738A>G	ENSP00000389383:p.His269Arg	172.0	0.0	2267	116.0	5.0	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Missense_Mutation	SNP	ENST00000456909.1	hg19		.	.	.	.	.	.	.	.	.	.	A	19.14	3.769271	0.69992	.	.	ENSG00000144589	ENST00000456909;ENST00000426736;ENST00000295641	T;T	0.21361	2.01;2.01	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.49932	0.1586	M	0.85197	2.74	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.993;0.999;0.997	T	0.56481	-0.7972	10	0.59425	D	0.04	-19.893	13.5291	0.61611	1.0:0.0:0.0:0.0	.	280;280;280;280	B4DUE4;B4DII2;Q8N1F8-2;Q8N1F8	.;.;.;S11IP_HUMAN	R	269;280;280	ENSP00000389383:H269R;ENSP00000295641:H280R	ENSP00000295641:H280R	H	+	2	0	STK11IP	220178982	1.000000	0.71417	1.000000	0.80357	0.485000	0.33311	7.325000	0.79124	2.061000	0.61500	0.533000	0.62120	CAC	.	.		0.602	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902	
COL4A3	1285	hgsc.bcm.edu	37	2	228162401	228162401	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:228162401G>T	ENST00000396578.3	+	42	3739	c.3577G>T	c.(3577-3579)Gac>Tac	p.D1193Y	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000439598.2_RNA|COL4A3_ENST00000468753.1_3'UTR|AC097662.2_ENST00000396588.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	1193	Triple-helical region.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		AGCCAAAGGAGACAGGGGAGC	0.507																																					p.D1193Y		Atlas-SNP	.											.	COL4A3	293	.	0			c.G3577T						.						15.0	17.0	16.0					2																	228162401		1830	4078	5908	SO:0001583	missense	1285	exon42			AAAGGAGACAGGG		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"""Collagens"""	2204	protein-coding gene	gene with protein product	"""tumstatin"""	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.3577G>T	chr2.hg19:g.228162401G>T	ENSP00000379823:p.Asp1193Tyr	144.0	0.0		95.0	4.0	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	hg19	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	G	8.583	0.882715	0.17467	.	.	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.96334	-3.98	5.54	1.06	0.20224	.	0.309908	0.27581	N	0.018735	D	0.93864	0.8037	M	0.76170	2.325	0.44702	D	0.997699	B;B;B;B	0.17667	0.009;0.009;0.023;0.015	B;B;B;B	0.19946	0.016;0.016;0.016;0.027	D	0.88052	0.2788	10	0.42905	T	0.14	.	5.9189	0.19070	0.3025:0.0:0.5647:0.1328	.	1193;1193;1193;1193	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	Y	1193	ENSP00000379823:D1193Y	ENSP00000323334:D1193Y	D	+	1	0	COL4A3	227870645	0.922000	0.31269	0.999000	0.59377	0.186000	0.23388	1.560000	0.36331	0.281000	0.22233	0.462000	0.41574	GAC	.	.		0.507	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
HTR2B	3357	hgsc.bcm.edu	37	2	231973880	231973880	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:231973880G>A	ENST00000258400.3	-	4	1309	c.797C>T	c.(796-798)aCa>aTa	p.T266I	PSMD1_ENST00000373635.4_Intron|PSMD1_ENST00000308696.6_Intron|PSMD1_ENST00000409643.1_Intron	NM_000867.4	NP_000858.3	P41595	5HT2B_HUMAN	5-hydroxytryptamine (serotonin) receptor 2B, G protein-coupled	266					activation of phospholipase C activity (GO:0007202)|behavior (GO:0007610)|calcium-mediated signaling (GO:0019722)|cardiac muscle hypertrophy (GO:0003300)|cellular calcium ion homeostasis (GO:0006874)|cellular response to temperature stimulus (GO:0071502)|cGMP biosynthetic process (GO:0006182)|embryonic morphogenesis (GO:0048598)|ERK1 and ERK2 cascade (GO:0070371)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway (GO:0007186)|heart morphogenesis (GO:0003007)|intestine smooth muscle contraction (GO:0014827)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell death (GO:0060548)|neural crest cell differentiation (GO:0014033)|neural crest cell migration (GO:0001755)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphorylation (GO:0016310)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	drug binding (GO:0008144)|G-protein alpha-subunit binding (GO:0001965)|Ras GTPase activator activity (GO:0005099)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	11		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;4.48e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0141)	Amoxapine(DB00543)|Apomorphine(DB00714)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Dihydroergotamine(DB00320)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Lisuride(DB00589)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Ropinirole(DB00268)|Triflupromazine(DB00508)|Yohimbine(DB01392)	TTGGAAAACTGTAGACACAGT	0.458																																					p.T266I	Ovarian(155;1331 1891 12853 14038 34991)	Atlas-SNP	.											.	HTR2B	33	.	0			c.C797T						.						167.0	148.0	154.0					2																	231973880		2203	4300	6503	SO:0001583	missense	3357	exon4			AAAACTGTAGACA		CCDS2483.1	2q36.3-q37.1	2012-08-08	2012-02-03		ENSG00000135914	ENSG00000135914		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5294	protein-coding gene	gene with protein product		601122	"""5-hydroxytryptamine (serotonin) receptor 2B"""			8143856	Standard	NM_000867		Approved	5-HT(2B), 5-HT2B	uc002vro.3	P41595	OTTHUMG00000133222	ENST00000258400.3:c.797C>T	chr2.hg19:g.231973880G>A	ENSP00000258400:p.Thr266Ile	248.0	0.0		147.0	57.0	NM_000867	B2R9D5|Q53TI1|Q62221|Q6P523	Missense_Mutation	SNP	ENST00000258400.3	hg19	CCDS2483.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.664060	0.67700	.	.	ENSG00000135914	ENST00000258400	T	0.61742	0.08	5.61	5.61	0.85477	GPCR, rhodopsin-like superfamily (1);	0.049844	0.85682	D	0.000000	T	0.73434	0.3586	M	0.63428	1.95	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.68483	0.958;0.917	T	0.68895	-0.5288	10	0.30854	T	0.27	.	19.6415	0.95760	0.0:0.0:1.0:0.0	.	81;266	B3VRC5;P41595	.;5HT2B_HUMAN	I	266	ENSP00000258400:T266I	ENSP00000258400:T266I	T	-	2	0	HTR2B	231682124	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	9.869000	0.99810	2.638000	0.89438	0.650000	0.86243	ACA	.	.		0.458	HTR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256957.2	NM_000867	
NCL	4691	hgsc.bcm.edu	37	2	232325390	232325390	+	Silent	SNP	C	C	T	rs371798454		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:232325390C>T	ENST00000322723.4	-	4	1041	c.801G>A	c.(799-801)gaG>gaA	p.E267E	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	267	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		CTTCCTCCTCCTCTTCTTCCT	0.413																																					p.E267E		Atlas-SNP	.											.	NCL	80	.	0			c.G801A						.	C		1,4405	2.1+/-5.4	0,1,2202	239.0	208.0	219.0		801	-3.1	0.5	2		219	0,8600		0,0,4300	no	coding-synonymous	NCL	NM_005381.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		267/711	232325390	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4691	exon4			CTCCTCCTCTTCT		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"""RNA binding motif (RRM) containing"""	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.801G>A	chr2.hg19:g.232325390C>T		318.0	0.0		208.0	17.0	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Silent	SNP	ENST00000322723.4	hg19	CCDS33397.1																																																																																			.	.		0.413	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381	
TRPM8	79054	hgsc.bcm.edu	37	2	234854669	234854669	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:234854669T>C	ENST00000324695.4	+	7	909	c.869T>C	c.(868-870)aTt>aCt	p.I290T	TRPM8_ENST00000433712.2_5'UTR|AC005538.5_ENST00000455991.1_RNA	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	290					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.I290N(1)		breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	GAGCGCACTATTCAAGGTCAG	0.473																																					p.I290T		Atlas-SNP	.											TRPM8,NS,carcinoma,0,1	TRPM8	146	.	1	Substitution - Missense(1)	lung(1)	c.T869C						.						71.0	62.0	65.0					2																	234854669		2203	4300	6503	SO:0001583	missense	79054	exon7			GCACTATTCAAGG	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.869T>C	chr2.hg19:g.234854669T>C	ENSP00000323926:p.Ile290Thr	95.0	0.0		77.0	4.0	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	hg19	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	T	6.697	0.497211	0.12762	.	.	ENSG00000144481	ENST00000324695	T	0.37058	1.22	5.75	4.65	0.58169	.	0.419814	0.24438	N	0.038539	T	0.25269	0.0614	L	0.33339	1.005	0.48830	D	0.999716	B	0.02656	0.0	B	0.06405	0.002	T	0.06716	-1.0811	10	0.41790	T	0.15	-8.8753	6.4808	0.22061	0.0:0.0859:0.2025:0.7117	.	290	Q7Z2W7	TRPM8_HUMAN	T	290	ENSP00000323926:I290T	ENSP00000323926:I290T	I	+	2	0	TRPM8	234519408	0.995000	0.38212	0.936000	0.37596	0.814000	0.46013	2.049000	0.41288	1.091000	0.41335	0.533000	0.62120	ATT	.	.		0.473	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
ACKR3	57007	hgsc.bcm.edu	37	2	237489664	237489664	+	Missense_Mutation	SNP	G	G	T	rs143561143	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:237489664G>T	ENST00000272928.3	+	2	866	c.556G>T	c.(556-558)Gtc>Ttc	p.V186F		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	186					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)	p.V186F(1)|p.V186I(1)									CCTGAAGACCGTCACGTCTGC	0.587																																					p.V186F		Atlas-SNP	.											CXCR7_ENST00000272928,caecum,carcinoma,0,2	CXCR7	72	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G556T						.						148.0	132.0	138.0					2																	237489664		2203	4300	6503	SO:0001583	missense	57007	exon2			AAGACCGTCACGT	BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : Atypical"""	23692	protein-coding gene	gene with protein product		610376	"""chemokine orphan receptor 1"", ""chemokine (C-X-C motif) receptor 7"""	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.556G>T	chr2.hg19:g.237489664G>T	ENSP00000272928:p.Val186Phe	85.0	0.0		89.0	4.0	NM_020311	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	hg19	CCDS2516.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.579509	0.65878	.	.	ENSG00000144476	ENST00000447924;ENST00000272928	T;T	0.37752	1.18;1.18	5.7	1.92	0.25849	GPCR, rhodopsin-like superfamily (1);	0.207947	0.39687	N	0.001293	T	0.40979	0.1139	L	0.45352	1.415	0.43372	D	0.995466	D	0.60160	0.987	P	0.62089	0.898	T	0.21143	-1.0254	10	0.11182	T	0.66	.	10.2608	0.43425	0.3193:0.0:0.6806:0.0	.	186	P25106	CXCR7_HUMAN	F	186	ENSP00000405945:V186F;ENSP00000272928:V186F	ENSP00000272928:V186F	V	+	1	0	CXCR7	237154403	0.999000	0.42202	0.961000	0.40146	0.988000	0.76386	2.813000	0.48002	0.773000	0.33404	-0.137000	0.14449	GTC	.	G|0.999;A|0.001		0.587	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311	
SEPT2	4735	hgsc.bcm.edu	37	2	242287583	242287583	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr2:242287583A>G	ENST00000391973.2	+	11	1489	c.961A>G	c.(961-963)Atc>Gtc	p.I321V	SEPT2_ENST00000360051.3_Missense_Mutation_p.I321V|SEPT2_ENST00000401990.1_Missense_Mutation_p.I331V|SEPT2_ENST00000402092.2_Missense_Mutation_p.I321V|SEPT2_ENST00000407971.1_Missense_Mutation_p.I281V|SEPT2_ENST00000391971.2_Missense_Mutation_p.I321V	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN	septin 2	321					cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|neuron projection development (GO:0031175)|regulation of L-glutamate transport (GO:0002036)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|synapse (GO:0045202)	enzyme regulator activity (GO:0030234)|GTP binding (GO:0005525)			central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|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;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		TAAAGACCAGATCTTGCTGGA	0.383																																					p.I321V		Atlas-SNP	.											.	SEPT2	33	.	0			c.A961G						.						170.0	172.0	171.0					2																	242287583		2203	4300	6503	SO:0001583	missense	4735	exon12			GACCAGATCTTGC	D28540	CCDS2548.1, CCDS63195.1, CCDS74682.1	2q37.3	2013-01-21	2005-01-11	2005-01-12	ENSG00000168385	ENSG00000168385		"""Septins"""	7729	protein-coding gene	gene with protein product		601506	"""neural precursor cell expressed, developmentally down-regulated 5"""	DIFF6, NEDD5		8697812	Standard	XM_005247011		Approved	KIAA0158, hNedd5, Pnutl3	uc002wbd.3	Q15019	OTTHUMG00000133394	ENST00000391973.2:c.961A>G	chr2.hg19:g.242287583A>G	ENSP00000375834:p.Ile321Val	160.0	0.0		100.0	4.0	NM_001008491	B4DGE8|Q14132|Q53QU3|Q8IUK9|Q96CB0	Missense_Mutation	SNP	ENST00000391973.2	hg19	CCDS2548.1	.	.	.	.	.	.	.	.	.	.	A	17.62	3.433859	0.62955	.	.	ENSG00000168385	ENST00000391973;ENST00000360051;ENST00000391971;ENST00000401990;ENST00000407971;ENST00000402092;ENST00000391972;ENST00000421717	T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.73;0.73;0.72;0.94	6.07	6.07	0.98685	.	0.099286	0.64402	D	0.000003	T	0.47801	0.1465	M	0.71036	2.16	0.80722	D	1	B;B;B	0.27192	0.171;0.103;0.124	B;B;B	0.31869	0.137;0.023;0.075	T	0.48305	-0.9047	10	0.02654	T	1	.	16.6288	0.85011	1.0:0.0:0.0:0.0	.	356;281;321	Q15019-2;B5MCX3;Q15019	.;.;SEPT2_HUMAN	V	321;321;321;331;281;321;356;148	ENSP00000375834:I321V;ENSP00000353157:I321V;ENSP00000375832:I321V;ENSP00000385109:I331V;ENSP00000384525:I281V;ENSP00000385172:I321V;ENSP00000408296:I148V	ENSP00000353157:I321V	I	+	1	0	SEPT2	241936256	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	8.414000	0.90238	2.326000	0.78906	0.533000	0.62120	ATC	.	.		0.383	SEPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323177.3	NM_006155	
SSUH2	51066	hgsc.bcm.edu	37	3	8669446	8669446	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:8669446T>C	ENST00000317371.4	-	15	1771	c.546A>G	c.(544-546)ggA>ggG	p.G182G	SSUH2_ENST00000544814.1_Silent_p.G204G|SSUH2_ENST00000341795.3_Silent_p.G182G|SSUH2_ENST00000415132.1_Silent_p.G182G			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	182	Cys-rich.					cytoplasm (GO:0005737)											TGCGCTTGGCTCCGCAGCAGG	0.662																																					p.G204G		Atlas-SNP	.											.	.	.	.	0			c.A612G						.						59.0	55.0	56.0					3																	8669446		2203	4300	6503	SO:0001819	synonymous_variant	51066	exon8			CTTGGCTCCGCAG	AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 32"""	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.546A>G	chr3.hg19:g.8669446T>C		138.0	0.0		132.0	7.0	NM_001256748	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Silent	SNP	ENST00000317371.4	hg19	CCDS2568.1																																																																																			.	.		0.662	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931	
SRGAP3	9901	hgsc.bcm.edu	37	3	9146431	9146431	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:9146431A>G	ENST00000383836.3	-	3	783	c.356T>C	c.(355-357)aTc>aCc	p.I119T	SRGAP3_ENST00000433332.3_5'UTR|SRGAP3_ENST00000360413.3_Missense_Mutation_p.I119T	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	119	F-BAR domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		GTTCATGAAGATGTCATTGAG	0.542			T	RAF1	pilocytic astrocytoma																																p.I119T		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.T356C						.						151.0	137.0	142.0					3																	9146431		2203	4300	6503	SO:0001583	missense	9901	exon3			ATGAAGATGTCAT	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"""Rho GTPase activating proteins"""	19744	protein-coding gene	gene with protein product		606525	"""SLIT-ROBO Rho GTPase activating protein 2"""	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.356T>C	chr3.hg19:g.9146431A>G	ENSP00000373347:p.Ile119Thr	110.0	0.0		99.0	4.0	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	hg19	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.644603	0.87859	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.12984	2.63;2.63	5.69	5.69	0.88448	Fps/Fes/Fer/CIP4 homology (1);	0.000000	0.85682	D	0.000000	T	0.32823	0.0842	M	0.70903	2.155	0.80722	D	1	D;B;P	0.57571	0.98;0.403;0.458	P;B;B	0.58130	0.833;0.221;0.328	T	0.03166	-1.1065	10	0.56958	D	0.05	.	15.6084	0.76692	1.0:0.0:0.0:0.0	.	119;119;119	C7TPG7;O43295-2;O43295	.;.;SRGP2_HUMAN	T	119	ENSP00000373347:I119T;ENSP00000353587:I119T	ENSP00000353587:I119T	I	-	2	0	SRGAP3	9121431	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.224000	0.95209	2.157000	0.67596	0.528000	0.53228	ATC	.	.		0.542	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3		
CAND2	23066	hgsc.bcm.edu	37	3	12854590	12854590	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:12854590A>G	ENST00000456430.2	+	6	900	c.859A>G	c.(859-861)Agg>Ggg	p.R287G	CAND2_ENST00000295989.5_Missense_Mutation_p.R194G	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	287					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GGCCTTCTTGAGGAAGTATGT	0.577																																					p.R287G	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.A859G						.						26.0	28.0	27.0					3																	12854590		1907	4128	6035	SO:0001583	missense	23066	exon6			TTCTTGAGGAAGT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.859A>G	chr3.hg19:g.12854590A>G	ENSP00000387641:p.Arg287Gly	116.0	0.0		90.0	4.0	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	hg19	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	A	14.46	2.542060	0.45280	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.32515	1.45;1.45	4.34	3.14	0.36123	Armadillo-like helical (1);Armadillo-type fold (1);	0.060935	0.64402	D	0.000005	T	0.42200	0.1192	L	0.49699	1.58	0.80722	D	1	P;D	0.57899	0.791;0.981	B;D	0.69142	0.231;0.962	T	0.12889	-1.0530	10	0.21014	T	0.42	-10.4408	9.068	0.36475	0.8141:0.1858:0.0:0.0	.	287;194	O75155;O75155-2	CAND2_HUMAN;.	G	194;287	ENSP00000295989:R194G;ENSP00000387641:R287G	ENSP00000295989:R194G	R	+	1	2	CAND2	12829590	1.000000	0.71417	0.998000	0.56505	0.904000	0.53231	3.319000	0.51983	0.494000	0.27859	0.379000	0.24179	AGG	.	.		0.577	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
TOP2B	7155	hgsc.bcm.edu	37	3	25654010	25654010	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:25654010T>C	ENST00000264331.4	-	28	3781	c.3782A>G	c.(3781-3783)aAg>aGg	p.K1261R	TOP2B_ENST00000475717.1_5'Flank|TOP2B_ENST00000540199.1_Missense_Mutation_p.K113R|TOP2B_ENST00000542520.1_Missense_Mutation_p.K113R|TOP2B_ENST00000435706.2_Missense_Mutation_p.K1256R	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	1261					ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	TCATACCTTCTTCTTCTTCAG	0.338																																					p.K1256R		Atlas-SNP	.											.	TOP2B	98	.	0			c.A3767G						.						131.0	126.0	127.0					3																	25654010		1848	4077	5925	SO:0001583	missense	7155	exon28			ACCTTCTTCTTCT	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"""topoisomerase (DNA) II beta (180kD)"""			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.3782A>G	chr3.hg19:g.25654010T>C	ENSP00000264331:p.Lys1261Arg	90.0	0.0		102.0	5.0	NM_001068	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	hg19		.	.	.	.	.	.	.	.	.	.	T	13.86	2.361890	0.41801	.	.	ENSG00000077097	ENST00000542520;ENST00000435706;ENST00000264331;ENST00000540199	T;T;T;T	0.54071	0.59;0.82;0.82;0.59	6.16	5.01	0.66863	.	0.040493	0.85682	N	0.000000	T	0.47432	0.1445	L	0.48642	1.525	0.58432	D	0.999991	B;B	0.32010	0.001;0.351	B;B	0.36567	0.001;0.228	T	0.32955	-0.9887	10	0.21540	T	0.41	-12.2423	12.3261	0.55011	0.0:0.0654:0.0:0.9346	.	1261;1256	Q02880;Q02880-2	TOP2B_HUMAN;.	R	113;1256;1261;113	ENSP00000446023:K113R;ENSP00000396704:K1256R;ENSP00000264331:K1261R;ENSP00000437352:K113R	ENSP00000264331:K1261R	K	-	2	0	TOP2B	25629014	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.755000	0.62198	1.155000	0.42497	0.528000	0.53228	AAG	.	.		0.338	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
LRRC3B	116135	hgsc.bcm.edu	37	3	26751506	26751506	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:26751506T>C	ENST00000396641.2	+	2	935	c.343T>C	c.(343-345)Ttg>Ctg	p.L115L	LRRC3B_ENST00000456208.2_Silent_p.L115L|LRRC3B_ENST00000417744.1_Silent_p.L115L|AC114877.3_ENST00000446601.1_lincRNA	NM_052953.2	NP_443185.1	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	115						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	21						AGCTGAAACCTTGCAGACTCT	0.453																																					p.L115L		Atlas-SNP	.											.	LRRC3B	51	.	0			c.T343C						.						64.0	60.0	61.0					3																	26751506		2203	4300	6503	SO:0001819	synonymous_variant	116135	exon2			GAAACCTTGCAGA	AF396933	CCDS2644.1	3p24	2004-07-12			ENSG00000179796	ENSG00000179796			28105	protein-coding gene	gene with protein product							Standard	NM_052953		Approved	LRP15	uc003cdp.3	Q96PB8	OTTHUMG00000130572	ENST00000396641.2:c.343T>C	chr3.hg19:g.26751506T>C		76.0	0.0		81.0	4.0	NM_052953	Q5M8T0	Silent	SNP	ENST00000396641.2	hg19	CCDS2644.1																																																																																			.	.		0.453	LRRC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252997.2	NM_052953	
LRRC3B	116135	hgsc.bcm.edu	37	3	26751740	26751740	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:26751740G>T	ENST00000396641.2	+	2	1169	c.577G>T	c.(577-579)Gac>Tac	p.D193Y	LRRC3B_ENST00000456208.2_Missense_Mutation_p.D193Y|LRRC3B_ENST00000417744.1_Missense_Mutation_p.D193Y|AC114877.3_ENST00000446601.1_lincRNA	NM_052953.2	NP_443185.1	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	193	LRRCT.					integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	21						CAACGACGCTGACCTTTGTAA	0.468																																					p.D193Y		Atlas-SNP	.											.	LRRC3B	51	.	0			c.G577T						.						78.0	71.0	73.0					3																	26751740		2203	4300	6503	SO:0001583	missense	116135	exon2			GACGCTGACCTTT	AF396933	CCDS2644.1	3p24	2004-07-12			ENSG00000179796	ENSG00000179796			28105	protein-coding gene	gene with protein product							Standard	NM_052953		Approved	LRP15	uc003cdp.3	Q96PB8	OTTHUMG00000130572	ENST00000396641.2:c.577G>T	chr3.hg19:g.26751740G>T	ENSP00000379880:p.Asp193Tyr	197.0	0.0		146.0	10.0	NM_052953	Q5M8T0	Missense_Mutation	SNP	ENST00000396641.2	hg19	CCDS2644.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.666595	0.67814	.	.	ENSG00000179796	ENST00000396641;ENST00000417744;ENST00000456208	T;T;T	0.61742	0.08;0.08;0.08	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.70561	0.3238	L	0.41824	1.3	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	T	0.70103	-0.4964	10	0.72032	D	0.01	-18.9203	19.8676	0.96824	0.0:0.0:1.0:0.0	.	193	Q96PB8	LRC3B_HUMAN	Y	193	ENSP00000379880:D193Y;ENSP00000406370:D193Y;ENSP00000394940:D193Y	ENSP00000379880:D193Y	D	+	1	0	LRRC3B	26726744	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.062000	0.89475	2.941000	0.99782	0.655000	0.94253	GAC	.	.		0.468	LRRC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252997.2	NM_052953	
ZNF860	344787	hgsc.bcm.edu	37	3	32030625	32030625	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:32030625T>C	ENST00000360311.4	+	2	603	c.54T>C	c.(52-54)gcT>gcC	p.A18A		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	18					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)|lung(4)|ovary(1)	8						CAGGCATGGCTCTTCCTCAGG	0.493																																					p.A18A		Atlas-SNP	.											.	ZNF860	96	.	0			c.T54C						.						47.0	42.0	44.0					3																	32030625		692	1591	2283	SO:0001819	synonymous_variant	344787	exon2			CATGGCTCTTCCT	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.54T>C	chr3.hg19:g.32030625T>C		206.0	0.0		124.0	5.0	NM_001137674	B4DFA4	Silent	SNP	ENST00000360311.4	hg19	CCDS46784.1																																																																																			.	.		0.493	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
ZNF860	344787	hgsc.bcm.edu	37	3	32032133	32032133	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:32032133A>G	ENST00000360311.4	+	2	2111	c.1562A>G	c.(1561-1563)cAa>cGa	p.Q521R		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	521					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)|lung(4)|ovary(1)	8						GTTTTTAATCAACAAGCAACC	0.403																																					p.Q521R		Atlas-SNP	.											.	ZNF860	96	.	0			c.A1562G						.						40.0	35.0	37.0					3																	32032133		692	1591	2283	SO:0001583	missense	344787	exon2			TTAATCAACAAGC	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1562A>G	chr3.hg19:g.32032133A>G	ENSP00000373274:p.Gln521Arg	141.0	0.0		107.0	5.0	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	hg19	CCDS46784.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-2.965020	0.00049	.	.	ENSG00000197385	ENST00000360311	T	0.14893	2.47	0.309	-0.618	0.11576	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05273	0.0140	N	0.02658	-0.545	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40739	-0.9547	8	.	.	.	.	4.8639	0.13598	0.7388:0.0:0.2612:0.0	.	521	A6NHJ4	ZN860_HUMAN	R	521	ENSP00000373274:Q521R	.	Q	+	2	0	ZNF860	32007137	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.656000	0.05342	-1.377000	0.02123	-1.381000	0.01174	CAA	.	.		0.403	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
XYLB	9942	hgsc.bcm.edu	37	3	38442465	38442465	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:38442465G>A	ENST00000207870.3	+	18	1612	c.1522G>A	c.(1522-1524)Gga>Aga	p.G508R	XYLB_ENST00000542835.1_Missense_Mutation_p.G371R|XYLB_ENST00000472721.1_3'UTR	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	508					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)		CCCAAGCCCGGGAGCTTCTCA	0.488																																					p.G508R		Atlas-SNP	.											.	XYLB	50	.	0			c.G1522A						.						119.0	113.0	115.0					3																	38442465		2203	4300	6503	SO:0001583	missense	9942	exon18			AGCCCGGGAGCTT	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.1522G>A	chr3.hg19:g.38442465G>A	ENSP00000207870:p.Gly508Arg	134.0	0.0		98.0	4.0	NM_005108	B2RAW4|B4DDT2|B9EH64	Missense_Mutation	SNP	ENST00000207870.3	hg19	CCDS2678.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.824271	0.50739	.	.	ENSG00000093217	ENST00000207870;ENST00000542835	T;T	0.43294	0.95;0.95	5.5	5.5	0.81552	.	0.301489	0.30979	N	0.008498	T	0.37705	0.1013	L	0.46157	1.445	0.45676	D	0.998592	B;B	0.15719	0.006;0.014	B;B	0.17722	0.013;0.019	T	0.08027	-1.0742	10	0.27082	T	0.32	.	14.7704	0.69671	0.0:0.0:1.0:0.0	.	371;508	B4DDT2;O75191	.;XYLB_HUMAN	R	508;371	ENSP00000207870:G508R;ENSP00000443659:G371R	ENSP00000207870:G508R	G	+	1	0	XYLB	38417469	1.000000	0.71417	0.931000	0.37212	0.815000	0.46073	4.629000	0.61290	2.861000	0.98227	0.655000	0.94253	GGA	.	.		0.488	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108	
EXOG	9941	hgsc.bcm.edu	37	3	38539163	38539164	+	Missense_Mutation	DNP	AA	AA	TT			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:38539163_38539164AA>TT	ENST00000287675.5	+	2	303_304	c.207_208AA>TT	c.(205-210)ttAAct>ttTTct	p.69_70LT>FS	EXOG_ENST00000358249.2_5'UTR|EXOG_ENST00000422077.2_Intron	NM_005107.3	NP_005098.2	Q9Y2C4	EXOG_HUMAN	endo/exonuclease (5'-3'), endonuclease G-like	69					DNA catabolic process, endonucleolytic (GO:0000737)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			central_nervous_system(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	17						GATTCCCTTTAACTGGAACAGA	0.401																																					p.L69F|p.T70S		Atlas-SNP	.											.	EXOG	29	.	0			c.A207T|c.A208T						.																																			SO:0001583	missense	9941	exon2			CCCTTTAACTGGA|CCTTTAACTGGAA	AB020523	CCDS2680.1, CCDS46795.1	3p21.3	2010-05-07	2009-01-08	2009-01-08	ENSG00000157036	ENSG00000157036	3.1.30.-		3347	protein-coding gene	gene with protein product		604051	"""endonuclease G-like 1"", ""endonuclease G-like 2"""	ENDOGL1, ENDOGL2		10231028, 18187503	Standard	NM_005107		Approved	ENGL-a, ENGL, ENGL-b	uc003cih.2	Q9Y2C4	OTTHUMG00000131295	Exception_encountered	chr3.hg19:g.38539163_38539164delinsTT	ENSP00000287675:p.L69_T70delinsFS	115.0|117.0	0.0		81.0	5.0|4.0	NM_005107	A8K242|B4DVG2|Q3SXM9|Q9Y2C8	Missense_Mutation	SNP	ENST00000287675.5	hg19	CCDS2680.1																																																																																			.	.		0.401	EXOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254063.2	NM_005107	
RPSA	3921	hgsc.bcm.edu	37	3	39453157	39453157	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:39453157T>C	ENST00000301821.6	+	5	625	c.516T>C	c.(514-516)ggT>ggC	p.G172G	RPSA_ENST00000478027.1_3'UTR|RPSA_ENST00000443003.1_Silent_p.G177G|SNORA62_ENST00000365493.1_RNA	NM_001012321.1|NM_002295.4	NP_001012321.1|NP_002286.2			ribosomal protein SA											endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.0509)|Kidney(284;0.064)		ACTCAGTGGGTTTGATGTGGT	0.512																																					p.G172G		Atlas-SNP	.											.	RPSA	15	.	0			c.T516C						.						151.0	151.0	151.0					3																	39453157		2203	4300	6503	SO:0001819	synonymous_variant	3921	exon4			AGTGGGTTTGATG	S37431	CCDS2686.1	3p21.3	2014-09-17	2002-08-29	2005-02-11	ENSG00000168028	ENSG00000168028			6502	protein-coding gene	gene with protein product		150370	"""laminin receptor 1 (67kD, ribosomal protein SA)"""	LAMR1		1534510, 8760291	Standard	NM_001012321		Approved	LRP, 37LRP, p40, SA	uc003cjp.3	P08865	OTTHUMG00000131296	ENST00000301821.6:c.516T>C	chr3.hg19:g.39453157T>C		112.0	0.0		83.0	4.0	NM_001012321		Silent	SNP	ENST00000301821.6	hg19	CCDS2686.1																																																																																			.	.		0.512	RPSA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254064.3	NM_002295	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266104	41266104	+	Missense_Mutation	SNP	G	G	T	rs28931589|rs121913416		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:41266104G>T	ENST00000349496.5	+	3	381	c.101G>T	c.(100-102)gGa>gTa	p.G34V	CTNNB1_ENST00000396185.3_Missense_Mutation_p.G34V|CTNNB1_ENST00000405570.1_Missense_Mutation_p.G34V|CTNNB1_ENST00000453024.1_Missense_Mutation_p.G27V|CTNNB1_ENST00000396183.3_Missense_Mutation_p.G34V	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	34			G -> E (in PTR). {ECO:0000269|PubMed:10192393}.|G -> R (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|G -> V (in hepatoblastoma; dbSNP:rs28931589). {ECO:0000269|PubMed:9927029}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.G34E(73)|p.G34V(72)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D32_H36>D(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.D32_H36del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CTGGACTCTGGAATCCATTCT	0.488	G34E(AGS_STOMACH)	15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												p.G34V	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	CTNNB1,gallbladder,other,0,161	CTNNB1	4904	.	276	Substitution - Missense(145)|Deletion - In frame(105)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(146)|endometrium(30)|large_intestine(27)|stomach(21)|central_nervous_system(20)|skin(8)|pancreas(8)|ovary(6)|small_intestine(2)|lung(2)|adrenal_gland(1)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|pituitary(1)|prostate(1)|bone(1)	c.G101T						.						93.0	78.0	83.0					3																	41266104		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACTCTGGAATCCA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.101G>T	chr3.hg19:g.41266104G>T	ENSP00000344456:p.Gly34Val	260.0	1.0		209.0	13.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.450603	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-31.2232	19.9596	0.97236	0.0:0.0:1.0:0.0	rs28931589	34	P35222	CTNB1_HUMAN	V	27;34;34;34;34;27;34;34;34	ENSP00000400508:G27V;ENSP00000385604:G34V;ENSP00000412219:G34V;ENSP00000379486:G34V;ENSP00000344456:G34V;ENSP00000411226:G27V;ENSP00000379488:G34V;ENSP00000409302:G34V;ENSP00000401599:G34V	ENSP00000344456:G34V	G	+	2	0	CTNNB1	41241108	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.726000	0.93360	0.655000	0.94253	GGA	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
LRRC2	79442	hgsc.bcm.edu	37	3	46569020	46569020	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:46569020A>G	ENST00000395905.3	-	7	1217	c.825T>C	c.(823-825)ctT>ctC	p.L275L	LRRC2_ENST00000296144.3_Silent_p.L275L	NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	275										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	17		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		TGGAATAGGGAAGGTAGGTCA	0.458																																					p.L275L		Atlas-SNP	.											.	LRRC2	37	.	0			c.T825C						.						107.0	100.0	102.0					3																	46569020		2203	4300	6503	SO:0001819	synonymous_variant	79442	exon7			ATAGGGAAGGTAG	AJ308569	CCDS2741.1	3p21.3	2014-07-30	2003-11-19		ENSG00000163827	ENSG00000163827			14676	protein-coding gene	gene with protein product		607180	"""leucine-rich repeat-containing 2"""			11896456	Standard	NM_024512		Approved		uc010hji.3	Q9BYS8	OTTHUMG00000133479	ENST00000395905.3:c.825T>C	chr3.hg19:g.46569020A>G		99.0	0.0		100.0	4.0	NM_024512	B2RDQ7|Q96LT5	Silent	SNP	ENST00000395905.3	hg19	CCDS2741.1																																																																																			.	.		0.458	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257375.2		
ALS2CL	259173	hgsc.bcm.edu	37	3	46722798	46722798	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:46722798C>T	ENST00000318962.4	-	13	1457	c.1374G>A	c.(1372-1374)agG>agA	p.R458R	ALS2CL_ENST00000415953.1_Silent_p.R458R	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	458					endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		GGCCCGTGTACCTGAAGGGCT	0.662																																					p.R458R		Atlas-SNP	.											.	ALS2CL	78	.	0			c.G1374A						.						78.0	85.0	82.0					3																	46722798		2203	4300	6503	SO:0001819	synonymous_variant	259173	exon13			CGTGTACCTGAAG	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.1374G>A	chr3.hg19:g.46722798C>T		211.0	0.0		152.0	53.0	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Silent	SNP	ENST00000318962.4	hg19	CCDS2743.1																																																																																			.	.		0.662	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	
NBEAL2	23218	hgsc.bcm.edu	37	3	47043918	47043918	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:47043918A>T	ENST00000450053.3	+	32	5388	c.5209A>T	c.(5209-5211)Atg>Ttg	p.M1737L	NBEAL2_ENST00000292309.5_Missense_Mutation_p.M1553L|NBEAL2_ENST00000383740.2_Missense_Mutation_p.M16L	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1737					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CCACGACCTTATGTCAGGTTT	0.587																																					p.M1737L		Atlas-SNP	.											.	NBEAL2	267	.	0			c.A5209T						.						75.0	77.0	76.0					3																	47043918		2099	4206	6305	SO:0001583	missense	23218	exon32			GACCTTATGTCAG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.5209A>T	chr3.hg19:g.47043918A>T	ENSP00000415034:p.Met1737Leu	92.0	0.0		91.0	26.0	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	hg19	CCDS46817.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	25.8|25.8|25.8	4.679318|4.679318|4.679318	0.88542|0.88542|0.88542	.|.|.	.|.|.	ENSG00000160796|ENSG00000160796|ENSG00000160796	ENST00000416683|ENST00000292309;ENST00000383740;ENST00000450053|ENST00000443829	T|T;T;T|.	0.58060|0.56776|.	0.36|0.5;1.14;0.44|.	4.84|4.84|4.84	4.84|4.84|4.84	0.62591|0.62591|0.62591	.|.|.	.|0.046774|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|T	0.63498|0.63498|0.63498	0.2516|0.2516|0.2516	L|L|L	0.54323|0.54323|0.54323	1.7|1.7|1.7	0.53688|0.53688|0.53688	D|D|D	0.999971|0.999971|0.999971	.|B;P|.	.|0.34462|.	.|0.264;0.454|.	.|B;B|.	.|0.37601|.	.|0.082;0.254|.	T|T|T	0.62091|0.62091|0.62091	-0.6927|-0.6927|-0.6927	7|10|5	0.54805|0.36615|.	T|T|.	0.06|0.2|.	.|.|.	13.4524|13.4524|13.4524	0.61178|0.61178|0.61178	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.|.	.|1553;1737|.	.|Q6ZNJ1-2;Q6ZNJ1|.	.|.;NBEL2_HUMAN|.	F|L|F	1024|1553;16;1737|105	ENSP00000410405:L1024F|ENSP00000292309:M1553L;ENSP00000373246:M16L;ENSP00000415034:M1737L|.	ENSP00000410405:L1024F|ENSP00000292309:M1553L|.	L|M|Y	+|+|+	3|1|2	2|0|0	NBEAL2|NBEAL2|NBEAL2	47018922|47018922|47018922	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.974000|0.974000|0.974000	0.67602|0.67602|0.67602	9.106000|9.106000|9.106000	0.94253|0.94253|0.94253	2.045000|2.045000|2.045000	0.60652|0.60652|0.60652	0.529000|0.529000|0.529000	0.55759|0.55759|0.55759	TTA|ATG|TAT	.	.		0.587	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
PTPN23	25930	hgsc.bcm.edu	37	3	47454662	47454662	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:47454662T>C	ENST00000265562.4	+	25	4975	c.4898T>C	c.(4897-4899)cTc>cCc	p.L1633P	PTPN23_ENST00000431726.1_Missense_Mutation_p.L1507P	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1633					cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTCTGGACACTCAACAAGACC	0.572																																					p.L1633P		Atlas-SNP	.											.	PTPN23	85	.	0			c.T4898C						.						71.0	72.0	71.0					3																	47454662		2202	4291	6493	SO:0001583	missense	25930	exon25			GGACACTCAACAA	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.4898T>C	chr3.hg19:g.47454662T>C	ENSP00000265562:p.Leu1633Pro	94.0	0.0		87.0	4.0	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	hg19	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.970869	0.53614	.	.	ENSG00000076201	ENST00000265562	T	0.13901	2.55	4.35	4.35	0.52113	.	0.000000	0.64402	D	0.000017	T	0.25791	0.0628	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.01988	-1.1234	10	0.87932	D	0	-26.5951	12.6561	0.56788	0.0:0.0:0.0:1.0	.	1633	Q9H3S7	PTN23_HUMAN	P	1633	ENSP00000265562:L1633P	ENSP00000265562:L1633P	L	+	2	0	PTPN23	47429666	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.147000	0.77382	1.805000	0.52779	0.460000	0.39030	CTC	.	.		0.572	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	
LAMB2	3913	hgsc.bcm.edu	37	3	49162306	49162306	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:49162306T>C	ENST00000418109.1	-	22	3101	c.2937A>G	c.(2935-2937)ccA>ccG	p.P979P	LAMB2_ENST00000305544.4_Silent_p.P979P|LAMB2_ENST00000464891.1_5'UTR	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	979	Laminin EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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)		ACCGGCCACCTGGCCTTGATG	0.602																																					p.P979P		Atlas-SNP	.											.	LAMB2	156	.	0			c.A2937G						.						87.0	77.0	81.0					3																	49162306		2203	4300	6503	SO:0001819	synonymous_variant	3913	exon21			GCCACCTGGCCTT		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.2937A>G	chr3.hg19:g.49162306T>C		54.0	0.0		43.0	4.0	NM_002292	Q16321	Silent	SNP	ENST00000418109.1	hg19	CCDS2789.1																																																																																			.	.		0.602	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	
GNAT1	2779	hgsc.bcm.edu	37	3	50231568	50231568	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:50231568A>G	ENST00000433068.1	+	6	678	c.622A>G	c.(622-624)Atc>Gtc	p.I208V	GNAT1_ENST00000232461.3_Missense_Mutation_p.I208V|GNAT1_ENST00000481246.1_3'UTR	NM_000172.3	NP_000163.2	P11488	GNAT1_HUMAN	guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1	208					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell proliferation (GO:0008283)|cellular response to electrical stimulus (GO:0071257)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|phototransduction, visible light (GO:0007603)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to light intensity (GO:0009642)|response to light stimulus (GO:0009416)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	acyl binding (GO:0000035)|G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		CAAGAAGTGGATCCACTGCTT	0.667																																					p.I208V		Atlas-SNP	.											.	GNAT1	39	.	0			c.A622G						.						65.0	59.0	61.0					3																	50231568		2203	4300	6503	SO:0001583	missense	2779	exon6			AAGTGGATCCACT		CCDS2812.1	3p21	2014-01-28			ENSG00000114349	ENSG00000114349			4393	protein-coding gene	gene with protein product		139330					Standard	NM_000172		Approved	CSNBAD3	uc003cyl.2	P11488	OTTHUMG00000156808	ENST00000433068.1:c.622A>G	chr3.hg19:g.50231568A>G	ENSP00000387555:p.Ile208Val	91.0	0.0		88.0	4.0	NM_144499	Q4VBN2	Missense_Mutation	SNP	ENST00000433068.1	hg19	CCDS2812.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.193651	0.78902	.	.	ENSG00000114349	ENST00000232461;ENST00000433068	D;D	0.88509	-2.39;-2.39	4.49	4.49	0.54785	.	0.048531	0.85682	D	0.000000	D	0.90696	0.7081	M	0.85099	2.735	0.58432	D	0.999997	B	0.31459	0.324	B	0.37601	0.254	D	0.91411	0.5151	10	0.87932	D	0	.	12.9261	0.58260	1.0:0.0:0.0:0.0	.	208	P11488	GNAT1_HUMAN	V	208	ENSP00000232461:I208V;ENSP00000387555:I208V	ENSP00000232461:I208V	I	+	1	0	GNAT1	50206572	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.894000	0.92506	1.908000	0.55244	0.459000	0.35465	ATC	.	.		0.667	GNAT1-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345957.1	NM_000172	
SLC38A3	10991	hgsc.bcm.edu	37	3	50251833	50251833	+	RNA	SNP	A	A	G	rs397812056|rs5848902|rs201228948		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:50251833A>G	ENST00000420502.1	+	0	255									solute carrier family 38, member 3											breast(1)|cervix(1)|endometrium(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)		CTGTGCCTACAGGTCGAGGAC	0.607																																					.		Atlas-SNP	.											.	SLC38A3	22	.	0			c.102-1A>G						.						23.0	27.0	26.0					3																	50251833		2041	4186	6227			10991	exon3			GCCTACAGGTCGA	U49082	CCDS74940.1	3p21.3	2013-05-22			ENSG00000188338	ENSG00000188338		"""Solute carriers"""	18044	protein-coding gene	gene with protein product		604437				10619430, 10823827	Standard	XM_006712954		Approved	G17, SN1	uc003cyn.4	Q99624	OTTHUMG00000156764		chr3.hg19:g.50251833A>G		68.0	0.0		61.0	5.0	NM_006841		Splice_Site	SNP	ENST00000420502.1	hg19																																																																																				.	.		0.607	SLC38A3-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000345635.2	NM_006841	
ZMYND10	51364	hgsc.bcm.edu	37	3	50380447	50380447	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:50380447A>G	ENST00000231749.3	-	7	1874	c.602T>C	c.(601-603)cTc>cCc	p.L201P	ZMYND10_ENST00000360165.3_Intron|RASSF1_ENST00000488024.1_5'Flank|ZMYND10-AS1_ENST00000440013.1_RNA|RASSF1_ENST00000357043.2_5'Flank|ZMYND10_ENST00000490675.1_5'Flank|RASSF1_ENST00000359365.4_5'Flank	NM_015896.2	NP_056980.2	O75800	ZMY10_HUMAN	zinc finger, MYND-type containing 10	201					inner dynein arm assembly (GO:0036159)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)	centriolar satellite (GO:0034451)|cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|urinary_tract(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GCTGAGAGAGAGGCTAGGGGC	0.627										TSP Lung(30;0.18)																											p.L201P		Atlas-SNP	.											.	ZMYND10	37	.	0			c.T602C						.						144.0	131.0	135.0					3																	50380447		2203	4300	6503	SO:0001583	missense	51364	exon7			AGAGAGAGGCTAG	U70824	CCDS2825.1	3p21.3	2014-02-03			ENSG00000004838	ENSG00000004838		"""Zinc fingers, MYND-type"""	19412	protein-coding gene	gene with protein product		607070				12629521, 23891469	Standard	NM_015896		Approved	BLU, CILD22	uc003dag.1	O75800	OTTHUMG00000156874	ENST00000231749.3:c.602T>C	chr3.hg19:g.50380447A>G	ENSP00000231749:p.Leu201Pro	172.0	0.0		143.0	6.0	NM_015896	A6NK41|B3KU54|O14570|O75801|Q53FE6|Q8N4R6|Q8NDN6	Missense_Mutation	SNP	ENST00000231749.3	hg19	CCDS2825.1	.	.	.	.	.	.	.	.	.	.	A	18.39	3.612870	0.66672	.	.	ENSG00000004838	ENST00000231749;ENST00000442887	T;T	0.30448	1.53;1.53	5.55	5.55	0.83447	.	0.218577	0.38217	N	0.001775	T	0.54727	0.1876	M	0.88241	2.94	0.80722	D	1	P	0.49862	0.929	P	0.53102	0.718	T	0.64931	-0.6291	10	0.87932	D	0	-11.4017	14.8803	0.70528	1.0:0.0:0.0:0.0	.	201	O75800	ZMY10_HUMAN	P	201;158	ENSP00000231749:L201P;ENSP00000393687:L158P	ENSP00000231749:L201P	L	-	2	0	ZMYND10	50355451	1.000000	0.71417	1.000000	0.80357	0.540000	0.34992	6.998000	0.76277	2.122000	0.65172	0.459000	0.35465	CTC	.	.		0.627	ZMYND10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346376.1	NM_015896	
TLR9	54106	hgsc.bcm.edu	37	3	52257674	52257674	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:52257674A>G	ENST00000360658.2	-	2	1291	c.658T>C	c.(658-660)Tcc>Ccc	p.S220P	TLR9_ENST00000494383.1_Missense_Mutation_p.F373S|TLR9_ENST00000597542.1_Missense_Mutation_p.S244P	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	220					defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	TCCAGGCTGGAAGGCAGGTTG	0.632																																					p.S220P		Atlas-SNP	.											.	TLR9	72	.	0			c.T658C						.						39.0	32.0	34.0					3																	52257674		2203	4300	6503	SO:0001583	missense	54106	exon2			GGCTGGAAGGCAG	AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"""CD molecules"""	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.658T>C	chr3.hg19:g.52257674A>G	ENSP00000353874:p.Ser220Pro	113.0	0.0		87.0	4.0	NM_017442	B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Missense_Mutation	SNP	ENST00000360658.2	hg19	CCDS2848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	3.388|3.388	-0.124873|-0.124873	0.06795|0.06795	.|.	.|.	ENSG00000173366|ENSG00000239732	ENST00000494383|ENST00000360658	.|T	.|0.57436	.|0.4	5.57|5.57	3.64|3.64	0.41730|0.41730	.|.	.|0.468826	.|0.15943	.|N	.|0.237118	T|T	0.32793|0.32793	0.0841|0.0841	N|N	0.21545|0.21545	0.675|0.675	0.26498|0.26498	N|N	0.974812|0.974812	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.15263|0.15263	-1.0443|-1.0443	5|10	.|0.16896	.|T	.|0.51	.|.	6.5276|6.5276	0.22309|0.22309	0.1879:0.1646:0.6475:0.0|0.1879:0.1646:0.6475:0.0	.|.	.|317;220	.|B4E0A1;Q9NR96	.|.;TLR9_HUMAN	S|P	373|220	.|ENSP00000353874:S220P	.|ENSP00000353874:S220P	F|S	-|-	2|1	0|0	RP11-330H6.5|TLR9	52232714|52232714	0.000000|0.000000	0.05858|0.05858	1.000000|1.000000	0.80357|0.80357	0.547000|0.547000	0.35210|0.35210	-0.426000|-0.426000	0.07008|0.07008	1.329000|1.329000	0.45376|0.45376	-0.242000|-0.242000	0.12053|0.12053	TTC|TCC	.	.		0.632	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1		
RFT1	91869	hgsc.bcm.edu	37	3	53126534	53126534	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:53126534A>G	ENST00000296292.3	-	12	1370	c.1309T>C	c.(1309-1311)Ttt>Ctt	p.F437L	RFT1_ENST00000394738.3_Missense_Mutation_p.F398L|RP11-894J14.5_ENST00000607203.1_Intron	NM_052859.3	NP_443091.1	Q96AA3	RFT1_HUMAN	RFT1 homolog (S. cerevisiae)	437					carbohydrate transport (GO:0008643)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)	lipid transporter activity (GO:0005319)			NS(1)|breast(1)|kidney(1)|lung(5)|skin(2)|urinary_tract(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)		CCCATGTTAAAGCAGTTGGCC	0.562																																					p.F437L		Atlas-SNP	.											.	RFT1	34	.	0			c.T1309C						.						83.0	71.0	75.0					3																	53126534		2203	4300	6503	SO:0001583	missense	91869	exon12			TGTTAAAGCAGTT	AJ318099	CCDS2869.1	3p21.1	2014-02-06	2005-01-26		ENSG00000163933	ENSG00000163933			30220	protein-coding gene	gene with protein product	"""congenital disorder of glycosylation 1N"""	611908	"""RFT1, requiring fifty three 1 homolog (S. cerevisiae)"""			12477932	Standard	NM_052859		Approved	CDG1N	uc003dgj.3	Q96AA3	OTTHUMG00000074035	ENST00000296292.3:c.1309T>C	chr3.hg19:g.53126534A>G	ENSP00000296292:p.Phe437Leu	78.0	0.0		83.0	4.0	NM_052859	Q96J03	Missense_Mutation	SNP	ENST00000296292.3	hg19	CCDS2869.1	.	.	.	.	.	.	.	.	.	.	A	7.966	0.748034	0.15710	.	.	ENSG00000163933	ENST00000296292;ENST00000394738	D;D	0.82893	-1.66;-1.66	5.33	4.16	0.48862	.	0.320109	0.38381	N	0.001717	T	0.61527	0.2354	N	0.03930	-0.32	0.44061	D	0.996801	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.51896	-0.8647	10	0.15499	T	0.54	.	10.3826	0.44121	0.9203:0.0:0.0797:0.0	.	398;437	B5MDE0;Q96AA3	.;RFT1_HUMAN	L	437;398	ENSP00000296292:F437L;ENSP00000378223:F398L	ENSP00000296292:F437L	F	-	1	0	RFT1	53101574	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.064000	0.49986	0.851000	0.35264	0.379000	0.24179	TTT	.	.		0.562	RFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157136.2	NM_052859	
ADAMTS9	56999	hgsc.bcm.edu	37	3	64524966	64524966	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:64524966A>G	ENST00000498707.1	-	37	5868	c.5526T>C	c.(5524-5526)acT>acC	p.T1842T	ADAMTS9_ENST00000295903.4_Silent_p.T1814T	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1842	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				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)		ACTGTAAGTCAGTGGCTGTGG	0.537																																					p.T1842T		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.T5526C						.						96.0	85.0	88.0					3																	64524966		2203	4300	6503	SO:0001819	synonymous_variant	56999	exon37			TAAGTCAGTGGCT	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.5526T>C	chr3.hg19:g.64524966A>G		105.0	0.0		88.0	5.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Silent	SNP	ENST00000498707.1	hg19	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	A	8.017	0.758879	0.15846	.	.	ENSG00000163638	ENST00000481060	.	.	.	5.62	-11.2	0.00127	.	.	.	.	.	T	0.35307	0.0927	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47799	-0.9089	4	.	.	.	.	4.6343	0.12516	0.2499:0.4312:0.2303:0.0886	.	.	.	.	P	898	.	.	L	-	2	0	ADAMTS9	64500006	0.052000	0.20516	0.896000	0.35187	0.734000	0.41952	-0.556000	0.05992	-1.368000	0.02149	-0.468000	0.05107	CTG	.	.		0.537	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1		
MAGI1	9223	hgsc.bcm.edu	37	3	65342529	65342529	+	Missense_Mutation	SNP	T	T	C	rs544348166		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:65342529T>C	ENST00000402939.2	-	23	3912	c.3913A>G	c.(3913-3915)Agg>Ggg	p.R1305G	RP11-88H12.2_ENST00000602316.1_RNA|MAGI1_ENST00000330909.8_3'UTR	NM_001033057.1	NP_001028229.1	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	1334					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		TGCGCGTCCCTCCGTCCCTCC	0.682													T|||	1	0.000199681	0.0	0.0	5008	,	,		11789	0.0		0.0	False		,,,				2504	0.001				p.R1305G		Atlas-SNP	.											.	MAGI1	481	.	0			c.A3913G						.						55.0	56.0	56.0					3																	65342529		2203	4300	6503	SO:0001583	missense	9223	exon23			CGTCCCTCCGTCC	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000402939.2:c.3913A>G	chr3.hg19:g.65342529T>C	ENSP00000385450:p.Arg1305Gly	146.0	0.0		161.0	11.0	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000402939.2	hg19	CCDS33780.1	.	.	.	.	.	.	.	.	.	.	T	1.874	-0.459500	0.04508	.	.	ENSG00000151276	ENST00000402939	T	0.13089	2.62	5.04	5.04	0.67666	.	0.128295	0.50627	D	0.000102	T	0.10294	0.0252	L	0.32530	0.975	0.45284	D	0.998283	B	0.24721	0.11	B	0.19391	0.025	T	0.18085	-1.0348	10	0.20046	T	0.44	-15.7152	10.6071	0.45400	0.0:0.0:0.3038:0.6962	.	1305	Q96QZ7-2	.	G	1305	ENSP00000385450:R1305G	ENSP00000385450:R1305G	R	-	1	2	MAGI1	65317569	0.997000	0.39634	0.616000	0.29078	0.026000	0.11368	2.755000	0.47540	1.888000	0.54679	0.533000	0.62120	AGG	.	.		0.682	MAGI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349126.1	NM_004742	
IQCB1	9657	hgsc.bcm.edu	37	3	121527778	121527778	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:121527778C>A	ENST00000310864.6	-	6	686	c.472G>T	c.(472-474)Gaa>Taa	p.E158*	IQCB1_ENST00000349820.6_Nonsense_Mutation_p.E158*	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	158					cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)			NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		TGAATAAGTTCAACATGGCCT	0.338																																					p.E158X		Atlas-SNP	.											.	IQCB1	50	.	0			c.G472T						.						58.0	65.0	62.0					3																	121527778		2203	4300	6503	SO:0001587	stop_gained	9657	exon6			TAAGTTCAACATG	D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"""nephrocystin-5"""	609237	"""IQ calmodulin-binding motif containing 1"""			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.472G>T	chr3.hg19:g.121527778C>A	ENSP00000311505:p.Glu158*	240.0	0.0		271.0	103.0	NM_001023570	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Nonsense_Mutation	SNP	ENST00000310864.6	hg19	CCDS33837.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.344418	0.82022	.	.	ENSG00000173226	ENST00000310864;ENST00000349820	.	.	.	5.54	4.67	0.58626	.	0.380726	0.32935	N	0.005467	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-6.5529	12.1582	0.54089	0.0:0.1807:0.8193:0.0	.	.	.	.	X	158	.	ENSP00000311505:E158X	E	-	1	0	IQCB1	123010468	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	3.495000	0.53280	1.579000	0.49836	-0.171000	0.13296	GAA	.	.		0.338	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642	
HEG1	57493	hgsc.bcm.edu	37	3	124724182	124724182	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:124724182T>C	ENST00000311127.4	-	9	3291	c.3224A>G	c.(3223-3225)aAg>aGg	p.K1075R		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	1075					cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						AAAAGTTCTCTTTAATTTAAA	0.348																																					p.K1075R		Atlas-SNP	.											.	HEG1	109	.	0			c.A3224G						.						67.0	66.0	66.0					3																	124724182		1829	4090	5919	SO:0001583	missense	57493	exon9			GTTCTCTTTAATT	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.3224A>G	chr3.hg19:g.124724182T>C	ENSP00000311502:p.Lys1075Arg	88.0	0.0		58.0	4.0	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	hg19	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.004702	0.35320	.	.	ENSG00000173706	ENST00000311127	D	0.88509	-2.39	5.08	3.92	0.45320	.	0.184817	0.25419	U	0.030811	T	0.77075	0.4077	N	0.17082	0.46	0.25578	N	0.986825	B	0.27882	0.192	B	0.24701	0.055	T	0.66396	-0.5934	10	0.45353	T	0.12	.	5.8174	0.18500	0.0:0.096:0.1719:0.7321	.	1075	Q9ULI3	HEG1_HUMAN	R	1075	ENSP00000311502:K1075R	ENSP00000311502:K1075R	K	-	2	0	HEG1	126206872	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	1.973000	0.40550	2.144000	0.66660	0.460000	0.39030	AAG	.	.		0.348	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
CCDC37	348807	hgsc.bcm.edu	37	3	126152005	126152005	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:126152005A>G	ENST00000352312.1	+	14	1479	c.1380A>G	c.(1378-1380)aaA>aaG	p.K460K	CCDC37_ENST00000393425.1_Silent_p.K461K|CCDC37_ENST00000505024.1_Silent_p.K461K	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	460										NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		TGGAGCTCAAAGCCCGAGTCT	0.602																																					p.K460K		Atlas-SNP	.											.	CCDC37	69	.	0			c.A1380G						.						135.0	122.0	126.0					3																	126152005		2203	4300	6503	SO:0001819	synonymous_variant	348807	exon14			GCTCAAAGCCCGA	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.1380A>G	chr3.hg19:g.126152005A>G		113.0	0.0		100.0	4.0	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	hg19	CCDS3037.1																																																																																			.	.		0.602	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628	
COPG1	22820	hgsc.bcm.edu	37	3	128984637	128984637	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:128984637T>C	ENST00000314797.6	+	14	1572		c.e14+2			NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1						COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)										TCCGGGCAGGTAGGTCTGAGC	0.542																																					.		Atlas-SNP	.											.	.	.	.	0			c.1468+2T>C						.						44.0	37.0	40.0					3																	128984637		2203	4300	6503	SO:0001630	splice_region_variant	22820	exon14			GGCAGGTAGGTCT	AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"""coat protein gamma-cop"""	615525	"""coatomer protein complex, subunit gamma"""	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.1468+2T>C	chr3.hg19:g.128984637T>C		123.0	0.0		96.0	4.0	NM_016128	A8K6M8|B3KMF6|Q54AC4	Splice_Site	SNP	ENST00000314797.6	hg19	CCDS33851.1	.	.	.	.	.	.	.	.	.	.	T	12.91	2.079215	0.36662	.	.	ENSG00000181789	ENST00000314797	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4129	0.67128	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	COPG	130467327	1.000000	0.71417	0.933000	0.37362	0.172000	0.22775	7.827000	0.86722	2.288000	0.76882	0.533000	0.62120	.	.	.		0.542	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128	Intron
COL6A5	256076	hgsc.bcm.edu	37	3	130174346	130174346	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:130174346T>C	ENST00000432398.2	+	37	7120	c.6626T>C	c.(6625-6627)aTt>aCt	p.I2209T	COL6A5_ENST00000265379.6_Missense_Mutation_p.I2209T	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2209	Nonhelical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						AATGGCTTCATTGGCCAAGAA	0.378																																					p.I2209T		Atlas-SNP	.											.	COL6A5	205	.	0			c.T6626C						.						43.0	43.0	43.0					3																	130174346		1807	4068	5875	SO:0001583	missense	256076	exon37			GCTTCATTGGCCA	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.6626T>C	chr3.hg19:g.130174346T>C	ENSP00000390895:p.Ile2209Thr	301.0	0.0		277.0	38.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	hg19		.	.	.	.	.	.	.	.	.	.	T	3.259	-0.151527	0.06585	.	.	ENSG00000172752	ENST00000432398;ENST00000265379;ENST00000373157;ENST00000512482	D;D;T;T	0.90324	-2.56;-2.65;-1.06;-0.91	4.38	0.641	0.17759	.	1.544370	0.04444	N	0.371447	D	0.84000	0.5376	L	0.44542	1.39	0.09310	N	1	B;B	0.15473	0.008;0.013	B;B	0.19391	0.011;0.025	T	0.64968	-0.6282	10	0.07482	T	0.82	.	3.6008	0.08024	0.0:0.2095:0.1963:0.5943	.	2209;2209	A8TX70;A8TX70-2	CO6A5_HUMAN;.	T	2209;2209;152;44	ENSP00000390895:I2209T;ENSP00000265379:I2209T;ENSP00000362250:I152T;ENSP00000424968:I44T	ENSP00000265379:I2209T	I	+	2	0	COL6A5	131657036	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.018000	0.12568	0.022000	0.15160	-0.299000	0.09455	ATT	.	.		0.378	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
DNAJC13	23317	hgsc.bcm.edu	37	3	132172158	132172158	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:132172158A>G	ENST00000260818.6	+	7	802	c.554A>G	c.(553-555)gAg>gGg	p.E185G	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	185					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						TTTGCGTCAGAGCAAAGAGAA	0.343																																					p.E185G		Atlas-SNP	.											.	DNAJC13	253	.	0			c.A554G						.						39.0	40.0	40.0					3																	132172158		2201	4300	6501	SO:0001583	missense	23317	exon7			CGTCAGAGCAAAG	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.554A>G	chr3.hg19:g.132172158A>G	ENSP00000260818:p.Glu185Gly	119.0	0.0		118.0	5.0	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	hg19	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	A	16.16	3.044640	0.55110	.	.	ENSG00000138246	ENST00000260818	T	0.42513	0.97	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.59865	0.2225	L	0.58810	1.83	0.80722	D	1	P;D	0.57899	0.67;0.981	B;D	0.67900	0.328;0.954	T	0.56565	-0.7958	10	0.35671	T	0.21	.	16.2214	0.82262	1.0:0.0:0.0:0.0	.	185;185	A7E2Y5;O75165	.;DJC13_HUMAN	G	185	ENSP00000260818:E185G	ENSP00000260818:E185G	E	+	2	0	DNAJC13	133654848	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.730000	0.91510	2.219000	0.72066	0.528000	0.53228	GAG	.	.		0.343	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
CEP63	80254	hgsc.bcm.edu	37	3	134270790	134270790	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:134270790C>T	ENST00000337090.3	+	12	1576	c.1403C>T	c.(1402-1404)tCa>tTa	p.S468L	CEP63_ENST00000354446.3_Missense_Mutation_p.S422L|CEP63_ENST00000332047.5_Missense_Mutation_p.S422L|CEP63_ENST00000513612.2_Missense_Mutation_p.S468L|CEP63_ENST00000606977.1_Missense_Mutation_p.S468L|CEP63_ENST00000383229.3_Missense_Mutation_p.S468L			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	468					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CAGCTGGAGTCACTCAAATTA	0.308																																					p.S468L		Atlas-SNP	.											.	CEP63	56	.	0			c.C1403T						.						82.0	93.0	89.0					3																	134270790		2203	4296	6499	SO:0001583	missense	80254	exon13			TGGAGTCACTCAA	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.1403C>T	chr3.hg19:g.134270790C>T	ENSP00000336524:p.Ser468Leu	83.0	0.0		93.0	4.0	NM_025180	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	hg19	CCDS3086.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.77|15.77	2.932417|2.932417	0.52866|0.52866	.|.	.|.	ENSG00000182923|ENSG00000182923	ENST00000504929|ENST00000332047;ENST00000354446;ENST00000337090;ENST00000383229;ENST00000513612;ENST00000514678	.|T;T;T;T;T;T	.|0.32515	.|1.52;1.91;2.27;1.54;2.27;1.45	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	.|0.148621	.|0.42821	.|D	.|0.000660	T|T	0.43523|0.43523	0.1251|0.1251	L|L	0.54323|0.54323	1.7|1.7	0.34030|0.34030	D|D	0.653712|0.653712	.|D;B;P;B	.|0.57899	.|0.981;0.034;0.825;0.16	.|P;B;B;B	.|0.54026	.|0.74;0.023;0.175;0.088	T|T	0.53436|0.53436	-0.8439|-0.8439	5|10	.|0.41790	.|T	.|0.15	-3.0335|-3.0335	16.877|16.877	0.86054|0.86054	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|468;468;422;422	.|Q96MT8;Q96MT8-2;Q96MT8-4;Q96MT8-3	.|CEP63_HUMAN;.;.;.	Y|L	157|422;422;468;468;468;141	.|ENSP00000328382:S422L;ENSP00000346432:S422L;ENSP00000336524:S468L;ENSP00000372716:S468L;ENSP00000426129:S468L;ENSP00000427526:S141L	.|ENSP00000328382:S422L	H|S	+|+	1|2	0|0	CEP63|CEP63	135753480|135753480	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.459000|0.459000	0.32528|0.32528	5.075000|5.075000	0.64407|0.64407	2.724000|2.724000	0.93272|0.93272	0.585000|0.585000	0.79938|0.79938	CAC|TCA	.	.		0.308	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180	
ATR	545	hgsc.bcm.edu	37	3	142226796	142226796	+	Missense_Mutation	SNP	G	G	T	rs139135398		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:142226796G>T	ENST00000350721.4	-	28	5129	c.5008C>A	c.(5008-5010)Cag>Aag	p.Q1670K	ATR_ENST00000383101.3_Missense_Mutation_p.Q1606K	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1670	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						AGATGTTCCTGAATATTTTGC	0.333								Other conserved DNA damage response genes																													p.Q1670K		Atlas-SNP	.											.	ATR	285	.	0			c.C5008A						.						58.0	59.0	59.0					3																	142226796		2203	4300	6503	SO:0001583	missense	545	exon28			GTTCCTGAATATT	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.5008C>A	chr3.hg19:g.142226796G>T	ENSP00000343741:p.Gln1670Lys	111.0	0.0		92.0	4.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.916713	0.92249	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.20881	2.04;2.04	5.42	5.42	0.78866	PIK-related kinase (1);Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.40322	0.1112	M	0.72894	2.215	0.80722	D	1	D	0.59357	0.985	P	0.57960	0.83	T	0.15150	-1.0447	10	0.12103	T	0.63	-7.2528	19.2145	0.93770	0.0:0.0:1.0:0.0	.	1670	Q13535	ATR_HUMAN	K	1670;1606	ENSP00000343741:Q1670K;ENSP00000372581:Q1606K	ENSP00000343741:Q1670K	Q	-	1	0	ATR	143709486	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.605000	0.98321	2.536000	0.85505	0.591000	0.81541	CAG	.	G|1.000;C|0.000		0.333	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
ATR	545	hgsc.bcm.edu	37	3	142226823	142226823	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:142226823A>G	ENST00000350721.4	-	28	5102	c.4981T>C	c.(4981-4983)Ttt>Ctt	p.F1661L	ATR_ENST00000383101.3_Missense_Mutation_p.F1597L	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1661	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						TCTGTAATAAATGATTCAAAG	0.373								Other conserved DNA damage response genes																													p.F1661L		Atlas-SNP	.											.	ATR	285	.	0			c.T4981C						.						70.0	71.0	70.0					3																	142226823		2203	4300	6503	SO:0001583	missense	545	exon28			TAATAAATGATTC	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.4981T>C	chr3.hg19:g.142226823A>G	ENSP00000343741:p.Phe1661Leu	139.0	0.0		114.0	5.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	A	18.47	3.630358	0.67015	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.22539	1.95;1.95	5.42	5.42	0.78866	PIK-related kinase (1);Tetratricopeptide-like helical (1);	0.117930	0.64402	D	0.000013	T	0.19765	0.0475	L	0.56769	1.78	0.58432	D	0.999999	P	0.46064	0.872	B	0.35114	0.196	T	0.06679	-1.0813	10	0.20046	T	0.44	-21.118	15.4559	0.75314	1.0:0.0:0.0:0.0	.	1661	Q13535	ATR_HUMAN	L	1661;1597	ENSP00000343741:F1661L;ENSP00000372581:F1597L	ENSP00000343741:F1661L	F	-	1	0	ATR	143709513	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.140000	0.71738	2.051000	0.60960	0.482000	0.46254	TTT	.	.		0.373	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
ATR	545	hgsc.bcm.edu	37	3	142272231	142272231	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:142272231T>C	ENST00000350721.4	-	13	2764	c.2643A>G	c.(2641-2643)aaA>aaG	p.K881K	ATR_ENST00000383101.3_Silent_p.K817K	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	881					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CCAAATCTCCTTTTGCGGCCC	0.393								Other conserved DNA damage response genes																													p.K881K		Atlas-SNP	.											.	ATR	285	.	0			c.A2643G						.						52.0	51.0	51.0					3																	142272231		2203	4300	6503	SO:0001819	synonymous_variant	545	exon13			ATCTCCTTTTGCG	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.2643A>G	chr3.hg19:g.142272231T>C		112.0	0.0		97.0	4.0	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.		0.393	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
AADAC	13	hgsc.bcm.edu	37	3	151545789	151545789	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:151545789T>C	ENST00000232892.7	+	5	1155	c.1029T>C	c.(1027-1029)gaT>gaC	p.D343D	RP11-454C18.2_ENST00000483843.2_RNA|RP11-454C18.2_ENST00000475855.1_RNA	NM_001086.2	NP_001077.2	P22760	AAAD_HUMAN	arylacetamide deacetylase	343					positive regulation of triglyceride catabolic process (GO:0010898)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|deacetylase activity (GO:0019213)|lipase activity (GO:0016298)|serine hydrolase activity (GO:0017171)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(5)|skin(2)	19		Myeloproliferative disorder(1037;0.0255)|all_neural(597;0.112)	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			GTCAATATGATCTCTTAAGAG	0.463																																					p.D343D	Ovarian(30;839 841 2699 32801 46334)	Atlas-SNP	.											.	AADAC	49	.	0			c.T1029C						.						97.0	88.0	91.0					3																	151545789		2203	4300	6503	SO:0001819	synonymous_variant	13	exon5			ATATGATCTCTTA	L32179	CCDS33877.1	3q25.1	2014-03-18	2012-07-13		ENSG00000114771	ENSG00000114771	3.1.1.3		17	protein-coding gene	gene with protein product		600338	"""arylacetamide deacetylase (esterase)"""			8063807	Standard	XM_005247103		Approved	DAC, CES5A1	uc003eze.3	P22760	OTTHUMG00000159876	ENST00000232892.7:c.1029T>C	chr3.hg19:g.151545789T>C		164.0	0.0		98.0	4.0	NM_001086	A8K3L3|D3DNJ6|Q8N1A9	Silent	SNP	ENST00000232892.7	hg19	CCDS33877.1																																																																																			.	.		0.463	AADAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357883.2	NM_001086	
DHX36	170506	hgsc.bcm.edu	37	3	153998561	153998561	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:153998561T>C	ENST00000496811.1	-	21	2547	c.2467A>G	c.(2467-2469)Ata>Gta	p.I823V	DHX36_ENST00000308361.6_Missense_Mutation_p.I794V|DHX36_ENST00000329463.5_Missense_Mutation_p.I809V|DHX36_ENST00000544526.1_Missense_Mutation_p.I809V	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	823					ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			CCTGAATTTATATTAGATTCT	0.383																																					p.I823V		Atlas-SNP	.											.	DHX36	98	.	0			c.A2467G						.						100.0	106.0	104.0					3																	153998561		2203	4300	6503	SO:0001583	missense	170506	exon21			AATTTATATTAGA	AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"""DEAH-boxes"""	14410	protein-coding gene	gene with protein product		612767	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"""	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.2467A>G	chr3.hg19:g.153998561T>C	ENSP00000417078:p.Ile823Val	109.0	0.0		88.0	4.0	NM_020865	B2RB00|Q70JU3|Q8IYE5|Q9P240	Missense_Mutation	SNP	ENST00000496811.1	hg19	CCDS3171.1	.	.	.	.	.	.	.	.	.	.	T	7.755	0.704075	0.15172	.	.	ENSG00000174953	ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	T;T;T;T;T	0.03152	4.2;4.11;4.03;4.03;4.19	5.65	4.49	0.54785	Domain of unknown function DUF1605 (1);	0.175651	0.64402	N	0.000011	T	0.02494	0.0076	N	0.11756	0.17	0.38706	D	0.953092	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.50600	-0.8809	10	0.16420	T	0.52	.	11.5378	0.50648	0.0:0.0699:0.0:0.9301	.	809;794;823	Q9H2U1-2;Q9H2U1-3;Q9H2U1	.;.;DHX36_HUMAN	V	823;794;809;809;737	ENSP00000417078:I823V;ENSP00000309296:I794V;ENSP00000444247:I809V;ENSP00000330113:I809V;ENSP00000419862:I737V	ENSP00000309296:I794V	I	-	1	0	DHX36	155481255	1.000000	0.71417	0.994000	0.49952	0.986000	0.74619	2.773000	0.47686	0.974000	0.38366	0.528000	0.53228	ATA	.	.		0.383	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865	
GMPS	8833	hgsc.bcm.edu	37	3	155629067	155629067	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:155629067A>G	ENST00000496455.2	+	7	1220	c.885A>G	c.(883-885)aaA>aaG	p.K295K	GMPS_ENST00000295920.7_Splice_Site_p.K196K	NM_003875.2	NP_003866.1	P49915	GUAA_HUMAN	guanine monphosphate synthase	295	GMPS ATP-PPase. {ECO:0000255|PROSITE- ProRule:PRU00886}.				glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|GMP synthase (glutamine-hydrolyzing) activity (GO:0003922)|GMP synthase activity (GO:0003921)|pyrophosphatase activity (GO:0016462)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamine(DB00130)	TTCAGGTCAAAGGTATTGAAG	0.358			T	MLL	AML																																p.K295K	Ovarian(153;896 1876 4149 15499 28134)	Atlas-SNP	.		Dom	yes		3	3q24	8833	guanine monphosphate synthetase		L	.	GMPS	70	.	0			c.A885G						.						62.0	57.0	58.0					3																	155629067		1839	4096	5935	SO:0001630	splice_region_variant	8833	exon7			GGTCAAAGGTATT	U10860	CCDS46941.1	3q25.31	2013-06-18	2013-06-18		ENSG00000163655	ENSG00000163655	6.3.5.2		4378	protein-coding gene	gene with protein product	"""GMP synthase"""	600358	"""guanine monphosphate synthetase"""			8089153, 9195163	Standard	NM_003875		Approved		uc003faq.3	P49915	OTTHUMG00000158551	ENST00000496455.2:c.886+1A>G	chr3.hg19:g.155629067A>G		117.0	0.0		89.0	4.0	NM_003875	A8K639|B4DXV7|F8W720	Silent	SNP	ENST00000496455.2	hg19	CCDS46941.1																																																																																			.	.		0.358	GMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351260.2		Silent
SLITRK3	22865	hgsc.bcm.edu	37	3	164906629	164906629	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:164906629A>G	ENST00000475390.1	-	2	2433	c.1990T>C	c.(1990-1992)Ttt>Ctt	p.F664L	SLITRK3_ENST00000241274.3_Missense_Mutation_p.F664L			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	664					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						GCTGAGAAAAACAGAACCAGC	0.532										HNSCC(40;0.11)																											p.F664L		Atlas-SNP	.											.	SLITRK3	263	.	0			c.T1990C						.						47.0	48.0	47.0					3																	164906629		2203	4300	6503	SO:0001583	missense	22865	exon2			AGAAAAACAGAAC	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.1990T>C	chr3.hg19:g.164906629A>G	ENSP00000420091:p.Phe664Leu	109.0	0.0		98.0	4.0	NM_014926	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	hg19	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.609455	0.46527	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.57436	0.4;0.4	4.85	4.85	0.62838	.	0.000000	0.35040	N	0.003490	T	0.45418	0.1341	L	0.55017	1.72	0.47994	D	0.999561	P	0.38827	0.649	B	0.33042	0.157	T	0.45745	-0.9240	10	0.33940	T	0.23	-15.6811	13.8456	0.63466	1.0:0.0:0.0:0.0	.	664	O94933	SLIK3_HUMAN	L	664	ENSP00000420091:F664L;ENSP00000241274:F664L	ENSP00000241274:F664L	F	-	1	0	SLITRK3	166389323	0.999000	0.42202	0.971000	0.41717	0.691000	0.40173	4.273000	0.58914	2.144000	0.66660	0.533000	0.62120	TTT	.	.		0.532	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926	
TBCCD1	55171	hgsc.bcm.edu	37	3	186272765	186272765	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:186272765C>T	ENST00000424280.1	-	5	1447	c.968G>A	c.(967-969)aGc>aAc	p.S323N	TBCCD1_ENST00000479590.1_5'Flank|TBCCD1_ENST00000338733.5_Missense_Mutation_p.S323N|TBCCD1_ENST00000446782.1_Missense_Mutation_p.S227N	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	323	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		AGTGTCTGAGCTCTTAGCCAG	0.468																																					p.S323N		Atlas-SNP	.											.	TBCCD1	42	.	0			c.G968A						.						121.0	110.0	113.0					3																	186272765		2203	4300	6503	SO:0001583	missense	55171	exon5			TCTGAGCTCTTAG	BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.968G>A	chr3.hg19:g.186272765C>T	ENSP00000411253:p.Ser323Asn	171.0	0.0		156.0	12.0	NM_001134415	B3KW69|D3DNU6|G5E9J4	Missense_Mutation	SNP	ENST00000424280.1	hg19	CCDS3276.1	.	.	.	.	.	.	.	.	.	.	C	17.95	3.514052	0.64522	.	.	ENSG00000113838	ENST00000424280;ENST00000338733;ENST00000446782	D;D;D	0.84516	-1.84;-1.84;-1.86	5.88	5.88	0.94601	C-CAP/cofactor C-like domain (1);	0.146462	0.64402	D	0.000007	D	0.89343	0.6688	M	0.67953	2.075	0.39658	D	0.970572	D;P	0.53462	0.96;0.872	P;B	0.54706	0.759;0.342	D	0.88212	0.2891	10	0.35671	T	0.21	-15.5751	17.791	0.88552	0.0:1.0:0.0:0.0	.	227;323	G5E9J4;Q9NVR7	.;TBCC1_HUMAN	N	323;323;227	ENSP00000411253:S323N;ENSP00000341652:S323N;ENSP00000397091:S227N	ENSP00000341652:S323N	S	-	2	0	TBCCD1	187755459	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	4.737000	0.62066	2.805000	0.96524	0.552000	0.68991	AGC	.	.		0.468	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138	
IL1RAP	3556	hgsc.bcm.edu	37	3	190366343	190366343	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr3:190366343T>C	ENST00000412504.2	+	11	1814	c.1562T>C	c.(1561-1563)cTc>cCc	p.L521P	IL1RAP_ENST00000447382.1_Missense_Mutation_p.L521P|IL1RAP_ENST00000072516.3_Missense_Mutation_p.L521P|IL1RAP_ENST00000439062.1_Missense_Mutation_p.L521P|IL1RAP_ENST00000317757.3_Intron|IL1RAP_ENST00000443369.2_Intron			Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein	521	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-2 biosynthetic process (GO:0042094)|protein complex assembly (GO:0006461)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		AAGACGGTGCTCACGGTCATT	0.498																																					p.L521P		Atlas-SNP	.											.	IL1RAP	96	.	0			c.T1562C						.						101.0	102.0	101.0					3																	190366343		2203	4300	6503	SO:0001583	missense	3556	exon11			CGGTGCTCACGGT	AB006537	CCDS3298.1, CCDS46982.1, CCDS54696.1	3q28	2013-01-11			ENSG00000196083	ENSG00000196083		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5995	protein-coding gene	gene with protein product		602626				9479509, 9065432	Standard	NM_002182		Approved	IL-1RAcP, IL1R3, C3orf13	uc003fsq.3	Q9NPH3	OTTHUMG00000156211	ENST00000412504.2:c.1562T>C	chr3.hg19:g.190366343T>C	ENSP00000412053:p.Leu521Pro	140.0	0.0		81.0	4.0	NM_001167929	B1NLD0|D3DNW0|O14915|Q86WJ7	Missense_Mutation	SNP	ENST00000412504.2	hg19	CCDS3298.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.369863	0.82573	.	.	ENSG00000196083	ENST00000072516;ENST00000412504;ENST00000439062;ENST00000447382	T;T;T;T	0.09538	2.97;2.97;2.97;2.97	6.03	6.03	0.97812	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.433509	0.22103	N	0.064584	T	0.37679	0.1012	M	0.82823	2.61	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.17258	-1.0375	10	0.62326	D	0.03	.	15.7535	0.78005	0.0:0.0:0.0:1.0	.	521	Q9NPH3	IL1AP_HUMAN	P	521	ENSP00000072516:L521P;ENSP00000412053:L521P;ENSP00000401132:L521P;ENSP00000390541:L521P	ENSP00000072516:L521P	L	+	2	0	IL1RAP	191849037	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.591000	0.82666	2.313000	0.78055	0.455000	0.32223	CTC	.	.		0.498	IL1RAP-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343497.1		
HTT	3064	hgsc.bcm.edu	37	4	3227454	3227454	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:3227454G>T	ENST00000355072.5	+	57	7977	c.7832G>T	c.(7831-7833)aGc>aTc	p.S2611I		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2611					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		GGGAGCATGAGCTACAAACTC	0.602																																					p.S2611I		Atlas-SNP	.											.	HTT	221	.	0			c.G7832T						.						28.0	32.0	31.0					4																	3227454		1997	4188	6185	SO:0001583	missense	3064	exon57			GCATGAGCTACAA	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.7832G>T	chr4.hg19:g.3227454G>T	ENSP00000347184:p.Ser2611Ile	136.0	0.0		123.0	5.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.587627	0.46110	.	.	ENSG00000197386	ENST00000355072	T	0.05258	3.47	3.97	3.97	0.46021	.	0.254344	0.43260	D	0.000581	T	0.04998	0.0134	N	0.22421	0.69	0.27258	N	0.95869	P	0.39903	0.694	B	0.37943	0.261	T	0.34179	-0.9839	10	0.37606	T	0.19	.	11.3151	0.49388	0.0935:0.0:0.9065:0.0	.	2611	P42858	HD_HUMAN	I	2611	ENSP00000347184:S2611I	ENSP00000347184:S2611I	S	+	2	0	HTT	3197252	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	4.833000	0.62766	2.247000	0.74100	0.644000	0.83932	AGC	.	.		0.602	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
EVC2	132884	hgsc.bcm.edu	37	4	5624634	5624634	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:5624634T>C	ENST00000344408.5	-	14	2184	c.2131A>G	c.(2131-2133)Agg>Ggg	p.R711G	EVC2_ENST00000344938.1_Missense_Mutation_p.R711G|EVC2_ENST00000310917.2_Missense_Mutation_p.R631G	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	711					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						ATCAGGCTCCTCTTCTGGTGC	0.637																																					p.R711G		Atlas-SNP	.											.	EVC2	202	.	0			c.A2131G						.						63.0	62.0	62.0					4																	5624634		2203	4300	6503	SO:0001583	missense	132884	exon14			GGCTCCTCTTCTG	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.2131A>G	chr4.hg19:g.5624634T>C	ENSP00000342144:p.Arg711Gly	160.0	0.0		135.0	7.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	T	6.206	0.406161	0.11754	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.75050	-0.9;-0.89;-0.9	5.12	-0.339	0.12647	.	1.004860	0.08010	N	0.990129	T	0.60945	0.2308	N	0.22421	0.69	0.25800	N	0.984521	B	0.10296	0.003	B	0.08055	0.003	T	0.44802	-0.9304	10	0.39692	T	0.17	-27.8752	11.5804	0.50887	0.0:0.0941:0.205:0.7009	.	711	Q86UK5	LBN_HUMAN	G	711;631;711	ENSP00000339954:R711G;ENSP00000311683:R631G;ENSP00000342144:R711G	ENSP00000311683:R631G	R	-	1	2	EVC2	5675535	0.315000	0.24571	0.556000	0.28293	0.001000	0.01503	0.085000	0.14912	-0.478000	0.06823	-0.648000	0.03929	AGG	.	.		0.637	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
C1QTNF7	114905	hgsc.bcm.edu	37	4	15444246	15444246	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:15444246T>C	ENST00000444304.2	+	3	1019	c.693T>C	c.(691-693)gcT>gcC	p.A231A	C1QTNF7_ENST00000429690.1_Silent_p.A231A|C1QTNF7_ENST00000295297.4_Silent_p.A238A			Q9BXJ2	C1QT7_HUMAN	C1q and tumor necrosis factor related protein 7	231	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				protein homooligomerization (GO:0051260)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	16						ATGATGTGGCTTCGGGGTCCA	0.498																																					p.A238A		Atlas-SNP	.											.	C1QTNF7	36	.	0			c.T714C						.						88.0	91.0	90.0					4																	15444246		2203	4300	6503	SO:0001819	synonymous_variant	114905	exon3			TGTGGCTTCGGGG	AF329839	CCDS3414.1, CCDS47025.1	4p15.3	2008-08-29			ENSG00000163145	ENSG00000163145			14342	protein-coding gene	gene with protein product							Standard	NM_001135170		Approved	CTRP7	uc003gnp.3	Q9BXJ2	OTTHUMG00000097095	ENST00000444304.2:c.693T>C	chr4.hg19:g.15444246T>C		95.0	0.0		90.0	4.0	NM_001135170	B2RBT3|J3KPW3	Silent	SNP	ENST00000444304.2	hg19	CCDS3414.1																																																																																			.	.		0.498	C1QTNF7-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250891.2		
SEPSECS	51091	hgsc.bcm.edu	37	4	25156728	25156728	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:25156728A>G	ENST00000382103.2	-	5	665	c.593T>C	c.(592-594)cTg>cCg	p.L198P	SEPSECS_ENST00000302922.3_Missense_Mutation_p.L119P	NM_016955.3	NP_058651.3	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	198					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	pyridoxal phosphate binding (GO:0030170)|transferase activity, transferring selenium-containing groups (GO:0016785)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(2)|stomach(1)	8		Breast(46;0.173)				GTCTGTACGCAGCTCGTCACC	0.428																																					p.L198P		Atlas-SNP	.											.	SEPSECS	55	.	0			c.T593C						.						136.0	117.0	123.0					4																	25156728		2203	4300	6503	SO:0001583	missense	51091	exon5			GTACGCAGCTCGT	AJ238617	CCDS3432.1, CCDS3432.2	4p15.2	2008-10-27			ENSG00000109618	ENSG00000109618			30605	protein-coding gene	gene with protein product	"""soluble liver antigen/liver pancreas antigen"""	613009				16230358, 10931155, 17142313, 17194211	Standard	NM_016955		Approved	SLA/LP, SLA	uc003grg.3	Q9HD40	OTTHUMG00000128563	ENST00000382103.2:c.593T>C	chr4.hg19:g.25156728A>G	ENSP00000371535:p.Leu198Pro	109.0	0.0		101.0	11.0	NM_016955	A8K8W1|Q0D2P3|Q17RT1|Q9NXZ5|Q9UGM9|Q9Y353	Missense_Mutation	SNP	ENST00000382103.2	hg19	CCDS3432.2	.	.	.	.	.	.	.	.	.	.	A	22.8	4.333384	0.81801	.	.	ENSG00000109618	ENST00000302922;ENST00000382103	D;D	0.84370	-1.84;-1.84	5.37	5.37	0.77165	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.93387	0.7891	M	0.88842	2.985	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	0.94587	0.7784	10	0.87932	D	0	-5.2746	15.7032	0.77558	1.0:0.0:0.0:0.0	.	197;138;198	Q9HD40-3;A1A4F3;Q9HD40	.;.;SPCS_HUMAN	P	119;198	ENSP00000305956:L119P;ENSP00000371535:L198P	ENSP00000305956:L119P	L	-	2	0	SEPSECS	24765826	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	8.855000	0.92236	2.178000	0.69098	0.473000	0.43528	CTG	.	.		0.428	SEPSECS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250414.2	NM_016955	
TBC1D19	55296	hgsc.bcm.edu	37	4	26755500	26755500	+	Silent	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:26755500G>T	ENST00000264866.4	+	20	1772	c.1494G>T	c.(1492-1494)ctG>ctT	p.L498L	TBC1D19_ENST00000511789.1_Silent_p.L433L	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	498							Rab GTPase activator activity (GO:0005097)			breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				TGACATCACTGGCTGCAGCTG	0.483																																					p.L498L		Atlas-SNP	.											.	TBC1D19	53	.	0			c.G1494T						.						137.0	119.0	125.0					4																	26755500		2203	4300	6503	SO:0001819	synonymous_variant	55296	exon20			ATCACTGGCTGCA	AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	ENST00000264866.4:c.1494G>T	chr4.hg19:g.26755500G>T		113.0	0.0		97.0	4.0	NM_018317	B9A6M0|Q9NUX1	Silent	SNP	ENST00000264866.4	hg19	CCDS3439.1																																																																																			.	.		0.483	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2	NM_018317	
UGDH	7358	hgsc.bcm.edu	37	4	39510222	39510222	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:39510222A>G	ENST00000316423.6	-	7	1212	c.870T>C	c.(868-870)gcT>gcC	p.A290A	UGDH_ENST00000506179.1_Silent_p.A290A|UGDH_ENST00000507089.1_Silent_p.A193A|UGDH_ENST00000515398.1_5'Flank|UGDH_ENST00000501493.2_Silent_p.A223A	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	290					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						GCAAATTCAGAGCCTCACAGA	0.393																																					p.A290A		Atlas-SNP	.											.	UGDH	52	.	0			c.T870C						.						75.0	80.0	78.0					4																	39510222		2203	4300	6503	SO:0001819	synonymous_variant	7358	exon7			ATTCAGAGCCTCA	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.870T>C	chr4.hg19:g.39510222A>G		84.0	0.0		50.0	4.0	NM_003359	B3KUU2|B4DN25|O60589	Silent	SNP	ENST00000316423.6	hg19	CCDS3455.1																																																																																			.	.		0.393	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359	
GABRG1	2565	hgsc.bcm.edu	37	4	46067446	46067446	+	Silent	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:46067446G>A	ENST00000295452.4	-	4	644	c.477C>T	c.(475-477)caC>caT	p.H159H		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	159					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	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)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|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)	TTGTTATCCAGTGAGCATCAG	0.353																																					p.H159H		Atlas-SNP	.											.	GABRG1	172	.	0			c.C477T						.						97.0	95.0	96.0					4																	46067446		2203	4300	6503	SO:0001819	synonymous_variant	2565	exon4			TATCCAGTGAGCA	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4086	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma"""	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.477C>T	chr4.hg19:g.46067446G>A		117.0	0.0		77.0	4.0	NM_173536	Q5H9T8	Silent	SNP	ENST00000295452.4	hg19	CCDS3470.1																																																																																			.	.		0.353	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536	
NPFFR2	10886	hgsc.bcm.edu	37	4	73013093	73013093	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:73013093T>C	ENST00000308744.6	+	4	1231	c.1133T>C	c.(1132-1134)cTc>cCc	p.L378P	NPFFR2_ENST00000344413.5_3'UTR|NPFFR2_ENST00000506359.1_3'UTR|NPFFR2_ENST00000358749.3_Missense_Mutation_p.L276P|NPFFR2_ENST00000395999.1_Missense_Mutation_p.L279P	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	378					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)	p.L378H(1)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			ATTAAGATGCTCCTGATTGTG	0.502																																					p.L378P		Atlas-SNP	.											NPFFR2,NS,carcinoma,0,1	NPFFR2	98	.	1	Substitution - Missense(1)	lung(1)	c.T1133C						.						89.0	85.0	86.0					4																	73013093		2203	4300	6503	SO:0001583	missense	10886	exon4			AGATGCTCCTGAT	AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"""GPCR / Class A :  Neuropeptide receptors : FF/AF"", ""GPCR / Class A : RF amide peptide receptors"""	4525	protein-coding gene	gene with protein product	"""neuropeptide FF 2"""	607449	"""G protein-coupled receptor 74"""	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.1133T>C	chr4.hg19:g.73013093T>C	ENSP00000307822:p.Leu378Pro	117.0	0.0		75.0	3.0	NM_004885	Q96RV1|Q9NR49	Missense_Mutation	SNP	ENST00000308744.6	hg19	CCDS3551.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.873655	0.51695	.	.	ENSG00000056291	ENST00000308744;ENST00000395999;ENST00000358749	T;T;T	0.51574	0.7;0.7;0.7	5.82	5.82	0.92795	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000116	T	0.81819	0.4903	H	0.98951	4.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.89340	0.3653	10	0.87932	D	0	.	15.8418	0.78852	0.0:0.0:0.0:1.0	.	279;378	Q9Y5X5-3;Q9Y5X5	.;NPFF2_HUMAN	P	378;279;276	ENSP00000307822:L378P;ENSP00000379321:L279P;ENSP00000351599:L276P	ENSP00000307822:L378P	L	+	2	0	NPFFR2	73231957	1.000000	0.71417	0.970000	0.41538	0.076000	0.17211	7.911000	0.87458	2.214000	0.71695	0.482000	0.46254	CTC	.	.		0.502	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885	
ALB	213	hgsc.bcm.edu	37	4	74274385	74274385	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:74274385T>C	ENST00000295897.4	+	4	434	c.345T>C	c.(343-345)tgT>tgC	p.C115C	ALB_ENST00000415165.2_Intron|ALB_ENST00000503124.1_Intron|ALB_ENST00000401494.3_Intron|ALB_ENST00000509063.1_Silent_p.C115C|ALB_ENST00000505649.1_3'UTR	NM_000477.5	NP_000468.1	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)			CTGACTGCTGTGCAAAACAAG	0.438																																					p.C115C		Atlas-SNP	.											.	ALB	132	.	0			c.T345C						.						94.0	88.0	90.0					4																	74274385		2203	4300	6503	SO:0001819	synonymous_variant	213	exon4			CTGCTGTGCAAAA	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	ENST00000295897.4:c.345T>C	chr4.hg19:g.74274385T>C		212.0	0.0		118.0	5.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000295897.4	hg19	CCDS3555.1																																																																																			.	.		0.438	ALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252173.3	NM_000477	
RASSF6	166824	hgsc.bcm.edu	37	4	74459214	74459214	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:74459214A>G	ENST00000342081.3	-	4	467	c.337T>C	c.(337-339)Tct>Cct	p.S113P	RASSF6_ENST00000307439.5_Missense_Mutation_p.S81P|RASSF6_ENST00000335049.5_Missense_Mutation_p.S69P|RASSF6_ENST00000395777.2_Missense_Mutation_p.S81P	NM_201431.2	NP_958834.1	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family member 6	113					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)					breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|pancreas(2)|skin(2)	17	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			GTAAAAGAAGAGAATGGCTTC	0.363																																					p.S113P		Atlas-SNP	.											.	RASSF6	68	.	0			c.T337C						.						116.0	117.0	117.0					4																	74459214		2203	4300	6503	SO:0001583	missense	166824	exon4			AAGAAGAGAATGG	AY217664	CCDS3558.1, CCDS3559.1, CCDS58904.1, CCDS58905.1	4q21.1	2008-02-22	2008-02-22		ENSG00000169435	ENSG00000169435			20796	protein-coding gene	gene with protein product		612620					Standard	NM_177532		Approved		uc003hhd.2	Q6ZTQ3	OTTHUMG00000130007	ENST00000342081.3:c.337T>C	chr4.hg19:g.74459214A>G	ENSP00000340578:p.Ser113Pro	191.0	0.0		149.0	6.0	NM_201431	Q68DT2|Q6PDA6|Q86WG9|Q86WH0	Missense_Mutation	SNP	ENST00000342081.3	hg19	CCDS3558.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.707539	0.00712	.	.	ENSG00000169435	ENST00000307439;ENST00000342081;ENST00000395777;ENST00000335049	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	5.42	1.28	0.21552	.	0.468479	0.26217	N	0.025656	T	0.09158	0.0226	N	0.00879	-1.12	0.35790	D	0.822346	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.002;0.0;0.001	T	0.33701	-0.9858	10	0.06365	T	0.9	-0.3215	8.4588	0.32915	0.3129:0.0:0.6871:0.0	.	69;81;113	Q6ZTQ3-3;Q6ZTQ3-4;Q6ZTQ3	.;.;RASF6_HUMAN	P	81;113;81;69	ENSP00000303877:S81P;ENSP00000340578:S113P;ENSP00000379123:S81P;ENSP00000335582:S69P	ENSP00000303877:S81P	S	-	1	0	RASSF6	74678078	1.000000	0.71417	0.985000	0.45067	0.095000	0.18619	1.046000	0.30354	0.176000	0.19873	-0.407000	0.06327	TCT	.	.		0.363	RASSF6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252279.1	NM_177532	
C4orf22	255119	hgsc.bcm.edu	37	4	81283933	81283933	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:81283933T>C	ENST00000358105.3	+	2	186	c.137T>C	c.(136-138)gTg>gCg	p.V46A	C4orf22_ENST00000508675.1_Missense_Mutation_p.V46A|C4orf22_ENST00000512931.1_3'UTR	NM_152770.2	NP_689983.2	Q6V702	CD022_HUMAN	chromosome 4 open reading frame 22	46										NS(1)|large_intestine(3)|lung(5)|prostate(1)|skin(5)	15						CGCCAGTTGGTGGAGCTAGGC	0.448																																					p.V46A		Atlas-SNP	.											.	C4orf22	35	.	0			c.T137C						.						115.0	125.0	122.0					4																	81283933		2203	4300	6503	SO:0001583	missense	255119	exon2			AGTTGGTGGAGCT	BC034296	CCDS3587.1, CCDS56336.1	4q21.21	2008-02-05			ENSG00000197826	ENSG00000197826			28554	protein-coding gene	gene with protein product						12477932	Standard	NM_152770		Approved		uc010ijp.3	Q6V702	OTTHUMG00000130289	ENST00000358105.3:c.137T>C	chr4.hg19:g.81283933T>C	ENSP00000350818:p.Val46Ala	116.0	0.0		86.0	4.0	NM_152770	E7EQ13|Q6ZQY4|Q8N4G9	Missense_Mutation	SNP	ENST00000358105.3	hg19	CCDS3587.1	.	.	.	.	.	.	.	.	.	.	T	18.36	3.606437	0.66445	.	.	ENSG00000197826	ENST00000358105;ENST00000508675	T;T	0.34275	1.37;1.37	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000020	T	0.62816	0.2459	M	0.84683	2.71	0.44862	D	0.997874	D;P	0.89917	1.0;0.845	D;P	0.79784	0.993;0.646	T	0.65681	-0.6109	10	0.38643	T	0.18	.	14.3501	0.66694	0.0:0.0:0.0:1.0	.	46;46	E7EQ13;Q6V702	.;CD022_HUMAN	A	46	ENSP00000350818:V46A;ENSP00000425786:V46A	ENSP00000350818:V46A	V	+	2	0	C4orf22	81502957	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	5.413000	0.66399	2.091000	0.63221	0.477000	0.44152	GTG	.	.		0.448	C4orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252629.2	NM_152770	
WDFY3	23001	hgsc.bcm.edu	37	4	85731416	85731416	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:85731416A>G	ENST00000295888.4	-	14	2376	c.1969T>C	c.(1969-1971)Ttg>Ctg	p.L657L	WDFY3_ENST00000322366.6_Silent_p.L657L|WDFY3-AS1_ENST00000510449.1_RNA	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	657					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GCAACGAGCAAGGATGTAATG	0.443																																					p.L657L		Atlas-SNP	.											.	WDFY3	314	.	0			c.T1969C						.						68.0	63.0	65.0					4																	85731416		2203	4300	6503	SO:0001819	synonymous_variant	23001	exon14			CGAGCAAGGATGT	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.1969T>C	chr4.hg19:g.85731416A>G		87.0	0.0		47.0	4.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.		0.443	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
MEPE	56955	hgsc.bcm.edu	37	4	88766433	88766433	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:88766433A>G	ENST00000424957.3	+	4	486	c.413A>G	c.(412-414)gAc>gGc	p.D138G	MEPE_ENST00000497649.2_Missense_Mutation_p.D114G|MEPE_ENST00000540395.1_Missense_Mutation_p.D25G|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000560249.1_Missense_Mutation_p.D25G|MEPE_ENST00000361056.3_Missense_Mutation_p.D138G|MEPE_ENST00000395102.4_Missense_Mutation_p.D169G	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	138					biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		AAACTACATGACCAAGAAGAA	0.418																																					p.D138G		Atlas-SNP	.											.	MEPE	86	.	0			c.A413G						.						70.0	68.0	69.0					4																	88766433		2203	4300	6503	SO:0001583	missense	56955	exon4			TACATGACCAAGA	AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"""matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"""			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.413A>G	chr4.hg19:g.88766433A>G	ENSP00000416984:p.Asp138Gly	182.0	0.0		86.0	4.0	NM_020203	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	hg19	CCDS3625.1	.	.	.	.	.	.	.	.	.	.	A	12.72	2.021259	0.35701	.	.	ENSG00000152595	ENST00000535138;ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.57436	4.32;0.42;0.4;0.46;4.32	4.84	-2.83	0.05769	.	0.620480	0.15238	N	0.273009	T	0.40272	0.1110	M	0.62088	1.915	0.09310	N	0.999994	P	0.34800	0.469	B	0.34590	0.186	T	0.26258	-1.0108	10	0.39692	T	0.17	-3.4702	3.3001	0.06980	0.4063:0.0:0.1726:0.4211	.	138	Q9NQ76	MEPE_HUMAN	G	138;138;169;114;25;138	ENSP00000416984:D138G;ENSP00000378534:D169G;ENSP00000422747:D114G;ENSP00000443491:D25G;ENSP00000354341:D138G	ENSP00000354341:D138G	D	+	2	0	MEPE	88985457	0.499000	0.26083	0.044000	0.18714	0.107000	0.19398	0.257000	0.18369	-0.628000	0.05582	0.533000	0.62120	GAC	.	.		0.418	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1		
CCDC109B	55013	hgsc.bcm.edu	37	4	110580168	110580168	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:110580168T>C	ENST00000394650.4	+	2	234	c.101T>C	c.(100-102)gTt>gCt	p.V34A	CCDC109B_ENST00000515114.1_3'UTR	NM_017918.4	NP_060388.2	Q9NWR8	MCUB_HUMAN	coiled-coil domain containing 109B	34					mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)	calcium channel complex (GO:0034704)|integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of membrane (GO:0031224)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium channel inhibitor activity (GO:0019855)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(1)	9				OV - Ovarian serous cystadenocarcinoma(123;6.65e-06)		TTCTTGTAGGTTTTGCGTGTG	0.318																																					p.V34A		Atlas-SNP	.											.	CCDC109B	47	.	0			c.T101C						.						214.0	178.0	189.0					4																	110580168		692	1591	2283	SO:0001630	splice_region_variant	55013	exon2			TGTAGGTTTTGCG	BC002633	CCDS3683.2	4q25	2011-05-24			ENSG00000005059	ENSG00000005059			26076	protein-coding gene	gene with protein product						12477932	Standard	NM_017918		Approved	FLJ20647	uc011cfs.2	Q9NWR8	OTTHUMG00000161103	ENST00000394650.4:c.100-1T>C	chr4.hg19:g.110580168T>C		182.0	0.0		103.0	6.0	NM_017918	A8K4Y3|Q6IAC1	Missense_Mutation	SNP	ENST00000394650.4	hg19	CCDS3683.2	.	.	.	.	.	.	.	.	.	.	T	9.020	0.984555	0.18889	.	.	ENSG00000005059	ENST00000394650;ENST00000452915	T;T	0.55052	0.54;0.54	4.86	3.66	0.41972	.	0.812536	0.09859	U	0.746452	T	0.41305	0.1153	L	0.27053	0.805	0.23933	N	0.996424	B;P	0.44139	0.243;0.827	B;B	0.40901	0.079;0.343	T	0.12243	-1.0555	10	0.39692	T	0.17	-0.167	10.2263	0.43227	0.0:0.0:0.1671:0.8329	.	34;13	Q9NWR8;C9JTJ6	C109B_HUMAN;.	A	34;13	ENSP00000378145:V34A;ENSP00000414591:V13A	ENSP00000378145:V34A	V	+	2	0	CCDC109B	110799617	0.999000	0.42202	0.634000	0.29324	0.066000	0.16364	2.038000	0.41184	0.704000	0.31869	0.529000	0.55759	GTT	.	.		0.318	CCDC109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254865.1	NM_017918	Missense_Mutation
CASP6	839	hgsc.bcm.edu	37	4	110612018	110612018	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:110612018A>G	ENST00000265164.2	-	6	708	c.631T>C	c.(631-633)Tct>Cct	p.S211P	CASP6_ENST00000510324.1_5'UTR|CASP6_ENST00000352981.3_Missense_Mutation_p.S122P|AC004067.5_ENST00000608733.1_RNA	NM_001226.3	NP_001217.2	P55212	CASP6_HUMAN	caspase 6, apoptosis-related cysteine peptidase	211					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|epithelial cell differentiation (GO:0030855)|proteolysis (GO:0006508)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	8		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000171)		TCTGCAACAGAGTAACACATG	0.443																																					p.S211P		Atlas-SNP	.											.	CASP6	25	.	0			c.T631C						.						189.0	163.0	172.0					4																	110612018		2203	4300	6503	SO:0001583	missense	839	exon6			CAACAGAGTAACA	U20536	CCDS3684.1, CCDS3685.1	4q25	2008-02-05	2005-08-17		ENSG00000138794	ENSG00000138794		"""Caspases"""	1507	protein-coding gene	gene with protein product		601532	"""caspase 6, apoptosis-related cysteine protease"""			8780721, 7796396	Standard	XM_005263271		Approved	MCH2	uc003hzn.1	P55212	OTTHUMG00000131914	ENST00000265164.2:c.631T>C	chr4.hg19:g.110612018A>G	ENSP00000265164:p.Ser211Pro	105.0	0.0		104.0	5.0	NM_001226	Q9BQE7	Missense_Mutation	SNP	ENST00000265164.2	hg19	CCDS3684.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.756726	0.89843	.	.	ENSG00000138794	ENST00000352981;ENST00000265164	T;T	0.57436	0.4;3.39	5.48	5.48	0.80851	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);	0.052885	0.85682	D	0.000000	T	0.77592	0.4153	M	0.90309	3.105	0.80722	D	1	P;D	0.76494	0.684;0.999	P;D	0.77004	0.477;0.989	T	0.83009	-0.0173	10	0.87932	D	0	.	15.6181	0.76784	1.0:0.0:0.0:0.0	.	122;211	P55212-2;P55212	.;CASP6_HUMAN	P	122;211	ENSP00000285333:S122P;ENSP00000265164:S211P	ENSP00000265164:S211P	S	-	1	0	CASP6	110831467	1.000000	0.71417	0.994000	0.49952	0.892000	0.51952	8.933000	0.92911	2.101000	0.63845	0.529000	0.55759	TCT	.	.		0.443	CASP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254866.1	NM_001226	
CCNA2	890	hgsc.bcm.edu	37	4	122738818	122738818	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:122738818T>C	ENST00000274026.5	-	8	1577	c.1274A>G	c.(1273-1275)aAc>aGc	p.N425S		NM_001237.3	NP_001228	P20248	CCNA2_HUMAN	cyclin A2	425					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|organ regeneration (GO:0031100)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|response to estradiol (GO:0032355)|response to glucagon (GO:0033762)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	12						CTCTGGTGGGTTGAGGAGAGA	0.348																																					p.N425S		Atlas-SNP	.											.	CCNA2	30	.	0			c.A1274G						.						141.0	136.0	138.0					4																	122738818		2203	4300	6503	SO:0001583	missense	890	exon8			GGTGGGTTGAGGA		CCDS3723.1	4q27	2012-07-12			ENSG00000145386	ENSG00000145386			1578	protein-coding gene	gene with protein product		123835		CCNA, CCN1		1675006	Standard	NM_001237		Approved		uc003iec.4	P20248	OTTHUMG00000133072	ENST00000274026.5:c.1274A>G	chr4.hg19:g.122738818T>C	ENSP00000274026:p.Asn425Ser	104.0	0.0		86.0	4.0	NM_001237	A8K7B6|Q2M3U6|Q4W5P4|Q6LER8	Missense_Mutation	SNP	ENST00000274026.5	hg19	CCDS3723.1	.	.	.	.	.	.	.	.	.	.	T	9.432	1.085771	0.20390	.	.	ENSG00000145386	ENST00000274026	T	0.19532	2.14	6.16	3.73	0.42828	Cyclin, C-terminal (1);Cyclin-like (2);	0.393919	0.29508	N	0.011958	T	0.04861	0.0131	N	0.00453	-1.485	0.26776	N	0.969697	B	0.02656	0.0	B	0.01281	0.0	T	0.37407	-0.9707	10	0.12103	T	0.63	.	8.1586	0.31185	0.1208:0.0645:0.0:0.8147	.	425	P20248	CCNA2_HUMAN	S	425	ENSP00000274026:N425S	ENSP00000274026:N425S	N	-	2	0	CCNA2	122958268	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.712000	0.47186	0.547000	0.28938	0.528000	0.53228	AAC	.	.		0.348	CCNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256712.2	NM_001237	
KIAA1109	84162	hgsc.bcm.edu	37	4	123210267	123210267	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:123210267C>T	ENST00000264501.4	+	54	9681	c.9308C>T	c.(9307-9309)aCa>aTa	p.T3103I	KIAA1109_ENST00000455637.1_Missense_Mutation_p.T3103I|KIAA1109_ENST00000388738.3_Missense_Mutation_p.T3103I			Q2LD37	K1109_HUMAN	KIAA1109	3103					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						CATAATCTTACAACTGATCTT	0.313																																					p.T3103I		Atlas-SNP	.											.	KIAA1109	424	.	0			c.C9308T						.						141.0	129.0	132.0					4																	123210267		1832	4084	5916	SO:0001583	missense	84162	exon52			ATCTTACAACTGA	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.9308C>T	chr4.hg19:g.123210267C>T	ENSP00000264501:p.Thr3103Ile	165.0	0.0		113.0	5.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.417393	0.83449	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637	T;T;T	0.36520	1.25;1.25;1.25	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.60612	0.2282	M	0.70595	2.14	0.49798	D	0.999826	D;D	0.76494	0.997;0.999	P;D	0.63488	0.899;0.915	T	0.62243	-0.6895	10	0.87932	D	0	.	20.0119	0.97458	0.0:1.0:0.0:0.0	.	3103;3103	Q2LD37-6;Q2LD37	.;K1109_HUMAN	I	3103	ENSP00000264501:T3103I;ENSP00000373390:T3103I;ENSP00000389925:T3103I	ENSP00000264501:T3103I	T	+	2	0	KIAA1109	123429717	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.888000	0.69758	2.712000	0.92718	0.650000	0.86243	ACA	.	.		0.313	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
FAT4	79633	hgsc.bcm.edu	37	4	126371393	126371393	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:126371393T>C	ENST00000394329.3	+	9	9235	c.9222T>C	c.(9220-9222)acT>acC	p.T3074T	FAT4_ENST00000335110.5_Silent_p.T1372T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3074	Cadherin 29. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCCAAGCAACTGTTCACATAA	0.438																																					p.T3074T		Atlas-SNP	.											.	FAT4	1752	.	0			c.T9222C						.						98.0	93.0	94.0					4																	126371393		2203	4300	6503	SO:0001819	synonymous_variant	79633	exon9			AGCAACTGTTCAC	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.9222T>C	chr4.hg19:g.126371393T>C		135.0	0.0		97.0	4.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	hg19	CCDS3732.3																																																																																			.	.		0.438	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
JADE1	79960	hgsc.bcm.edu	37	4	129782996	129782996	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:129782996A>G	ENST00000226319.6	+	9	1399	c.1119A>G	c.(1117-1119)aaA>aaG	p.K373K	PHF17_ENST00000511647.1_Silent_p.K373K|PHF17_ENST00000452328.2_Silent_p.K361K|PHF17_ENST00000413543.2_Silent_p.K373K|PHF17_ENST00000512960.1_Silent_p.K373K	NM_199320.2	NP_955352.1														NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						CACATAGGAAACCCGAGGAGA	0.562																																					p.K373K		Atlas-SNP	.											.	PHF17	63	.	0			c.A1119G						.						103.0	116.0	112.0					4																	129782996		2203	4300	6503	SO:0001819	synonymous_variant	79960	exon9			TAGGAAACCCGAG																												ENST00000226319.6:c.1119A>G	chr4.hg19:g.129782996A>G		167.0	0.0		92.0	4.0	NM_199320		Silent	SNP	ENST00000226319.6	hg19	CCDS34062.1																																																																																			.	.		0.562	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1		
ARHGAP10	79658	hgsc.bcm.edu	37	4	148802995	148802995	+	Nonsense_Mutation	SNP	G	G	T	rs138388284		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:148802995G>T	ENST00000336498.3	+	10	1185	c.946G>T	c.(946-948)Gga>Tga	p.G316*	ARHGAP10_ENST00000414545.2_5'Flank	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		GCAGGGGGACGGAGAGGTGTT	0.413																																					p.G316X		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.G946T						.						154.0	150.0	152.0					4																	148802995		2203	4300	6503	SO:0001587	stop_gained	79658	exon10			GGGGACGGAGAGG	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"""Rho GTPase activating proteins"""	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.946G>T	chr4.hg19:g.148802995G>T	ENSP00000336923:p.Gly316*	187.0	0.0		110.0	38.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Nonsense_Mutation	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	G	38	6.804907	0.97853	.	.	ENSG00000071205	ENST00000336498	.	.	.	4.94	4.94	0.65067	.	0.110592	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	.	14.3287	0.66537	0.0:0.1492:0.8507:0.0	.	.	.	.	X	316	.	ENSP00000336923:G316X	G	+	1	0	ARHGAP10	149022445	0.085000	0.21516	0.783000	0.31826	0.053000	0.15095	1.461000	0.35255	2.284000	0.76573	0.591000	0.81541	GGA	.	G|1.000;A|0.000		0.413	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605	
ARHGAP10	79658	hgsc.bcm.edu	37	4	148984403	148984403	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:148984403C>A	ENST00000336498.3	+	21	2371	c.2132C>A	c.(2131-2133)cCt>cAt	p.P711H	ARHGAP10_ENST00000414545.2_Intron	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		GGGTCGTCCCCTTTCCCCTTT	0.562																																					p.P711H		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.C2132A						.						152.0	107.0	122.0					4																	148984403		2203	4300	6503	SO:0001583	missense	79658	exon21			CGTCCCCTTTCCC	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"""Rho GTPase activating proteins"""	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.2132C>A	chr4.hg19:g.148984403C>A	ENSP00000336923:p.Pro711His	148.0	0.0		131.0	30.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	C	14.18	2.458566	0.43634	.	.	ENSG00000071205	ENST00000336498	T	0.10288	2.89	5.56	5.56	0.83823	Src homology-3 domain (1);	1.151220	0.06032	N	0.653185	T	0.10252	0.0251	N	0.14661	0.345	0.80722	D	1	D;B;B	0.55172	0.97;0.016;0.0	B;B;B	0.40901	0.343;0.005;0.001	T	0.43294	-0.9400	10	0.45353	T	0.12	.	16.4441	0.83910	0.0:1.0:0.0:0.0	.	144;292;711	Q9H7G7;Q86T21;A1A4S6	.;.;RHG10_HUMAN	H	711	ENSP00000336923:P711H	ENSP00000336923:P711H	P	+	2	0	ARHGAP10	149203853	0.006000	0.16342	0.006000	0.13384	0.020000	0.10135	1.978000	0.40598	2.615000	0.88500	0.555000	0.69702	CCT	.	.		0.562	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605	
FAM160A1	729830	hgsc.bcm.edu	37	4	152571430	152571430	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:152571430C>T	ENST00000505231.1	+	9	2396	c.2237C>T	c.(2236-2238)cCg>cTg	p.P746L	FAM160A1_ENST00000435205.1_Missense_Mutation_p.P746L			Q05DH4	F16A1_HUMAN	family with sequence similarity 160, member A1	746	Glu-rich.									endometrium(2)|kidney(1)	3						GCCGCCCACCCGGAGAGCGAG	0.567																																					p.P746L		Atlas-SNP	.											.	FAM160A1	60	.	0			c.C2237T						.						66.0	77.0	74.0					4																	152571430		692	1591	2283	SO:0001583	missense	729830	exon11			CCCACCCGGAGAG		CCDS47146.1	4q31.3	2012-11-30			ENSG00000164142	ENSG00000164142			34237	protein-coding gene	gene with protein product							Standard	NM_001109977		Approved	FLJ43373	uc003imj.2	Q05DH4	OTTHUMG00000161675	ENST00000505231.1:c.2237C>T	chr4.hg19:g.152571430C>T	ENSP00000421580:p.Pro746Leu	87.0	0.0		79.0	4.0	NM_001109977	Q6ZUS2	Missense_Mutation	SNP	ENST00000505231.1	hg19	CCDS47146.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.108568	0.37242	.	.	ENSG00000164142	ENST00000435205;ENST00000505231	T;T	0.11712	2.75;2.75	5.08	4.24	0.50183	.	.	.	.	.	T	0.12732	0.0309	L	0.54323	1.7	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.20273	-1.0280	9	0.21540	T	0.41	.	13.6038	0.62035	0.0:0.9246:0.0:0.0754	.	746	Q05DH4	F16A1_HUMAN	L	746	ENSP00000413196:P746L;ENSP00000421580:P746L	ENSP00000413196:P746L	P	+	2	0	FAM160A1	152790880	0.001000	0.12720	0.004000	0.12327	0.002000	0.02628	1.044000	0.30329	1.268000	0.44264	0.655000	0.94253	CCG	.	.		0.567	FAM160A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365691.1	NM_001109977	
FHDC1	85462	hgsc.bcm.edu	37	4	153884235	153884235	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:153884235A>G	ENST00000511601.1	+	8	1170	c.982A>G	c.(982-984)Aca>Gca	p.T328A	FHDC1_ENST00000260008.3_Missense_Mutation_p.T328A			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	328	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.								ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					ATTGGCAGACACAAAAGCAAA	0.398																																					p.T328A		Atlas-SNP	.											.	FHDC1	102	.	0			c.A982G						.						114.0	122.0	119.0					4																	153884235		2203	4300	6503	SO:0001583	missense	85462	exon7			GCAGACACAAAAG	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.982A>G	chr4.hg19:g.153884235A>G	ENSP00000427567:p.Thr328Ala	93.0	0.0		68.0	4.0	NM_033393		Missense_Mutation	SNP	ENST00000511601.1	hg19	CCDS34081.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.714560	0.89112	.	.	ENSG00000137460	ENST00000511601;ENST00000260008	T;T	0.21361	2.01;2.01	5.43	5.43	0.79202	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	T	0.55721	0.1938	M	0.92026	3.265	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.66548	-0.5896	10	0.66056	D	0.02	.	15.5039	0.75722	1.0:0.0:0.0:0.0	.	328	Q9C0D6	FHDC1_HUMAN	A	328	ENSP00000427567:T328A;ENSP00000260008:T328A	ENSP00000260008:T328A	T	+	1	0	FHDC1	154103685	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.062000	0.61559	0.459000	0.35465	ACA	.	.		0.398	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393	
TRIM2	23321	hgsc.bcm.edu	37	4	154216477	154216477	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:154216477C>T	ENST00000437508.2	+	6	919	c.718C>T	c.(718-720)Cag>Tag	p.Q240*	TRIM2_ENST00000494872.1_3'UTR|TRIM2_ENST00000338700.5_Nonsense_Mutation_p.Q267*	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	240					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		CCTCCAGTCGCAGCTGGATAC	0.652																																					p.Q267X		Atlas-SNP	.											TRIM2_ENST00000338700,colon,carcinoma,0,2	TRIM2	105	.	0			c.C799T						.						22.0	21.0	22.0					4																	154216477		2203	4300	6503	SO:0001587	stop_gained	23321	exon6			CAGTCGCAGCTGG	AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	15974	protein-coding gene	gene with protein product		614141	"""tripartite motif-containing 2"""			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.718C>T	chr4.hg19:g.154216477C>T	ENSP00000415812:p.Gln240*	63.0	0.0		49.0	3.0	NM_015271	D3DP09|O60272|Q9BSI9|Q9UFZ1	Nonsense_Mutation	SNP	ENST00000437508.2	hg19	CCDS47147.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.993509	0.93167	.	.	ENSG00000109654	ENST00000437508;ENST00000338700	.	.	.	5.31	5.31	0.75309	.	0.102561	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	1.0038	19.3326	0.94297	0.0:1.0:0.0:0.0	.	.	.	.	X	240;267	.	ENSP00000339659:Q267X	Q	+	1	0	TRIM2	154435927	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.411000	0.80078	2.639000	0.89480	0.561000	0.74099	CAG	.	.		0.652	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1		
IRF2	3660	hgsc.bcm.edu	37	4	185340657	185340657	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:185340657A>G	ENST00000393593.3	-	3	360	c.153T>C	c.(151-153)gaT>gaC	p.D51D	IRF2_ENST00000512020.1_5'UTR	NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	51					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		AGAGTGGTGCATCTTTTTCCA	0.393																																					p.D51D		Atlas-SNP	.											.	IRF2	53	.	0			c.T153C						.						140.0	141.0	141.0					4																	185340657		2203	4300	6503	SO:0001819	synonymous_variant	3660	exon3			TGGTGCATCTTTT		CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.153T>C	chr4.hg19:g.185340657A>G		96.0	0.0		74.0	4.0	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Silent	SNP	ENST00000393593.3	hg19	CCDS3835.1																																																																																			.	.		0.393	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1		
TRIML1	339976	hgsc.bcm.edu	37	4	189068092	189068092	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr4:189068092G>A	ENST00000332517.3	+	6	1113	c.973G>A	c.(973-975)Gac>Aac	p.D325N	TRIML1_ENST00000507581.1_3'UTR	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	325	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.D325H(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		GGAAAGATTTGACCAGTCTGC	0.547																																					p.D325N	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											TRIML1,NS,carcinoma,0,1	TRIML1	126	.	1	Substitution - Missense(1)	endometrium(1)	c.G973A						.						105.0	99.0	101.0					4																	189068092		2203	4300	6503	SO:0001583	missense	339976	exon6			AGATTTGACCAGT	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"""RING-type (C3HC4) zinc fingers"""	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.973G>A	chr4.hg19:g.189068092G>A	ENSP00000327738:p.Asp325Asn	127.0	0.0		109.0	5.0	NM_178556	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	hg19	CCDS3851.1	.	.	.	.	.	.	.	.	.	.	g	19.93	3.917648	0.73098	.	.	ENSG00000184108	ENST00000332517	T	0.15952	2.38	4.92	4.07	0.47477	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.000000	0.56097	D	0.000026	T	0.23410	0.0566	L	0.50919	1.6	0.37246	D	0.906365	D	0.57899	0.981	P	0.56514	0.8	T	0.01869	-1.1257	10	0.26408	T	0.33	-38.8901	6.7704	0.23591	0.1815:0.0:0.8185:0.0	.	325	Q8N9V2	TRIML_HUMAN	N	325	ENSP00000327738:D325N	ENSP00000327738:D325N	D	+	1	0	TRIML1	189305086	0.032000	0.19561	1.000000	0.80357	0.838000	0.47535	1.110000	0.31147	2.749000	0.94314	0.550000	0.68814	GAC	.	.		0.547	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556	
EXOC3	11336	hgsc.bcm.edu	37	5	466898	466898	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:466898A>G	ENST00000512944.1	+	13	2312	c.2123A>G	c.(2122-2124)aAg>aGg	p.K708R	EXOC3_ENST00000315013.5_Missense_Mutation_p.K708R|CTD-2228K2.5_ENST00000510714.1_Intron	NM_007277.4	NP_009208.2	O60645	EXOC3_HUMAN	exocyst complex component 3	719					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|secretory granule membrane (GO:0030667)				breast(2)|cervix(1)|endometrium(4)|large_intestine(1)|lung(13)|ovary(1)|urinary_tract(1)	23		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			CGTGACATGAAGCAGACCATC	0.647																																					p.K708R		Atlas-SNP	.											.	EXOC3	54	.	0			c.A2123G						.						47.0	57.0	54.0					5																	466898		2167	4257	6424	SO:0001583	missense	11336	exon13			ACATGAAGCAGAC	BC034427	CCDS54830.1	5p15.33	2013-01-22	2005-11-01	2005-11-01	ENSG00000180104	ENSG00000180104			30378	protein-coding gene	gene with protein product		608186	"""SEC6-like 1 (S. cerevisiae)"""	SEC6L1		8619474	Standard	XM_005248238		Approved	Sec6p	uc003jba.3	O60645	OTTHUMG00000162205	ENST00000512944.1:c.2123A>G	chr5.hg19:g.466898A>G	ENSP00000425587:p.Lys708Arg	147.0	0.0		109.0	6.0	NM_007277	Q6P2E8|Q8TEN6|Q8WUW0|Q96DI4	Missense_Mutation	SNP	ENST00000512944.1	hg19	CCDS54830.1	.	.	.	.	.	.	.	.	.	.	A	8.734	0.917369	0.17982	.	.	ENSG00000180104	ENST00000512944;ENST00000315013;ENST00000340158	T;T	0.05996	3.36;3.36	5.49	5.49	0.81192	.	0.047847	0.85682	D	0.000000	T	0.02970	0.0088	N	0.02802	-0.49	0.45554	D	0.998505	B	0.14012	0.009	B	0.16289	0.015	T	0.47699	-0.9097	10	0.09843	T	0.71	-43.9352	13.5419	0.61679	1.0:0.0:0.0:0.0	.	719	O60645	EXOC3_HUMAN	R	708;708;603	ENSP00000425587:K708R;ENSP00000323377:K708R	ENSP00000323377:K708R	K	+	2	0	EXOC3	519898	1.000000	0.71417	1.000000	0.80357	0.495000	0.33615	5.054000	0.64275	2.091000	0.63221	0.254000	0.18369	AAG	.	.		0.647	EXOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367882.1	NM_007277	
BRD9	65980	hgsc.bcm.edu	37	5	864653	864653	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:864653T>C	ENST00000467963.1	-	16	1890	c.1724A>G	c.(1723-1725)cAg>cGg	p.Q575R	BRD9_ENST00000483173.1_Missense_Mutation_p.Q522R|BRD9_ENST00000323510.4_Missense_Mutation_p.Q479R|BRD9_ENST00000388890.4_Missense_Mutation_p.Q459R	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9	575					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			GACGTCTGGCTGCTCCCCGAC	0.557																																					p.Q575R		Atlas-SNP	.											.	BRD9	113	.	0			c.A1724G						.						73.0	74.0	74.0					5																	864653		2203	4300	6503	SO:0001583	missense	65980	exon16			TCTGGCTGCTCCC	AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310			25818	protein-coding gene	gene with protein product						12477932	Standard	NM_023924		Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.1724A>G	chr5.hg19:g.864653T>C	ENSP00000419765:p.Gln575Arg	70.0	0.0		63.0	4.0	NM_023924	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	Missense_Mutation	SNP	ENST00000467963.1	hg19	CCDS34127.2	.	.	.	.	.	.	.	.	.	.	t	18.51	3.639436	0.67244	.	.	ENSG00000028310	ENST00000323510;ENST00000388890;ENST00000483173;ENST00000467963	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.58680	0.2139	M	0.63428	1.95	0.80722	D	1	D;D;P;P	0.52996	0.957;0.957;0.921;0.921	P;P;P;P	0.52710	0.608;0.608;0.707;0.707	T	0.63717	-0.6574	10	0.87932	D	0	.	15.2034	0.73159	0.0:0.0:0.0:1.0	.	522;575;479;459	B4DMQ2;Q9H8M2;Q9H8M2-1;Q9H8M2-3	.;BRD9_HUMAN;.;.	R	479;459;522;575	ENSP00000323557:Q479R;ENSP00000373542:Q459R;ENSP00000419845:Q522R;ENSP00000419765:Q575R	ENSP00000323557:Q479R	Q	-	2	0	BRD9	917653	1.000000	0.71417	1.000000	0.80357	0.183000	0.23260	5.037000	0.64170	2.078000	0.62432	0.459000	0.35465	CAG	.	.		0.557	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354113.1	NM_023924	
LPCAT1	79888	hgsc.bcm.edu	37	5	1463792	1463792	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:1463792T>C	ENST00000283415.3	-	14	1711	c.1579A>G	c.(1579-1581)Aag>Gag	p.K527E	LPCAT1_ENST00000503252.1_5'UTR	NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	527					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		CGAACAGGCTTCCGCCCAGCG	0.597																																					p.K527E		Atlas-SNP	.											.	LPCAT1	70	.	0			c.A1579G						.						56.0	59.0	58.0					5																	1463792		2203	4300	6503	SO:0001583	missense	79888	exon14			CAGGCTTCCGCCC	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"""EF-hand domain containing"""	25718	protein-coding gene	gene with protein product		610472	"""acyltransferase like 2"""	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.1579A>G	chr5.hg19:g.1463792T>C	ENSP00000283415:p.Lys527Glu	115.0	0.0		90.0	4.0	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Missense_Mutation	SNP	ENST00000283415.3	hg19	CCDS3864.1	.	.	.	.	.	.	.	.	.	.	T	10.65	1.410349	0.25465	.	.	ENSG00000153395	ENST00000283415	T	0.70045	-0.45	4.29	0.528	0.17089	.	0.693642	0.14799	N	0.297753	T	0.37945	0.1022	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.15150	-1.0447	10	0.21540	T	0.41	-7.8716	4.4181	0.11466	0.0:0.2028:0.1961:0.6011	.	527	Q8NF37	PCAT1_HUMAN	E	527	ENSP00000283415:K527E	ENSP00000283415:K527E	K	-	1	0	LPCAT1	1516792	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.428000	0.21395	-0.155000	0.11098	0.459000	0.35465	AAG	.	.		0.597	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830	
ICE1	23379	hgsc.bcm.edu	37	5	5461628	5461628	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:5461628A>G	ENST00000296564.7	+	13	2403	c.2181A>G	c.(2179-2181)aaA>aaG	p.K727K		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		727					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						AATATACAAAAGTAGTAAAAG	0.388																																					p.K727K		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A2181G						.						54.0	51.0	52.0					5																	5461628		1851	4093	5944	SO:0001819	synonymous_variant	23379	exon13			TACAAAAGTAGTA																												ENST00000296564.7:c.2181A>G	chr5.hg19:g.5461628A>G		116.0	0.0		102.0	5.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	hg19	CCDS47187.1																																																																																			.	.		0.388	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
ICE1	23379	hgsc.bcm.edu	37	5	5461675	5461675	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:5461675T>C	ENST00000296564.7	+	13	2450	c.2228T>C	c.(2227-2229)tTt>tCt	p.F743S		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		743					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						CGGTCAGTATTTATGAAAGCT	0.363																																					p.F743S		Atlas-SNP	.											.	KIAA0947	301	.	0			c.T2228C						.						59.0	51.0	54.0					5																	5461675		1874	4096	5970	SO:0001583	missense	23379	exon13			CAGTATTTATGAA																												ENST00000296564.7:c.2228T>C	chr5.hg19:g.5461675T>C	ENSP00000296564:p.Phe743Ser	99.0	0.0		81.0	4.0	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	hg19	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.147369	0.77888	.	.	ENSG00000164151	ENST00000296564	T	0.12361	2.69	5.26	2.63	0.31362	.	0.545813	0.19575	N	0.111005	T	0.20981	0.0505	L	0.32530	0.975	0.09310	N	1	D	0.71674	0.998	D	0.69654	0.965	T	0.04693	-1.0933	10	0.34782	T	0.22	-21.5527	8.8379	0.35123	0.0:0.0:0.3738:0.6262	.	743	Q9Y2F5	K0947_HUMAN	S	743	ENSP00000296564:F743S	ENSP00000296564:F743S	F	+	2	0	KIAA0947	5514675	0.535000	0.26370	0.007000	0.13788	0.857000	0.48899	1.607000	0.36836	0.807000	0.34208	0.254000	0.18369	TTT	.	.		0.363	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
SEMA5A	9037	hgsc.bcm.edu	37	5	9122917	9122917	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:9122917A>G	ENST00000382496.5	-	14	2297	c.1632T>C	c.(1630-1632)ggT>ggC	p.G544G		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	544	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GAGACCACACACCAAAGTGCC	0.557																																					p.G544G		Atlas-SNP	.											.	SEMA5A	236	.	0			c.T1632C						.						63.0	63.0	63.0					5																	9122917		2203	4300	6503	SO:0001819	synonymous_variant	9037	exon14			CCACACACCAAAG	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.1632T>C	chr5.hg19:g.9122917A>G		158.0	0.0		135.0	6.0	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	hg19	CCDS3875.1																																																																																			.	.		0.557	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		
FBXL7	23194	hgsc.bcm.edu	37	5	15936656	15936656	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:15936656G>A	ENST00000504595.1	+	4	1318	c.837G>A	c.(835-837)atG>atA	p.M279I	FBXL7_ENST00000329673.7_Missense_Mutation_p.M267I|MIR887_ENST00000401258.1_RNA|FBXL7_ENST00000510662.1_Missense_Mutation_p.M232I	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	279					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						ACCTGGACATGACGGACTGCT	0.612																																					p.M279I		Atlas-SNP	.											.	FBXL7	138	.	0			c.G837A						.						72.0	73.0	72.0					5																	15936656		2183	4285	6468	SO:0001583	missense	23194	exon4			GGACATGACGGAC	AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"""F-boxes / Leucine-rich repeats"""	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.837G>A	chr5.hg19:g.15936656G>A	ENSP00000423630:p.Met279Ile	62.0	0.0		63.0	4.0	NM_012304	B9EGF1|D6RDY7|O94926	Missense_Mutation	SNP	ENST00000504595.1	hg19	CCDS54833.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.369911	0.61624	.	.	ENSG00000183580	ENST00000504595;ENST00000510662;ENST00000329673	T;T;T	0.49139	0.79;0.79;0.79	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.35307	0.0927	N	0.24115	0.695	0.80722	D	1	P	0.35844	0.524	B	0.29862	0.108	T	0.20773	-1.0265	10	0.41790	T	0.15	.	18.6513	0.91431	0.0:0.0:1.0:0.0	.	279	Q9UJT9	FBXL7_HUMAN	I	279;232;267	ENSP00000423630:M279I;ENSP00000425184:M232I;ENSP00000329632:M267I	ENSP00000329632:M267I	M	+	3	0	FBXL7	15989656	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.414000	0.81942	0.655000	0.94253	ATG	.	.		0.612	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304	
CDH18	1016	hgsc.bcm.edu	37	5	19544066	19544066	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:19544066A>G	ENST00000507958.1	-	11	2292	c.1302T>C	c.(1300-1302)gaT>gaC	p.D434D	CDH18_ENST00000502796.1_Silent_p.D434D|CDH18_ENST00000274170.4_Silent_p.D434D|CDH18_ENST00000506372.1_Silent_p.D434D|CDH18_ENST00000511273.1_Silent_p.D434D|CDH18_ENST00000382275.1_Silent_p.D434D			Q13634	CAD18_HUMAN	cadherin 18, type 2	434	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CAGTATTGGCATCAATGTTGA	0.343																																					p.D434D		Atlas-SNP	.											.	CDH18	561	.	0			c.T1302C						.						124.0	117.0	119.0					5																	19544066		2203	4300	6503	SO:0001819	synonymous_variant	1016	exon9			ATTGGCATCAATG	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"""Cadherins / Major cadherins"""	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1302T>C	chr5.hg19:g.19544066A>G		169.0	0.0		114.0	6.0	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Silent	SNP	ENST00000507958.1	hg19	CCDS3889.1																																																																																			.	.		0.343	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934	
FYB	2533	hgsc.bcm.edu	37	5	39130699	39130699	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:39130699T>C	ENST00000351578.6	-	10	2023	c.1833A>G	c.(1831-1833)ggA>ggG	p.G611G	FYB_ENST00000540520.1_Silent_p.G621G|FYB_ENST00000512982.1_Silent_p.G611G|FYB_ENST00000515010.1_Silent_p.G611G|FYB_ENST00000505428.1_Silent_p.G611G	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	611					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			TACCTCCACTTCCACTCTGAC	0.333																																					p.G621G		Atlas-SNP	.											.	FYB	354	.	0			c.A1863G						.						77.0	71.0	73.0					5																	39130699		1891	4117	6008	SO:0001819	synonymous_variant	2533	exon10			TCCACTTCCACTC	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"""FYN-binding protein (FYB-120/130)"""			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1833A>G	chr5.hg19:g.39130699T>C		72.0	0.0		73.0	5.0	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Silent	SNP	ENST00000351578.6	hg19	CCDS47200.1																																																																																			.	.		0.333	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465	
FGF10	2255	hgsc.bcm.edu	37	5	44388683	44388683	+	Silent	SNP	A	A	G	rs140279180	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:44388683A>G	ENST00000264664.4	-	1	216	c.102T>C	c.(100-102)ccT>ccC	p.P34P	RP11-473L15.2_ENST00000502457.1_RNA	NM_004465.1	NP_004456.1	O15520	FGF10_HUMAN	fibroblast growth factor 10	34					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching morphogenesis of an epithelial tube (GO:0048754)|bronchiole morphogenesis (GO:0060436)|bud elongation involved in lung branching (GO:0060449)|bud outgrowth involved in lung branching (GO:0060447)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell migration (GO:0010631)|epithelial cell proliferation (GO:0050673)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|ERK1 and ERK2 cascade (GO:0070371)|establishment of mitotic spindle orientation (GO:0000132)|Fc-epsilon receptor signaling pathway (GO:0038095)|female genitalia morphogenesis (GO:0048807)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|hair follicle morphogenesis (GO:0031069)|Harderian gland development (GO:0070384)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte proliferation (GO:0043616)|lacrimal gland development (GO:0032808)|limb bud formation (GO:0060174)|lung epithelium development (GO:0060428)|lung proximal/distal axis specification (GO:0061115)|lung saccule development (GO:0060430)|male genitalia morphogenesis (GO:0048808)|mammary gland bud formation (GO:0060615)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal-epithelial cell signaling involved in lung development (GO:0060496)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|metanephros morphogenesis (GO:0003338)|muscle cell fate commitment (GO:0042693)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|pancreas development (GO:0031016)|phosphatidylinositol-mediated signaling (GO:0048015)|pituitary gland development (GO:0021983)|positive chemotaxis (GO:0050918)|positive regulation of ATPase activity (GO:0032781)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urothelial cell proliferation (GO:0050677)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of white fat cell proliferation (GO:0070352)|prostatic bud formation (GO:0060513)|protein localization to cell surface (GO:0034394)|radial glial cell differentiation (GO:0060019)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of saliva secretion (GO:0046877)|regulation of smoothened signaling pathway (GO:0008589)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|salivary gland development (GO:0007431)|secretion by lung epithelial cell involved in lung growth (GO:0061033)|semicircular canal fusion (GO:0060879)|smooth muscle cell differentiation (GO:0051145)|somatic stem cell maintenance (GO:0035019)|spleen development (GO:0048536)|submandibular salivary gland formation (GO:0060661)|tear secretion (GO:0070075)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tissue regeneration (GO:0042246)|Type II pneumocyte differentiation (GO:0060510)|urothelial cell proliferation (GO:0050674)|white fat cell differentiation (GO:0050872)|wound healing (GO:0042060)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chemoattractant activity (GO:0042056)|fibroblast growth factor receptor binding (GO:0005104)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|type 2 fibroblast growth factor receptor binding (GO:0005111)			haematopoietic_and_lymphoid_tissue(1)|lung(11)|skin(1)	13	Lung NSC(6;1.12e-06)					GGCAGGTGACAGGGACGGAAG	0.572																																					p.P34P		Atlas-SNP	.											.	FGF10	40	.	0			c.T102C						.						55.0	51.0	52.0					5																	44388683		2203	4300	6503	SO:0001819	synonymous_variant	2255	exon1			GGTGACAGGGACG		CCDS3950.1	5p13-p12	2008-02-05			ENSG00000070193	ENSG00000070193			3666	protein-coding gene	gene with protein product		602115				9287324	Standard	NM_004465		Approved		uc003jog.1	O15520	OTTHUMG00000131153	ENST00000264664.4:c.102T>C	chr5.hg19:g.44388683A>G		128.0	0.0		141.0	6.0	NM_004465	C7FDY0|Q6FHR3|Q6FHT6|Q96P59	Silent	SNP	ENST00000264664.4	hg19	CCDS3950.1																																																																																			.	A|1.000;C|0.000		0.572	FGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253845.2	NM_004465	
ADAMTS6	11174	hgsc.bcm.edu	37	5	64510631	64510631	+	IGR	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:64510631A>G								ADAMTS6 (16039 upstream) : ADAMTS6 (82403 downstream)																							CTCCAGCACAAGTAGCTGAGC	0.443																																					p.T855T		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.T2565C						.						130.0	114.0	119.0					5																	64510631		2203	4300	6503	SO:0001628	intergenic_variant	11174	exon20			AGCACAAGTAGCT																													chr5.hg19:g.64510631A>G		119.0	0.0		110.0	5.0	NM_197941		Silent	SNP		hg19																																																																																				.	.	0	0.443								
PPWD1	23398	hgsc.bcm.edu	37	5	64868003	64868003	+	Missense_Mutation	SNP	T	T	C	rs373825399		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:64868003T>C	ENST00000261308.5	+	5	931	c.859T>C	c.(859-861)Tgt>Cgt	p.C287R	PPWD1_ENST00000538977.1_Missense_Mutation_p.C131R|PPWD1_ENST00000535264.1_Missense_Mutation_p.C257R	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	287					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		AACCAGCGTATGTTTTTCACC	0.338																																					p.C287R		Atlas-SNP	.											.	PPWD1	47	.	0			c.T859C						.	T	ARG/CYS	1,4405	2.1+/-5.4	0,1,2202	65.0	71.0	68.0		859	5.6	1.0	5		68	0,8600		0,0,4300	no	missense	PPWD1	NM_015342.2	180	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	287/647	64868003	1,13005	2203	4300	6503	SO:0001583	missense	23398	exon5			AGCGTATGTTTTT	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"""WD repeat domain containing"""	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.859T>C	chr5.hg19:g.64868003T>C	ENSP00000261308:p.Cys287Arg	84.0	0.0		75.0	4.0	NM_015342	B4DWR9|Q15002|Q7KZ89	Missense_Mutation	SNP	ENST00000261308.5	hg19	CCDS3985.1	.	.	.	.	.	.	.	.	.	.	T	9.671	1.146709	0.21288	2.27E-4	0.0	ENSG00000113593	ENST00000261308;ENST00000535264;ENST00000538977;ENST00000505380	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.215721	0.48286	D	0.000195	T	0.35307	0.0927	N	0.05124	-0.11	0.58432	D	0.999994	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.19192	-1.0313	10	0.32370	T	0.25	.	11.5435	0.50679	0.1416:0.0:0.0:0.8584	.	257;287	F5H7P7;Q96BP3	.;PPWD1_HUMAN	R	287;257;131;206	ENSP00000261308:C287R;ENSP00000442371:C257R;ENSP00000444496:C131R;ENSP00000423234:C206R	ENSP00000261308:C287R	C	+	1	0	PPWD1	64903759	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.444000	0.44890	2.125000	0.65367	0.459000	0.35465	TGT	.	.		0.338	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342	
TRIM23	373	hgsc.bcm.edu	37	5	64890421	64890421	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:64890421T>C	ENST00000231524.9	-	10	1843	c.1472A>G	c.(1471-1473)cAc>cGc	p.H491R	TRIM23_ENST00000381018.3_Missense_Mutation_p.H491R|TRIM23_ENST00000274327.7_Missense_Mutation_p.H491R	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	491	ARF-like.				GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		AAGTTCGCTGTGTGCTTCACT	0.338																																					p.H491R		Atlas-SNP	.											.	TRIM23	73	.	0			c.A1472G						.						109.0	102.0	105.0					5																	64890421		2202	4300	6502	SO:0001583	missense	373	exon10			TCGCTGTGTGCTT	L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	660	protein-coding gene	gene with protein product		601747	"""ADP-ribosylation factor domain protein 1, 64kDa"", ""tripartite motif-containing 23"""	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.1472A>G	chr5.hg19:g.64890421T>C	ENSP00000231524:p.His491Arg	85.0	0.0		74.0	4.0	NM_033228	Q9BZY4|Q9BZY5	Missense_Mutation	SNP	ENST00000231524.9	hg19	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	T	9.197	1.027585	0.19512	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	T;T;T	0.61392	0.11;0.11;0.11	5.64	5.64	0.86602	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.30759	0.0775	N	0.01473	-0.845	0.58432	D	0.999998	B;B;B	0.16603	0.0;0.002;0.018	B;B;B	0.20955	0.01;0.002;0.032	T	0.26503	-1.0101	10	0.13470	T	0.59	.	15.8515	0.78934	0.0:0.0:0.0:1.0	.	491;491;491	P36406;P36406-2;P36406-3	TRI23_HUMAN;.;.	R	491	ENSP00000231524:H491R;ENSP00000370406:H491R;ENSP00000274327:H491R	ENSP00000231524:H491R	H	-	2	0	TRIM23	64926177	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.263000	0.72521	2.137000	0.66172	0.482000	0.46254	CAC	.	.		0.338	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656	
SV2C	22987	hgsc.bcm.edu	37	5	75505685	75505685	+	Missense_Mutation	SNP	A	A	C	rs370314313		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:75505685A>C	ENST00000502798.2	+	4	1328	c.886A>C	c.(886-888)Atg>Ctg	p.M296L	SV2C_ENST00000322285.7_Missense_Mutation_p.M296L	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	296					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)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CGCCTCTGCCATGGCCTGGGC	0.577																																					p.M296L		Atlas-SNP	.											.	SV2C	97	.	0			c.A886C						.	A	LEU/MET	0,4400		0,0,2200	55.0	58.0	57.0		886	5.1	1.0	5		57	1,8599	1.2+/-3.3	0,1,4299	no	missense	SV2C	NM_014979.1	15	0,1,6499	CC,CA,AA		0.0116,0.0,0.0077	possibly-damaging	296/728	75505685	1,12999	2200	4300	6500	SO:0001583	missense	22987	exon4			TCTGCCATGGCCT	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.886A>C	chr5.hg19:g.75505685A>C	ENSP00000423541:p.Met296Leu	106.0	0.0		79.0	4.0	NM_014979	Q496K1|Q9UPU8	Missense_Mutation	SNP	ENST00000502798.2	hg19	CCDS43331.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.314382	0.60414	0.0	1.16E-4	ENSG00000122012	ENST00000502798;ENST00000322285	T;T	0.50001	0.76;0.76	5.13	5.13	0.70059	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.31104	0.0786	N	0.16130	0.375	0.80722	D	1	B	0.13594	0.008	B	0.23150	0.044	T	0.11251	-1.0595	10	0.13108	T	0.6	-31.3584	14.6544	0.68823	1.0:0.0:0.0:0.0	.	296	Q496J9	SV2C_HUMAN	L	296	ENSP00000423541:M296L;ENSP00000316983:M296L	ENSP00000316983:M296L	M	+	1	0	SV2C	75541441	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.176000	0.94839	1.935000	0.56089	0.477000	0.44152	ATG	.	.		0.577	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4		
AP3B1	8546	hgsc.bcm.edu	37	5	77563357	77563357	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:77563357T>C	ENST00000255194.6	-	2	366	c.191A>G	c.(190-192)aAg>aGg	p.K64R	AP3B1_ENST00000519295.1_Missense_Mutation_p.K15R	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	64					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		AACAATCCGCTTCATAGCATC	0.289									Hermansky-Pudlak syndrome																												p.K64R		Atlas-SNP	.											.	AP3B1	94	.	0			c.A191G						.						94.0	95.0	94.0					5																	77563357		2203	4298	6501	SO:0001583	missense	8546	exon2	Familial Cancer Database	HPS, HPS1-8	ATCCGCTTCATAG	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.191A>G	chr5.hg19:g.77563357T>C	ENSP00000255194:p.Lys64Arg	94.0	0.0		88.0	4.0	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.150497	0.78001	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760	T;T	0.30981	1.51;1.51	5.29	5.29	0.74685	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.164274	0.51477	D	0.000088	T	0.51534	0.1680	L	0.58428	1.81	0.58432	D	0.999999	D	0.71674	0.998	D	0.77557	0.99	T	0.54397	-0.8300	10	0.87932	D	0	-19.2682	14.2078	0.65746	0.0:0.0:0.0:1.0	.	64	O00203	AP3B1_HUMAN	R	64;15;64	ENSP00000255194:K64R;ENSP00000430597:K15R	ENSP00000255194:K64R	K	-	2	0	AP3B1	77599113	1.000000	0.71417	0.999000	0.59377	0.949000	0.60115	4.593000	0.61034	1.990000	0.58119	0.482000	0.46254	AAG	.	.		0.289	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
RASGRF2	5924	hgsc.bcm.edu	37	5	80511700	80511700	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:80511700A>G	ENST00000265080.4	+	24	3427	c.3360A>G	c.(3358-3360)aaA>aaG	p.K1120K	CKMT2-AS1_ENST00000511495.1_RNA|CKMT2-AS1_ENST00000503483.2_RNA	NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	1120	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.|Responsible of the affinity for farnesylated versus geranylgeranylated Ras. {ECO:0000250}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		TTTAGACAAAAGCTCTAATGG	0.289																																					p.K1120K		Atlas-SNP	.											.	RASGRF2	165	.	0			c.A3360G						.						15.0	16.0	16.0					5																	80511700		2118	4226	6344	SO:0001819	synonymous_variant	5924	exon24			GACAAAAGCTCTA	AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.3360A>G	chr5.hg19:g.80511700A>G		105.0	0.0		86.0	4.0	NM_006909	B9EG89|Q9UK56	Silent	SNP	ENST00000265080.4	hg19	CCDS4052.1																																																																																			.	.		0.289	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909	
XRCC4	7518	hgsc.bcm.edu	37	5	82499472	82499472	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:82499472A>G	ENST00000511817.1	+	5	664	c.584A>G	c.(583-585)cAt>cGt	p.H195R	XRCC4_ENST00000282268.3_Missense_Mutation_p.H195R|XRCC4_ENST00000338635.6_Missense_Mutation_p.H195R|XRCC4_ENST00000509268.1_3'UTR|XRCC4_ENST00000396027.4_Missense_Mutation_p.H195R			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	195	Interacts with LIG4.				cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		AGAAGTTTGCATAATAAATTA	0.328								Non-homologous end-joining																													p.H195R		Atlas-SNP	.											.	XRCC4	37	.	0			c.A584G						.						69.0	75.0	73.0					5																	82499472		2203	4299	6502	SO:0001583	missense	7518	exon5			GTTTGCATAATAA	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"""X-ray repair, complementing defective, repair in Chinese hamster"", ""DNA repair protein XRCC4"""	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.584A>G	chr5.hg19:g.82499472A>G	ENSP00000421491:p.His195Arg	92.0	0.0		94.0	4.0	NM_003401	A8K3X4|Q9BS72|Q9UP94	Missense_Mutation	SNP	ENST00000511817.1	hg19	CCDS4059.1	.	.	.	.	.	.	.	.	.	.	A	3.577	-0.086504	0.07097	.	.	ENSG00000152422	ENST00000282268;ENST00000338635;ENST00000396027;ENST00000511817	T;T;T;T	0.26660	1.72;1.72;1.72;1.72	0.225	0.225	0.15325	.	0.212263	0.50627	N	0.000115	T	0.20170	0.0485	L	0.56769	1.78	0.25570	N	0.986905	B;B;B	0.15719	0.011;0.014;0.012	B;B;B	0.12837	0.005;0.008;0.007	T	0.15150	-1.0447	10	0.46703	T	0.11	-18.6796	4.823	0.13400	0.9998:0.0:2.0E-4:0.0	.	195;195;195	Q13426-2;Q13426;Q13426-3	.;XRCC4_HUMAN;.	R	195	ENSP00000282268:H195R;ENSP00000342011:H195R;ENSP00000379344:H195R;ENSP00000421491:H195R	ENSP00000282268:H195R	H	+	2	0	XRCC4	82535228	0.940000	0.31905	0.993000	0.49108	0.668000	0.39293	1.013000	0.29937	0.257000	0.21650	0.254000	0.18369	CAT	.	.		0.328	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550	
ERAP1	51752	hgsc.bcm.edu	37	5	96119656	96119656	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:96119656T>C	ENST00000443439.2	-	14	2138	c.2072A>G	c.(2071-2073)gAt>gGt	p.D691G	ERAP1_ENST00000514604.1_5'UTR|CTD-2260A17.1_ENST00000512856.1_RNA|ERAP1_ENST00000296754.3_Missense_Mutation_p.D691G|CTD-2260A17.1_ENST00000602972.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	691					angiogenesis (GO:0001525)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|fat cell differentiation (GO:0045444)|membrane protein ectodomain proteolysis (GO:0006509)|positive regulation of angiogenesis (GO:0045766)|regulation of blood pressure (GO:0008217)|regulation of innate immune response (GO:0045088)|response to bacterium (GO:0009617)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|interleukin-1, Type II receptor binding (GO:0005151)|interleukin-6 receptor binding (GO:0005138)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|stomach(2)	19		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TTCATTCATATCTCTTTTCTC	0.308																																					p.D691G		Atlas-SNP	.											.	ERAP1	59	.	0			c.A2072G						.						88.0	83.0	85.0					5																	96119656		2203	4300	6503	SO:0001583	missense	51752	exon14			TTCATATCTCTTT	AB011097	CCDS4085.1, CCDS47250.1	5q15	2014-04-07			ENSG00000164307	ENSG00000164307			18173	protein-coding gene	gene with protein product	"""aminopeptidase regulator of TNFR1 shedding"", ""adipocyte-derived leucine aminopeptidase"", ""puromycin-insensitive leucyl-specific aminopeptidase"""	606832				10220586, 12189246, 16286653	Standard	NM_001198541		Approved	ARTS-1, A-LAP, PILS-AP, KIAA0525, ERAAP1	uc003kml.3	Q9NZ08	OTTHUMG00000128721	ENST00000443439.2:c.2072A>G	chr5.hg19:g.96119656T>C	ENSP00000406304:p.Asp691Gly	110.0	0.0		89.0	4.0	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	hg19	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	T	10.29	1.309375	0.23821	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.06449	3.3;3.3	5.84	5.84	0.93424	.	0.262386	0.42420	D	0.000702	T	0.07954	0.0199	L	0.46614	1.455	0.58432	D	0.999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.12837	0.008;0.003;0.003	T	0.26985	-1.0087	10	0.17369	T	0.5	.	15.1933	0.73063	0.0:0.0:0.0:1.0	.	691;691;691	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	G	691	ENSP00000296754:D691G;ENSP00000406304:D691G	ENSP00000296754:D691G	D	-	2	0	ERAP1	96145412	1.000000	0.71417	0.994000	0.49952	0.988000	0.76386	4.552000	0.60747	2.232000	0.73038	0.533000	0.62120	GAT	.	.		0.308	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
ST8SIA4	7903	hgsc.bcm.edu	37	5	100222086	100222086	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:100222086T>C	ENST00000231461.5	-	3	774	c.464A>G	c.(463-465)gAa>gGa	p.E155G	ST8SIA4_ENST00000451528.2_Missense_Mutation_p.E155G|ST8SIA4_ENST00000507360.2_5'UTR	NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	155					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)		CTTTCCACATTCACTGTCTAA	0.388																																					p.E155G		Atlas-SNP	.											ST8SIA4,colon,carcinoma,0,2	ST8SIA4	77	.	0			c.A464G						.						83.0	83.0	83.0					5																	100222086		2203	4300	6503	SO:0001583	missense	7903	exon3			CCACATTCACTGT	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.464A>G	chr5.hg19:g.100222086T>C	ENSP00000231461:p.Glu155Gly	201.0	0.0		169.0	7.0	NM_175052	A8KA07|G3V104|Q8N1F4|Q92693	Missense_Mutation	SNP	ENST00000231461.5	hg19	CCDS4091.1	.	.	.	.	.	.	.	.	.	.	T	5.756	0.323932	0.10900	.	.	ENSG00000113532	ENST00000231461;ENST00000451528	T;T	0.28454	1.61;1.61	5.92	-1.81	0.07882	.	0.400705	0.26761	N	0.022637	T	0.05318	0.0141	N	0.00149	-1.99	0.25427	N	0.988219	B	0.02656	0.0	B	0.01281	0.0	T	0.43410	-0.9393	10	0.02654	T	1	-3.5454	13.1326	0.59391	0.0:0.6687:0.0:0.3313	.	155	Q92187	SIA8D_HUMAN	G	155	ENSP00000231461:E155G;ENSP00000428914:E155G	ENSP00000231461:E155G	E	-	2	0	ST8SIA4	100249985	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	0.871000	0.28023	-0.155000	0.11098	0.455000	0.32223	GAA	.	.		0.388	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250632.3	NM_005668	
MAN2A1	4124	hgsc.bcm.edu	37	5	109190938	109190938	+	Missense_Mutation	SNP	C	C	T	rs3217225|rs200723635	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:109190938C>T	ENST00000261483.4	+	20	4126	c.3074C>T	c.(3073-3075)tCc>tTc	p.S1025F	MAN2A1_ENST00000505313.1_3'UTR	NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	1025					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		AATAAGTTCTCCTCACCTACC	0.403																																					p.S1025F		Atlas-SNP	.											MAN2A1,colon,carcinoma,0,1	MAN2A1	136	.	0			c.C3074T						.						163.0	117.0	132.0					5																	109190938		2202	4295	6497	SO:0001583	missense	4124	exon20			AGTTCTCCTCACC		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.3074C>T	chr5.hg19:g.109190938C>T	ENSP00000261483:p.Ser1025Phe	3.0	0.0		26.0	15.0	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	C	9.575	1.122145	0.20877	.	.	ENSG00000112893	ENST00000261483	T	0.80738	-1.41	5.07	1.88	0.25563	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	1.184260	0.05825	N	0.616516	T	0.71609	0.3360	L	0.34521	1.04	0.09310	N	1	B	0.10296	0.003	B	0.19666	0.026	T	0.58521	-0.7622	10	0.56958	D	0.05	1.7459	5.1539	0.15025	0.5166:0.3102:0.0:0.1732	.	1025	Q16706	MA2A1_HUMAN	F	1025	ENSP00000261483:S1025F	ENSP00000261483:S1025F	S	+	2	0	MAN2A1	109218837	0.407000	0.25352	0.001000	0.08648	0.007000	0.05969	3.958000	0.56737	0.412000	0.25729	-0.373000	0.07131	TCC	.	.		0.403	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1		
YTHDC2	64848	hgsc.bcm.edu	37	5	112927702	112927702	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:112927702A>G	ENST00000161863.4	+	28	4252	c.4039A>G	c.(4039-4041)Agg>Ggg	p.R1347G		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1347	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GGGATTTTCTAGGATGTCTTC	0.418																																					p.R1347G		Atlas-SNP	.											.	YTHDC2	118	.	0			c.A4039G						.						47.0	45.0	46.0					5																	112927702		2201	4299	6500	SO:0001583	missense	64848	exon28			TTTTCTAGGATGT	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.4039A>G	chr5.hg19:g.112927702A>G	ENSP00000161863:p.Arg1347Gly	84.0	0.0		87.0	4.0	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	hg19	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	A	19.03	3.748349	0.69533	.	.	ENSG00000047188	ENST00000161863;ENST00000511372	T	0.36157	1.27	5.83	3.3	0.37823	YTH domain (2);	0.000000	0.85682	D	0.000000	T	0.57740	0.2074	M	0.79614	2.46	0.80722	D	1	D	0.57257	0.979	D	0.65233	0.933	T	0.61038	-0.7143	10	0.87932	D	0	.	12.9384	0.58329	0.613:0.387:0.0:0.0	.	1347	Q9H6S0	YTDC2_HUMAN	G	1347;1257	ENSP00000161863:R1347G	ENSP00000161863:R1347G	R	+	1	2	YTHDC2	112955601	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.692000	0.47018	0.399000	0.25367	0.528000	0.53228	AGG	.	.		0.418	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
DCANP1	140947	hgsc.bcm.edu	37	5	134785146	134785146	+	5'Flank	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:134785146A>G	ENST00000503143.2	-	0	0				TIFAB_ENST00000537858.1_Nonstop_Mutation_p.*162Q|CTB-138E5.1_ENST00000510230.1_RNA	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN								nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGGATCTGCTACCCTGAACCA	0.582																																					p.X162Q		Atlas-SNP	.											.	TIFAB	23	.	0			c.T484C						.						52.0	55.0	54.0					5																	134785146		1890	4117	6007	SO:0001631	upstream_gene_variant	497189	exon2			TCTGCTACCCTGA																													chr5.hg19:g.134785146A>G	Exception_encountered	90.0	0.0		81.0	4.0	NM_001099221		Missense_Mutation	SNP	ENST00000503143.2	hg19	CCDS4186.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-2.948404	0.00051	.	.	ENSG00000255833	ENST00000537858	.	.	.	5.28	-5.38	0.02673	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.3388	0.07111	0.085:0.2566:0.3544:0.3041	.	.	.	.	Q	162	.	.	X	-	1	0	TIFAB	134813045	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.454000	0.06770	-1.473000	0.01881	-1.525000	0.00928	TAG	.	.		0.582	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1		
PKD2L2	27039	hgsc.bcm.edu	37	5	137271514	137271514	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:137271514A>G	ENST00000508883.1	+	13	1726	c.1700A>G	c.(1699-1701)aAa>aGa	p.K567R	PKD2L2_ENST00000290431.5_Missense_Mutation_p.K567R|PKD2L2_ENST00000502810.1_Missense_Mutation_p.K545R|PKD2L2_ENST00000508638.1_Missense_Mutation_p.K466R|PKD2L2_ENST00000350250.4_Missense_Mutation_p.K533R			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	567					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)	integral component of membrane (GO:0016021)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			breast(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	28			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CAGATGAAAAAATGGAAAGAG	0.388																																					p.K567R		Atlas-SNP	.											.	PKD2L2	68	.	0			c.A1700G						.						77.0	75.0	76.0					5																	137271514		1839	4104	5943	SO:0001583	missense	27039	exon13			TGAAAAAATGGAA	AF118125	CCDS43367.1, CCDS58971.1, CCDS58972.1	5q31	2011-12-16			ENSG00000078795	ENSG00000078795		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9012	protein-coding gene	gene with protein product		604669				10602361	Standard	NM_014386		Approved	TRPP5	uc003lbw.1	Q9NZM6	OTTHUMG00000163306	ENST00000508883.1:c.1700A>G	chr5.hg19:g.137271514A>G	ENSP00000424725:p.Lys567Arg	71.0	0.0		92.0	4.0	NM_014386	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Missense_Mutation	SNP	ENST00000508883.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.86	1.469548	0.26423	.	.	ENSG00000078795	ENST00000350250;ENST00000508638;ENST00000502810;ENST00000508883;ENST00000290431	T;T;T;T;T	0.72835	-0.31;0.21;-0.69;-0.23;-0.24	5.63	3.24	0.37175	.	0.157314	0.44688	N	0.000431	T	0.48333	0.1494	N	0.17474	0.49	0.23282	N	0.997982	B;B;B	0.17038	0.001;0.02;0.011	B;B;B	0.13407	0.002;0.008;0.009	T	0.25745	-1.0123	10	0.25106	T	0.35	-7.9694	5.5578	0.17125	0.7359:0.1739:0.0902:0.0	.	567;466;567	Q9NZM6;E9PC91;Q9NZM6-5	PK2L2_HUMAN;.;.	R	533;466;545;567;567	ENSP00000344177:K533R;ENSP00000423382:K466R;ENSP00000425513:K545R;ENSP00000424725:K567R;ENSP00000290431:K567R	ENSP00000290431:K567R	K	+	2	0	PKD2L2	137299413	0.977000	0.34250	0.980000	0.43619	0.991000	0.79684	1.162000	0.31786	0.505000	0.28104	-0.313000	0.08912	AAA	.	.		0.388	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386	
PCDHA3	56145	hgsc.bcm.edu	37	5	140180864	140180864	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:140180864A>C	ENST00000522353.2	+	1	82	c.82A>C	c.(82-84)Agc>Cgc	p.S28R	PCDHA3_ENST00000532566.2_Missense_Mutation_p.S28R|PCDHA2_ENST00000520672.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	28					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGGTGGGGAGCGGCCAGCT	0.617																																					p.S28R		Atlas-SNP	.											.	PCDHA3	396	.	0			c.A82C						.						57.0	63.0	61.0					5																	140180864		2203	4300	6503	SO:0001583	missense	56145	exon1			GTGGGGAGCGGCC	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.82A>C	chr5.hg19:g.140180864A>C	ENSP00000429808:p.Ser28Arg	83.0	0.0		95.0	4.0	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	hg19	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	a	4.841	0.156425	0.09236	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.54071	0.67;0.59	4.65	3.49	0.39957	Cadherin (1);	0.000000	0.46758	U	0.000274	T	0.56601	0.1996	M	0.91768	3.24	0.20196	N	0.999921	B;B	0.26547	0.152;0.014	B;B	0.28709	0.093;0.031	T	0.57642	-0.7776	10	0.51188	T	0.08	.	4.7933	0.13259	0.6568:0.1611:0.1821:0.0	.	28;28	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	R	28	ENSP00000429808:S28R;ENSP00000434086:S28R	ENSP00000429808:S28R	S	+	1	0	PCDHA3	140161048	0.034000	0.19679	0.986000	0.45419	0.031000	0.12232	1.944000	0.40263	0.758000	0.33059	-0.333000	0.08304	AGC	.	.		0.617	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
PCDHA11	56138	hgsc.bcm.edu	37	5	140250200	140250200	+	Silent	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:140250200G>A	ENST00000398640.2	+	1	1512	c.1512G>A	c.(1510-1512)tcG>tcA	p.S504S	PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	504	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCGCTGTCGAGCTACGTGT	0.692																																					p.S504S		Atlas-SNP	.											.	PCDHA11	209	.	0			c.G1512A						.						61.0	67.0	65.0					5																	140250200		2203	4298	6501	SO:0001819	synonymous_variant	56138	exon1			GCTGTCGAGCTAC	AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"""Cadherins / Protocadherins : Clustered"""	8665	other	complex locus constituent	"""KIAA0345-like 3"", ""ortholog of mouse CNR7"""	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.1512G>A	chr5.hg19:g.140250200G>A		114.0	0.0		142.0	11.0	NM_018902	B2RN58|O75279	Silent	SNP	ENST00000398640.2	hg19	CCDS47284.1																																																																																			.	.		0.692	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902	
PCDHB3	56132	hgsc.bcm.edu	37	5	140480645	140480645	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:140480645A>G	ENST00000231130.2	+	1	412	c.412A>G	c.(412-414)Atg>Gtg	p.M138V	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	138	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGAAAATGAAATGCATCTGAA	0.398																																					p.M138V		Atlas-SNP	.											PCDHB3,colon,carcinoma,-1,1	PCDHB3	208	.	0			c.A412G						.						83.0	87.0	86.0					5																	140480645		2203	4300	6503	SO:0001583	missense	56132	exon1			AATGAAATGCATC	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"""Cadherins / Protocadherins : Clustered"""	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.412A>G	chr5.hg19:g.140480645A>G	ENSP00000231130:p.Met138Val	65.0	0.0		87.0	4.0	NM_018937	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	hg19	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	A	7.759	0.705025	0.15172	.	.	ENSG00000113205	ENST00000231130	T	0.19105	2.17	5.08	5.08	0.68730	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.18467	0.0443	L	0.35723	1.085	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.09751	-1.0660	9	0.45353	T	0.12	.	10.7425	0.46162	0.8576:0.0:0.0:0.1424	.	138	Q9Y5E6	PCDB3_HUMAN	V	138	ENSP00000231130:M138V	ENSP00000231130:M138V	M	+	1	0	PCDHB3	140460829	0.000000	0.05858	0.998000	0.56505	0.997000	0.91878	-0.490000	0.06482	2.036000	0.60181	0.533000	0.62120	ATG	.	.		0.398	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937	
KIF4B	285643	hgsc.bcm.edu	37	5	154394167	154394167	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:154394167A>C	ENST00000435029.4	+	1	908	c.748A>C	c.(748-750)Acc>Ccc	p.T250P		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	250	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)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			ACAGAAGAAAACCAAGGCTGA	0.428																																					p.T250P		Atlas-SNP	.											.	KIF4B	307	.	0			c.A748C						.						111.0	113.0	112.0					5																	154394167		2203	4300	6503	SO:0001583	missense	285643	exon1			AAGAAAACCAAGG	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.748A>C	chr5.hg19:g.154394167A>C	ENSP00000387875:p.Thr250Pro	227.0	0.0		269.0	19.0	NM_001099293		Missense_Mutation	SNP	ENST00000435029.4	hg19	CCDS47324.1	.	.	.	.	.	.	.	.	.	.	a	16.48	3.134160	0.56828	.	.	ENSG00000226650	ENST00000435029	T	0.77489	-1.1	1.73	1.73	0.24493	Kinesin, motor domain (5);	.	.	.	.	D	0.89694	0.6789	H	0.95850	3.73	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88917	0.3363	9	0.87932	D	0	.	7.4446	0.27203	1.0:0.0:0.0:0.0	.	250	Q2VIQ3	KIF4B_HUMAN	P	250	ENSP00000387875:T250P	ENSP00000387875:T250P	T	+	1	0	KIF4B	154374360	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.389000	0.59639	1.070000	0.40811	0.533000	0.62120	ACC	.	.		0.428	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1		
HAVCR1	26762	hgsc.bcm.edu	37	5	156479571	156479571	+	Missense_Mutation	SNP	C	C	T	rs6149307|rs386693994|rs183130208|rs141023871	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:156479571C>T	ENST00000339252.3	-	3	1006	c.474G>A	c.(472-474)atG>atA	p.M158I	HAVCR1_ENST00000523175.1_Missense_Mutation_p.M158I|HAVCR1_ENST00000425854.1_Missense_Mutation_p.M158I|HAVCR1_ENST00000522693.1_Missense_Mutation_p.M158I|HAVCR1_ENST00000544197.1_Missense_Mutation_p.M158I	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)			endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GAACAGTCGTCATTGGAACAG	0.488																																					p.M158I		Atlas-SNP	.											.	HAVCR1	84	.	0			c.G474A						.						413.0	302.0	340.0					5																	156479571		2079	3991	6070	SO:0001583	missense	26762	exon4			AGTCGTCATTGGA	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"""Immunoglobulin superfamily / V-set domain containing"""	17866	protein-coding gene	gene with protein product	"""T-cell immunoglobulin mucin family member 1"""	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.474G>A	chr5.hg19:g.156479571C>T	ENSP00000344844:p.Met158Ile	8.0	0.0		339.0	38.0	NM_001099414	O43656	Missense_Mutation	SNP	ENST00000339252.3	hg19	CCDS43392.1	.	.	.	.	.	.	.	.	.	.	C	2.575	-0.298775	0.05532	.	.	ENSG00000113249	ENST00000522693;ENST00000523175;ENST00000339252;ENST00000425854;ENST00000544197;ENST00000518745	T;T;T;T;T;T	0.13901	2.55;2.6;2.6;2.55;2.6;2.57	1.56	-3.12	0.05282	.	.	.	.	.	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.31392	-0.9945	7	0.62326	D	0.03	.	0.1239	0.00067	0.2901:0.1916:0.1631:0.3551	.	.	.	.	I	158	ENSP00000428524:M158I;ENSP00000427898:M158I;ENSP00000344844:M158I;ENSP00000403333:M158I;ENSP00000440258:M158I;ENSP00000428422:M158I	ENSP00000344844:M158I	M	-	3	0	HAVCR1	156412149	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	0.878000	0.28126	-1.479000	0.01867	-0.507000	0.04495	ATG	.	.		0.488	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1		
ADRA1B	147	hgsc.bcm.edu	37	5	159399016	159399016	+	Silent	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:159399016G>A	ENST00000306675.3	+	2	1203	c.1080G>A	c.(1078-1080)gtG>gtA	p.V360V		NM_000679.3	NP_000670.1	P35368	ADA1B_HUMAN	adrenoceptor alpha 1B	360					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|adult heart development (GO:0007512)|behavioral response to cocaine (GO:0048148)|blood vessel remodeling (GO:0001974)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|multicellular organismal development (GO:0007275)|negative regulation of glycogen catabolic process (GO:0045818)|organ growth (GO:0035265)|positive regulation of glycogen catabolic process (GO:0045819)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of the force of heart contraction by epinephrine-norepinephrine (GO:0001997)|regulation of cardiac muscle contraction (GO:0055117)|regulation of vasoconstriction (GO:0019229)|response to amphetamine (GO:0001975)|response to morphine (GO:0043278)|vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure (GO:0001987)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)|protein heterodimerization activity (GO:0046982)			endometrium(3)|large_intestine(6)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acepromazine(DB01614)|Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Dapiprazole(DB00298)|Desipramine(DB01151)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Ziprasidone(DB00246)	GCGCTTTCGTGCGCATCCTCG	0.697																																					p.V360V		Atlas-SNP	.											.	ADRA1B	39	.	0			c.G1080A						.						19.0	20.0	20.0					5																	159399016		2199	4291	6490	SO:0001819	synonymous_variant	147	exon2			TTTCGTGCGCATC	L31773	CCDS4347.1	5q33.3	2012-08-08	2012-05-09		ENSG00000170214	ENSG00000170214		"""GPCR / Class A : Adrenoceptors : alpha"""	278	protein-coding gene	gene with protein product		104220	"""adrenergic, alpha-1B-, receptor"""				Standard	XM_005265818		Approved		uc003lxt.1	P35368	OTTHUMG00000130327	ENST00000306675.3:c.1080G>A	chr5.hg19:g.159399016G>A		83.0	0.0		89.0	4.0	NM_000679	B0LPE1	Silent	SNP	ENST00000306675.3	hg19	CCDS4347.1																																																																																			.	.		0.697	ADRA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252676.1		
HK3	3101	hgsc.bcm.edu	37	5	176314004	176314004	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:176314004T>C	ENST00000292432.5	-	13	1947	c.1856A>G	c.(1855-1857)cAg>cGg	p.Q619R		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	619	Catalytic.|Glucose-binding. {ECO:0000255}.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCCCTCACCTGGTCTAGGCC	0.622																																					p.Q619R		Atlas-SNP	.											.	HK3	210	.	0			c.A1856G						.						55.0	48.0	50.0					5																	176314004		2203	4300	6503	SO:0001630	splice_region_variant	3101	exon13			CTCACCTGGTCTA		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1857+1A>G	chr5.hg19:g.176314004T>C		52.0	0.0		72.0	4.0	NM_002115	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	hg19	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.328492	0.41197	.	.	ENSG00000160883	ENST00000292432	D	0.98914	-5.23	5.0	5.0	0.66597	Hexokinase, conserved site (1);Hexokinase, N-terminal (1);	0.000000	0.51477	D	0.000096	D	0.95853	0.8650	N	0.11255	0.115	0.38068	D	0.936293	B	0.25719	0.132	B	0.34931	0.192	D	0.95163	0.8283	10	0.51188	T	0.08	-15.0804	14.6863	0.69052	0.0:0.0:0.0:1.0	.	619	P52790	HXK3_HUMAN	R	619	ENSP00000292432:Q619R	ENSP00000292432:Q619R	Q	-	2	0	HK3	176246610	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	2.609000	0.46317	1.880000	0.54463	0.454000	0.30748	CAG	.	.		0.622	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		Missense_Mutation
FGFR4	2264	hgsc.bcm.edu	37	5	176520392	176520392	+	Intron	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr5:176520392T>C	ENST00000292408.4	+	10	1496				FGFR4_ENST00000292410.3_Missense_Mutation_p.S373P|FGFR4_ENST00000393648.2_Intron|FGFR4_ENST00000393637.1_Missense_Mutation_p.S373P|FGFR4_ENST00000502906.1_Intron	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4						alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	CAGAACCAAGTCTCCCACTTT	0.627										TSP Lung(9;0.080)																											p.S373P		Atlas-SNP	.											.	FGFR4	174	.	0			c.T1117C						.						78.0	80.0	80.0					5																	176520392		2203	4300	6503	SO:0001627	intron_variant	2264	exon8			ACCAAGTCTCCCA	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1252-15T>C	chr5.hg19:g.176520392T>C		113.0	0.0		166.0	7.0	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	T	8.471	0.857541	0.17106	.	.	ENSG00000160867	ENST00000292410;ENST00000393637	T;T	0.78816	-1.21;-1.21	4.76	-2.17	0.07059	.	.	.	.	.	T	0.52025	0.1709	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29458	-1.0011	9	0.27082	T	0.32	.	5.301	0.15778	0.0:0.382:0.1581:0.4599	.	373	P22455-2	.	P	373	ENSP00000292410:S373P;ENSP00000377254:S373P	ENSP00000292410:S373P	S	+	1	0	FGFR4	176452998	0.008000	0.16893	0.001000	0.08648	0.671000	0.39405	0.419000	0.21247	-0.545000	0.06224	-0.451000	0.05528	TCT	.	.		0.627	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1		
CDYL	9425	hgsc.bcm.edu	37	6	4892284	4892284	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:4892284A>G	ENST00000328908.5	+	4	655	c.524A>G	c.(523-525)aAg>aGg	p.K175R	CDYL_ENST00000472453.1_Intron|CDYL_ENST00000397588.3_Missense_Mutation_p.K121R|CDYL_ENST00000449732.2_5'UTR|CDYL_ENST00000343762.5_5'UTR			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	175	Interaction with EZH2.				regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		AAGTTCAGGAAGAACACAGCT	0.507																																					p.K121R		Atlas-SNP	.											.	CDYL	74	.	0			c.A362G						.						89.0	93.0	91.0					6																	4892284		2203	4300	6503	SO:0001583	missense	9425	exon2			TCAGGAAGAACAC	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"""CDY-like, autosomal"", ""testis-specific chromodomain Y-like protein"""	603778	"""chromodomain protein, Y chromosome-like"""			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.524A>G	chr6.hg19:g.4892284A>G	ENSP00000330512:p.Lys175Arg	87.0	0.0		92.0	4.0	NM_004824	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	hg19		.	.	.	.	.	.	.	.	.	.	A	10.15	1.269882	0.23221	.	.	ENSG00000153046	ENST00000328908;ENST00000397588	T;T	0.55588	0.89;0.51	5.79	2.02	0.26589	.	2.341570	0.01986	N	0.045182	T	0.18173	0.0436	N	0.21448	0.665	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.001	T	0.24799	-1.0150	10	0.28530	T	0.3	.	4.2753	0.10806	0.6459:0.0:0.2176:0.1365	.	121;175	Q9Y232-2;Q9Y232	.;CDYL1_HUMAN	R	175;121	ENSP00000330512:K175R;ENSP00000380718:K121R	ENSP00000330512:K175R	K	+	2	0	CDYL	4837283	1.000000	0.71417	0.975000	0.42487	0.993000	0.82548	2.489000	0.45285	0.107000	0.17824	0.528000	0.53228	AAG	.	.		0.507	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824	
RIOK1	83732	hgsc.bcm.edu	37	6	7393524	7393524	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:7393524A>G	ENST00000379834.2	+	2	771	c.264A>G	c.(262-264)ggA>ggG	p.G88G		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	88							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					GGAATGGAGGAAGCAACCCAC	0.408																																					p.G88G		Atlas-SNP	.											.	RIOK1	36	.	0			c.A264G						.						132.0	124.0	126.0					6																	7393524		2203	4300	6503	SO:0001819	synonymous_variant	83732	exon2			TGGAGGAAGCAAC	BC006104	CCDS4500.1	6p24.3	2012-12-10	2012-12-10		ENSG00000124784	ENSG00000124784			18656	protein-coding gene	gene with protein product			"""RIO kinase 1 (yeast)"""				Standard	NM_031480		Approved	AD034, FLJ30006, bA288G3.1, RRP10	uc003mxn.3	Q9BRS2	OTTHUMG00000014207	ENST00000379834.2:c.264A>G	chr6.hg19:g.7393524A>G		133.0	0.0		141.0	8.0	NM_031480	B2RB28|Q8NDC8|Q96NV9	Silent	SNP	ENST00000379834.2	hg19	CCDS4500.1																																																																																			.	.		0.408	RIOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039780.2	NM_031480	
DSP	1832	hgsc.bcm.edu	37	6	7581098	7581098	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:7581098T>C	ENST00000379802.3	+	23	5016	c.4675T>C	c.(4675-4677)Ttc>Ctc	p.F1559L	DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1559	Central fibrous rod domain.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		TATCACGCGGTTCCAGAACTC	0.522																																					p.F1559L		Atlas-SNP	.											.	DSP	306	.	0			c.T4675C						.						76.0	81.0	79.0					6																	7581098		2203	4300	6503	SO:0001583	missense	1832	exon23			ACGCGGTTCCAGA	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.4675T>C	chr6.hg19:g.7581098T>C	ENSP00000369129:p.Phe1559Leu	82.0	0.0		99.0	4.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	hg19	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	T	0.104	-1.147277	0.01714	.	.	ENSG00000096696	ENST00000379802	T	0.65178	-0.14	5.58	3.05	0.35203	.	0.189188	0.37955	N	0.001865	T	0.07234	0.0183	N	0.00801	-1.175	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.42361	-0.9456	10	0.02654	T	1	.	3.6866	0.08331	0.2897:0.1438:0.0:0.5665	.	1559	P15924	DESP_HUMAN	L	1559	ENSP00000369129:F1559L	ENSP00000369129:F1559L	F	+	1	0	DSP	7526097	0.647000	0.27304	0.570000	0.28473	0.572000	0.35998	1.153000	0.31676	0.337000	0.23665	0.533000	0.62120	TTC	.	.		0.522	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
DSP	1832	hgsc.bcm.edu	37	6	7585893	7585893	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:7585893C>T	ENST00000379802.3	+	24	8739	c.8398C>T	c.(8398-8400)Ctg>Ttg	p.L2800L	DSP_ENST00000418664.2_Silent_p.L2201L	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2800	4.5 X 38 AA tandem repeats (Domain C).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		TATCACTGGGCTGCGCCTTCT	0.552																																					p.L2800L		Atlas-SNP	.											.	DSP	306	.	0			c.C8398T						.						130.0	147.0	141.0					6																	7585893		2203	4300	6503	SO:0001819	synonymous_variant	1832	exon24			ACTGGGCTGCGCC	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.8398C>T	chr6.hg19:g.7585893C>T		66.0	0.0		95.0	4.0	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.		0.552	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
ERVFRD-1	405754	hgsc.bcm.edu	37	6	11104838	11104838	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:11104838A>G	ENST00000472091.1	-	2	1081	c.706T>C	c.(706-708)Tct>Cct	p.S236P	ERVFRD-1_ENST00000542862.1_Missense_Mutation_p.S236P|SMIM13_ENST00000416247.2_Intron	NM_207582.2	NP_997465.1	P60508	SYCY2_HUMAN	endogenous retrovirus group FRD, member 1	236					syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(4)|stomach(1)	15						caaaaaagagaatttcgagtt	0.468																																					p.S236P		Atlas-SNP	.											.	ERVFRD-1	41	.	0			c.T706C						.						29.0	32.0	31.0					6																	11104838		2203	4300	6503	SO:0001583	missense	405754	exon2			AAAGAGAATTTCG	AK075092, AK123938, AY358244	CCDS4519.1	6p24.2	2014-05-02			ENSG00000244476	ENSG00000244476			33823	other	endogenous retrovirus		610524				12970426, 14557543, 15476554, 21542922	Standard	NM_207582		Approved	HERV-W/FRD, HERV-FRD, envFRD, ERVFRDE1, syncytin-2	uc003mzt.3	P60508	OTTHUMG00000159193	ENST00000472091.1:c.706T>C	chr6.hg19:g.11104838A>G	ENSP00000420174:p.Ser236Pro	57.0	0.0		91.0	4.0	NM_207582		Missense_Mutation	SNP	ENST00000472091.1	hg19	CCDS4519.1	.	.	.	.	.	.	.	.	.	.	A	13.63	2.295281	0.40594	.	.	ENSG00000244476	ENST00000472091;ENST00000542862	T;T	0.14516	2.5;2.5	0.225	0.225	0.15325	.	.	.	.	.	T	0.02649	0.0080	N	0.22421	0.69	0.20926	N	0.99982	B	0.10296	0.003	B	0.18263	0.021	T	0.45011	-0.9290	8	0.45353	T	0.12	.	.	.	.	.	236	P60508	EFRD1_HUMAN	P	236	ENSP00000420174:S236P;ENSP00000444461:S236P	ENSP00000420174:S236P	S	-	1	0	ERVFRD-1	11212824	0.973000	0.33851	0.891000	0.34965	0.891000	0.51852	0.349000	0.20055	0.257000	0.21650	0.254000	0.18369	TCT	.	.		0.468	ERVFRD-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353776.1	NM_207582	
EDN1	1906	hgsc.bcm.edu	37	6	12296284	12296284	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:12296284A>G	ENST00000379375.5	+	5	890	c.623A>G	c.(622-624)aAc>aGc	p.N208S		NM_001168319.1|NM_001955.4	NP_001161791.1|NP_001946.3	P05305	EDN1_HUMAN	endothelin 1	208					artery smooth muscle contraction (GO:0014824)|body fluid secretion (GO:0007589)|calcium-mediated signaling (GO:0019722)|cartilage development (GO:0051216)|cell growth (GO:0016049)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|dorsal/ventral pattern formation (GO:0009953)|epithelial fluid transport (GO:0042045)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose transport (GO:0015758)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|inositol phosphate-mediated signaling (GO:0048016)|leukocyte activation (GO:0045321)|maternal process involved in parturition (GO:0060137)|membrane depolarization (GO:0051899)|middle ear morphogenesis (GO:0042474)|multicellular organismal aging (GO:0010259)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of hormone secretion (GO:0046888)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|nitric oxide transport (GO:0030185)|patterning of blood vessels (GO:0001569)|peptide hormone secretion (GO:0030072)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase D-activating G-protein coupled receptor signaling pathway (GO:0031583)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of odontogenesis (GO:0042482)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of urine volume (GO:0035810)|prostaglandin biosynthetic process (GO:0001516)|protein kinase C deactivation (GO:0042313)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|respiratory gaseous exchange (GO:0007585)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to testosterone (GO:0033574)|rhythmic excitation (GO:0043179)|sensory perception of pain (GO:0019233)|superoxide anion generation (GO:0042554)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|endothelin A receptor binding (GO:0031707)|endothelin B receptor binding (GO:0031708)|hormone activity (GO:0005179)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	13	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)				GTGACCCACAACCGAGCACAT	0.547																																					p.N208S		Atlas-SNP	.											.	EDN1	23	.	0			c.A623G						.						131.0	122.0	125.0					6																	12296284		2203	4300	6503	SO:0001583	missense	1906	exon5			CCCACAACCGAGC	S56805	CCDS4522.1	6p24.1	2014-03-19			ENSG00000078401	ENSG00000078401		"""Endogenous ligands"""	3176	protein-coding gene	gene with protein product		131240					Standard	NM_001168319		Approved	ET1	uc003nae.4	P05305	OTTHUMG00000014266	ENST00000379375.5:c.623A>G	chr6.hg19:g.12296284A>G	ENSP00000368683:p.Asn208Ser	86.0	0.0		109.0	5.0	NM_001955	Q96DA1	Missense_Mutation	SNP	ENST00000379375.5	hg19	CCDS4522.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.035233	0.35893	.	.	ENSG00000078401	ENST00000379375	D	0.85088	-1.94	5.93	5.93	0.95920	.	0.258675	0.45126	D	0.000381	D	0.86024	0.5834	L	0.35854	1.095	0.41107	D	0.985715	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	D	0.87471	0.2414	10	0.51188	T	0.08	-3.2364	14.9508	0.71071	1.0:0.0:0.0:0.0	.	208;208	Q6FH53;P05305	.;EDN1_HUMAN	S	208	ENSP00000368683:N208S	ENSP00000368683:N208S	N	+	2	0	EDN1	12404270	1.000000	0.71417	1.000000	0.80357	0.340000	0.28889	5.705000	0.68355	2.271000	0.75665	0.533000	0.62120	AAC	.	.		0.547	EDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039872.1	NM_001955	
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156943	26156943	+	Nonsense_Mutation	SNP	A	A	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:26156943A>T	ENST00000304218.3	+	1	385	c.325A>T	c.(325-327)Aag>Tag	p.K109*	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	109	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						CAAACTCAACAAGAAGGCGGC	0.617																																					p.K109X		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.A325T						.						33.0	40.0	38.0					6																	26156943		2203	4300	6503	SO:0001587	stop_gained	3008	exon1			CTCAACAAGAAGG	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"""Histones / Replication-dependent"""	4718	protein-coding gene	gene with protein product		142220	"""H1 histone family, member 4"", ""histone 1, H1e"""	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.325A>T	chr6.hg19:g.26156943A>T	ENSP00000307705:p.Lys109*	119.0	0.0		141.0	52.0	NM_005321	Q4VB25	Nonsense_Mutation	SNP	ENST00000304218.3	hg19	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	35	5.588280	0.96590	.	.	ENSG00000168298	ENST00000304218	.	.	.	5.35	5.35	0.76521	.	0.105304	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.2553	14.7974	0.69886	1.0:0.0:0.0:0.0	.	.	.	.	X	109	.	ENSP00000307705:K109X	K	+	1	0	HIST1H1E	26264922	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.448000	0.80631	2.146000	0.66826	0.459000	0.35465	AAG	.	.		0.617	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156946	26156946	+	Nonsense_Mutation	SNP	A	A	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:26156946A>T	ENST00000304218.3	+	1	388	c.328A>T	c.(328-330)Aag>Tag	p.K110*	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	110					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						ACTCAACAAGAAGGCGGCCTC	0.627																																					p.K110X		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.A328T						.						33.0	39.0	37.0					6																	26156946		2203	4300	6503	SO:0001587	stop_gained	3008	exon1			AACAAGAAGGCGG	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"""Histones / Replication-dependent"""	4718	protein-coding gene	gene with protein product		142220	"""H1 histone family, member 4"", ""histone 1, H1e"""	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.328A>T	chr6.hg19:g.26156946A>T	ENSP00000307705:p.Lys110*	110.0	0.0		146.0	55.0	NM_005321	Q4VB25	Nonsense_Mutation	SNP	ENST00000304218.3	hg19	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	35	5.574334	0.96553	.	.	ENSG00000168298	ENST00000304218	.	.	.	5.35	5.35	0.76521	.	0.152047	0.41194	D	0.000922	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.1063	14.7974	0.69886	1.0:0.0:0.0:0.0	.	.	.	.	X	110	.	ENSP00000307705:K110X	K	+	1	0	HIST1H1E	26264925	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	6.134000	0.71689	2.146000	0.66826	0.459000	0.35465	AAG	.	.		0.627	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
TRIM39	56658	hgsc.bcm.edu	37	6	30297109	30297109	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:30297109T>C	ENST00000396547.1	+	2	175	c.15T>C	c.(13-15)agT>agC	p.S5S	HCG18_ENST00000454269.1_RNA|HCG18_ENST00000454129.1_RNA|TRIM39_ENST00000376656.4_Silent_p.S5S|HCG18_ENST00000444126.1_RNA|TRIM39-RPP21_ENST00000513556.1_5'Flank|TRIM39_ENST00000540416.1_Silent_p.S5S|TRIM39_ENST00000376659.5_Silent_p.S5S|HCG18_ENST00000412685.2_RNA|TRIM39_ENST00000396548.1_Silent_p.S5S|HCG18_ENST00000413358.2_RNA|HCG18_ENST00000602290.1_RNA|HCG18_ENST00000449544.1_RNA|HCG18_ENST00000426882.1_RNA|HCG18_ENST00000438412.1_RNA|HCG18_ENST00000602550.1_RNA|TRIM39_ENST00000396551.3_Silent_p.S5S			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	5					apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						CAGAGACAAGTCTGTTAGAGG	0.453																																					p.S5S		Atlas-SNP	.											.	TRIM39	56	.	0			c.T15C						.						134.0	175.0	160.0					6																	30297109		1508	2707	4215	SO:0001819	synonymous_variant	56658	exon3			GACAAGTCTGTTA	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10065	protein-coding gene	gene with protein product		605700	"""ring finger protein 23"", ""tripartite motif-containing 39"""	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.15T>C	chr6.hg19:g.30297109T>C		63.0	0.0		75.0	4.0	NM_172016	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Silent	SNP	ENST00000396547.1	hg19	CCDS34377.1																																																																																			.	.		0.453	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016	
ABCF1	23	hgsc.bcm.edu	37	6	30550931	30550931	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:30550931G>A	ENST00000326195.8	+	10	993	c.881G>A	c.(880-882)cGc>cAc	p.R294H	MIR877_ENST00000401282.1_RNA|ABCF1_ENST00000376545.3_Missense_Mutation_p.R256H|ABCF1_ENST00000396515.4_Intron	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	294					inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						ATGTCCTCCCGCCAAGCCATG	0.512																																					p.R294H		Atlas-SNP	.											.	ABCF1	61	.	0			c.G881A						.						94.0	100.0	98.0					6																	30550931		1510	2708	4218	SO:0001583	missense	23	exon10			CCTCCCGCCAAGC	AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"""ATP binding cassette transporters / subfamily F"""	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.881G>A	chr6.hg19:g.30550931G>A	ENSP00000313603:p.Arg294His	77.0	0.0		89.0	4.0	NM_001025091	A2BF75|O14897|Q69YP6	Missense_Mutation	SNP	ENST00000326195.8	hg19	CCDS34380.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.429787	0.83776	.	.	ENSG00000204574	ENST00000326195;ENST00000376545;ENST00000455943;ENST00000441867	T;T;T	0.53857	0.6;0.94;0.79	5.41	4.55	0.56014	.	0.057428	0.64402	D	0.000001	T	0.55986	0.1955	L	0.59436	1.845	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.64877	0.93;0.93;0.93	T	0.59553	-0.7433	10	0.48119	T	0.1	-9.7828	12.9326	0.58294	0.0798:0.0:0.9202:0.0	.	256;294;294	Q2L6I2;Q8NE71;A2BF75	.;ABCF1_HUMAN;.	H	294;256;295;295	ENSP00000313603:R294H;ENSP00000365728:R256H;ENSP00000405512:R295H	ENSP00000313603:R294H	R	+	2	0	ABCF1	30658910	1.000000	0.71417	0.994000	0.49952	0.960000	0.62799	8.704000	0.91351	1.301000	0.44836	0.313000	0.20887	CGC	.	.		0.512	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3		
IER3	8870	hgsc.bcm.edu	37	6	30709964	30709964	+	IGR	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:30709964C>T	ENST00000259874.5	-	0	1244				FLOT1_ENST00000456573.2_Start_Codon_SNP_p.M1I|XXbac-BPG252P9.10_ENST00000607333.1_RNA|FLOT1_ENST00000376389.3_Start_Codon_SNP_p.M1I|FLOT1_ENST00000470643.1_5'UTR	NM_003897.3	NP_003888.2	P46695	IEX1_HUMAN	immediate early response 3						anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glycolytic process (GO:0045820)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|negative regulation of systemic arterial blood pressure (GO:0003085)|positive regulation of protein catabolic process (GO:0045732)|regulation of DNA repair (GO:0006282)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of response to DNA damage stimulus (GO:2001020)|response to protozoan (GO:0001562)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)	1						AAGTGAAAAACATGGTTCAGG	0.597																																					p.M1I		Atlas-SNP	.											.	FLOT1	28	.	0			c.G3A						.						157.0	148.0	151.0					6																	30709964		1511	2709	4220	SO:0001628	intergenic_variant	10211	exon2			GAAAAACATGGTT	AF083421	CCDS4689.1	6p21.3	2010-02-17			ENSG00000137331	ENSG00000137331			5392	protein-coding gene	gene with protein product		602996				8603392, 9703517	Standard	NM_003897		Approved	IEX-1, DIF-2, PRG1, IEX-1L	uc003nrn.3	P46695	OTTHUMG00000031265		chr6.hg19:g.30709964C>T		72.0	0.0		93.0	4.0	NM_005803	Q5SU30|Q92691|Q93044	Missense_Mutation	SNP	ENST00000259874.5	hg19	CCDS4689.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.52|17.52	3.410420|3.410420	0.62399|0.62399	.|.	.|.	ENSG00000137312|ENSG00000137312	ENST00000418160|ENST00000376389;ENST00000456573;ENST00000438162;ENST00000445853;ENST00000416018;ENST00000454845	.|D;T;D;D;D;D	.|0.97352	.|-3.41;1.52;-3.8;-3.8;-4.35;-4.27	4.41|4.41	4.41|4.41	0.53225|0.53225	.|.	.|0.045756	.|0.85682	.|D	.|0.000000	D|D	0.92951|0.92951	0.7757|0.7757	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|B;B	.|0.24533	.|0.105;0.101	.|B;B	.|0.20955	.|0.032;0.02	D|D	0.92161|0.92161	0.5736|0.5736	5|9	0.87932|0.56958	D|D	0|0.05	0.6111|0.6111	14.8798|14.8798	0.70522|0.70522	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1;1	.|B4DVY7;O75955	.|.;FLOT1_HUMAN	Y|I	50|1	.|ENSP00000365569:M1I;ENSP00000394375:M1I;ENSP00000400615:M1I;ENSP00000398834:M1I;ENSP00000412058:M1I;ENSP00000391341:M1I	ENSP00000404300:C50Y|ENSP00000365569:M1I	C|M	-|-	2|3	0|0	FLOT1|FLOT1	30817943|30817943	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.651000|0.651000	0.38670|0.38670	6.264000|6.264000	0.72527|0.72527	2.435000|2.435000	0.82474|0.82474	0.462000|0.462000	0.41574|0.41574	TGT|ATG	.	.		0.597	IER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076578.2		
PRRC2A	7916	hgsc.bcm.edu	37	6	31599743	31599743	+	Missense_Mutation	SNP	C	C	T	rs545938957		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:31599743C>T	ENST00000376033.2	+	16	3527	c.3293C>T	c.(3292-3294)cCc>cTc	p.P1098L	PRRC2A_ENST00000376007.4_Missense_Mutation_p.P1098L	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1098	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GAGGAAATCCCCAAGCGGCGC	0.647																																					p.P1098L		Atlas-SNP	.											.	PRRC2A	152	.	0			c.C3293T						.						35.0	46.0	42.0					6																	31599743		1507	2708	4215	SO:0001583	missense	7916	exon16			AAATCCCCAAGCG	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3293C>T	chr6.hg19:g.31599743C>T	ENSP00000365201:p.Pro1098Leu	50.0	0.0		74.0	4.0	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	hg19	CCDS4708.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.28|13.28	2.188734|2.188734	0.38609|0.38609	.|.	.|.	ENSG00000204469|ENSG00000204469	ENST00000376007;ENST00000376033;ENST00000376010|ENST00000424184;ENST00000435052	T;T|.	0.33438|.	1.41;1.41|.	4.88|4.88	4.88|4.88	0.63580|0.63580	.|.	0.000000|0.000000	0.52532|0.52532	D|D	0.000075|0.000075	T|T	0.67031|0.67031	0.2850|0.2850	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.85130|.	0.997|.	T|T	0.70894|0.70894	-0.4748|-0.4748	10|7	0.87932|0.87932	D|D	0|0	-8.8398|-8.8398	16.9681|16.9681	0.86291|0.86291	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1098|.	P48634|.	PRC2A_HUMAN|.	L|S	1098;1098;323|1097;1086	ENSP00000365175:P1098L;ENSP00000365201:P1098L|.	ENSP00000365175:P1098L|ENSP00000407986:P1097S	P|P	+|+	2|1	0|0	PRRC2A|PRRC2A	31707722|31707722	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.940000|0.940000	0.58332|0.58332	7.314000|7.314000	0.78988|0.78988	2.562000|2.562000	0.86427|0.86427	0.655000|0.655000	0.94253|0.94253	CCC|CCA	.	.		0.647	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
APOM	55937	hgsc.bcm.edu	37	6	31623826	31623826	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:31623826A>C	ENST00000375916.3	+	1	579	c.83A>C	c.(82-84)cAa>cCa	p.Q28P	C6orf47-AS1_ENST00000422049.1_RNA|APOM_ENST00000375918.2_Intron|APOM_ENST00000375920.4_Intron	NM_019101.2	NP_061974.2	O95445	APOM_HUMAN	apolipoprotein M	28				MFHQIWAALLYFYGIILNSIYQCPEHSQLTTLGVDGKE -> RFPDSIWGSRSDTSGSPQVPKLYFCGARRESPQPQT (in Ref. 3; AAF29014). {ECO:0000305}.	cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|high-density lipoprotein particle assembly (GO:0034380)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein metabolic process (GO:0042157)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|response to glucose (GO:0009749)|reverse cholesterol transport (GO:0043691)	discoidal high-density lipoprotein particle (GO:0034365)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|lipid transporter activity (GO:0005319)|phospholipid binding (GO:0005543)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(1)	7						GAGCACAGTCAACTGACAACT	0.532																																					p.Q28P	Colon(39;129 858 13764 41453 42617)	Atlas-SNP	.											.	APOM	12	.	0			c.A83C						.						63.0	41.0	49.0					6																	31623826		1510	2709	4219	SO:0001583	missense	55937	exon1			ACAGTCAACTGAC	AJ245434	CCDS4710.1, CCDS59004.1	6p21	2014-01-22			ENSG00000204444	ENSG00000204444		"""Apolipoproteins"", ""Lipocalins"""	13916	protein-coding gene	gene with protein product		606907				10531326, 11418126	Standard	NM_019101		Approved	ApoM, G3a, NG20	uc003nvl.3	O95445	OTTHUMG00000031250	ENST00000375916.3:c.83A>C	chr6.hg19:g.31623826A>C	ENSP00000365081:p.Gln28Pro	158.0	0.0		208.0	41.0	NM_019101	B0UX98|Q5SRP4|Q9P046|Q9UMP6	Missense_Mutation	SNP	ENST00000375916.3	hg19	CCDS4710.1	.	.	.	.	.	.	.	.	.	.	A	11.16	1.557628	0.27827	.	.	ENSG00000204444	ENST00000375916	.	.	.	5.34	-2.35	0.06684	.	0.279884	0.30085	N	0.010446	T	0.09069	0.0224	N	0.20401	0.57	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32025	-0.9922	9	0.41790	T	0.15	-12.5912	8.4387	0.32801	0.3283:0.5869:0.0848:0.0	.	28	O95445	APOM_HUMAN	P	28	.	ENSP00000365081:Q28P	Q	+	2	0	APOM	31731805	0.021000	0.18746	0.461000	0.27105	0.905000	0.53344	0.040000	0.13905	-0.253000	0.09514	0.402000	0.26972	CAA	.	.		0.532	APOM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076527.3	NM_019101	
DAAM2	23500	hgsc.bcm.edu	37	6	39869662	39869662	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:39869662A>G	ENST00000398904.2	+	25	3238	c.3056A>G	c.(3055-3057)gAg>gGg	p.E1019G	DAAM2_ENST00000538976.1_Missense_Mutation_p.E1018G|RP11-61I13.3_ENST00000437947.1_RNA|DAAM2_ENST00000274867.4_Missense_Mutation_p.E1019G			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	1019	DAD. {ECO:0000255|PROSITE- ProRule:PRU00577}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					TCGCTGGAGGAGGGAGGAGAG	0.647																																					p.E1019G		Atlas-SNP	.											.	DAAM2	101	.	0			c.A3056G						.						32.0	41.0	38.0					6																	39869662		2109	4231	6340	SO:0001583	missense	23500	exon25			TGGAGGAGGGAGG	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.3056A>G	chr6.hg19:g.39869662A>G	ENSP00000381876:p.Glu1019Gly	26.0	0.0		66.0	11.0	NM_001201427	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	hg19	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.290024	0.59976	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.80824	-1.42;-1.42;-1.41	5.64	5.64	0.86602	Actin-binding FH2/DRF autoregulatory (1);Diaphanous autoregulatory (1);	0.068023	0.64402	D	0.000010	T	0.69242	0.3089	L	0.50333	1.59	0.80722	D	1	B;B	0.23891	0.042;0.093	B;B	0.26517	0.07;0.05	T	0.71062	-0.4701	10	0.56958	D	0.05	.	15.5198	0.75857	1.0:0.0:0.0:0.0	.	1018;1019	G5EA45;Q86T65	.;DAAM2_HUMAN	G	1019;1019;1018	ENSP00000274867:E1019G;ENSP00000381876:E1019G;ENSP00000437808:E1018G	ENSP00000274867:E1019G	E	+	2	0	DAAM2	39977640	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	5.425000	0.66470	2.145000	0.66743	0.533000	0.62120	GAG	.	.		0.647	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
PEX6	5190	hgsc.bcm.edu	37	6	42933450	42933450	+	Nonsense_Mutation	SNP	G	G	A	rs267608241		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:42933450G>A	ENST00000304611.8	-	13	2509	c.2440C>T	c.(2440-2442)Cga>Tga	p.R814*	PEX6_ENST00000244546.4_Silent_p.G731G	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	814					ATP catabolic process (GO:0006200)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix, translocation (GO:0016561)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(3)	15			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			TCTCCACTTCGCCCCCGGCTT	0.562																																					p.R814X		Atlas-SNP	.											.	PEX6	44	.	0			c.C2440T						.						160.0	177.0	171.0					6																	42933450		2203	4300	6503	SO:0001587	stop_gained	5190	exon13			CACTTCGCCCCCG	U56602	CCDS4877.1	6p22-p11	2010-04-21			ENSG00000124587	ENSG00000124587		"""ATPases / AAA-type"""	8859	protein-coding gene	gene with protein product		601498				8670792	Standard	NM_000287		Approved	PXAAA1, PAF-2	uc003otf.3	Q13608	OTTHUMG00000014713	ENST00000304611.8:c.2440C>T	chr6.hg19:g.42933450G>A	ENSP00000303511:p.Arg814*	148.0	0.0		184.0	17.0	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Nonsense_Mutation	SNP	ENST00000304611.8	hg19	CCDS4877.1	.	.	.	.	.	.	.	.	.	.	G	40	8.021076	0.98613	.	.	ENSG00000124587	ENST00000304611	.	.	.	5.76	5.76	0.90799	.	0.109084	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.5604	14.4359	0.67279	0.0:0.0:0.8525:0.1474	.	.	.	.	X	814	.	ENSP00000303511:R814X	R	-	1	2	PEX6	43041428	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.022000	0.57203	2.724000	0.93272	0.563000	0.77884	CGA	.	.		0.562	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287	
SPATS1	221409	hgsc.bcm.edu	37	6	44336153	44336153	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:44336153A>G	ENST00000288390.2	+	5	959	c.612A>G	c.(610-612)ccA>ccG	p.P204P	RP11-444E17.6_ENST00000505802.1_3'UTR|SPATS1_ENST00000323108.8_Silent_p.P204P			Q496A3	SPAS1_HUMAN	spermatogenesis associated, serine-rich 1	204										NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(5)|skin(1)|urinary_tract(1)	14	all_lung(25;0.00469)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AGTTAACTCCAGGCGACAATC	0.398																																					p.P204P		Atlas-SNP	.											.	SPATS1	61	.	0			c.A612G						.						122.0	119.0	120.0					6																	44336153		2203	4300	6503	SO:0001819	synonymous_variant	221409	exon6			AACTCCAGGCGAC	AK058171	CCDS4911.1	6p21.1	2003-08-08			ENSG00000249481	ENSG00000249481			22957	protein-coding gene	gene with protein product							Standard	NM_145026		Approved	SPATA8, FLJ25442, SRSP1	uc021yzz.1	Q496A3	OTTHUMG00000014764	ENST00000288390.2:c.612A>G	chr6.hg19:g.44336153A>G		62.0	0.0		88.0	4.0	NM_145026	Q496A2|Q496A5|Q96LJ0	Silent	SNP	ENST00000288390.2	hg19	CCDS4911.1																																																																																			.	.		0.398	SPATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040738.2	NM_145026	
CDC5L	988	hgsc.bcm.edu	37	6	44414375	44414375	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:44414375A>G	ENST00000371477.3	+	16	2635	c.2336A>G	c.(2335-2337)gAa>gGa	p.E779G		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	779	Interaction with PLRG1.				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)	p.E779G(1)		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)			CGACAACAAGAAAGAGAAAAG	0.294																																					p.E779G		Atlas-SNP	.											CDC5L,colon,carcinoma,0,1	CDC5L	86	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2336G						.						106.0	113.0	111.0					6																	44414375		2203	4300	6503	SO:0001583	missense	988	exon16			AACAAGAAAGAGA	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.2336A>G	chr6.hg19:g.44414375A>G	ENSP00000360532:p.Glu779Gly	58.0	0.0		70.0	3.0	NM_001253	Q76N46|Q99974	Missense_Mutation	SNP	ENST00000371477.3	hg19	CCDS4912.1	.	.	.	.	.	.	.	.	.	.	A	19.64	3.866052	0.71949	.	.	ENSG00000096401	ENST00000371477	T	0.48522	0.81	6.01	6.01	0.97437	.	0.225469	0.52532	D	0.000067	T	0.37128	0.0992	M	0.72479	2.2	0.80722	D	1	P	0.41313	0.745	B	0.36134	0.218	T	0.44997	-0.9291	10	0.52906	T	0.07	-10.0754	16.5285	0.84344	1.0:0.0:0.0:0.0	.	779	Q99459	CDC5L_HUMAN	G	779	ENSP00000360532:E779G	ENSP00000360532:E779G	E	+	2	0	CDC5L	44522353	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	8.065000	0.89485	2.307000	0.77673	0.528000	0.53228	GAA	.	.		0.294	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1		
GPR111	222611	hgsc.bcm.edu	37	6	47649442	47649442	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:47649442A>G	ENST00000296862.1	+	6	1147	c.1147A>G	c.(1147-1149)Aag>Gag	p.K383E	GPR111_ENST00000507065.1_Missense_Mutation_p.K315E|GPR111_ENST00000398742.2_Missense_Mutation_p.K315E			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	383					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						GATTTTTGAAAAGATCAGCAA	0.438																																					p.K315E		Atlas-SNP	.											.	GPR111	123	.	0			c.A943G						.						93.0	92.0	92.0					6																	47649442		1907	4137	6044	SO:0001583	missense	222611	exon7			TTTGAAAAGATCA	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.1147A>G	chr6.hg19:g.47649442A>G	ENSP00000296862:p.Lys383Glu	78.0	0.0		98.0	4.0	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Missense_Mutation	SNP	ENST00000296862.1	hg19		.	.	.	.	.	.	.	.	.	.	A	23.2	4.391015	0.82902	.	.	ENSG00000164393	ENST00000507065;ENST00000296862;ENST00000398742	T;T;T	0.38240	1.92;1.9;1.15	5.52	5.52	0.82312	.	0.000000	0.64402	D	0.000003	T	0.54902	0.1887	M	0.83774	2.66	0.35076	D	0.762988	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.64740	-0.6336	10	0.54805	T	0.06	.	14.8206	0.70070	1.0:0.0:0.0:0.0	.	315;383	Q8IZF7-2;Q8IZF7	.;GP111_HUMAN	E	315;383;315	ENSP00000422934:K315E;ENSP00000296862:K383E;ENSP00000381727:K315E	ENSP00000296862:K383E	K	+	1	0	GPR111	47757401	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.977000	0.88081	2.099000	0.63709	0.477000	0.44152	AAG	.	.		0.438	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
RIMS1	22999	hgsc.bcm.edu	37	6	72678720	72678720	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:72678720T>C	ENST00000521978.1	+	2	199	c.199T>C	c.(199-201)Tgc>Cgc	p.C67R	RIMS1_ENST00000520567.1_Missense_Mutation_p.C67R|RIMS1_ENST00000522291.1_Missense_Mutation_p.C67R|RIMS1_ENST00000264839.7_Missense_Mutation_p.C67R|RIMS1_ENST00000491071.2_Missense_Mutation_p.C67R|RIMS1_ENST00000517960.1_Missense_Mutation_p.C67R|RIMS1_ENST00000348717.5_Missense_Mutation_p.C67R|RIMS1_ENST00000518273.1_Missense_Mutation_p.C67R	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	67	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GCCTGCTGCCTGCAAAACACC	0.448																																					p.C67R		Atlas-SNP	.											.	RIMS1	278	.	0			c.T199C						.						132.0	137.0	136.0					6																	72678720		1936	4138	6074	SO:0001583	missense	22999	exon2			GCTGCCTGCAAAA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.199T>C	chr6.hg19:g.72678720T>C	ENSP00000428417:p.Cys67Arg	96.0	0.0		102.0	10.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.235682	0.58886	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978	T;T;T;T;T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91	5.31	4.14	0.48551	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);Zinc finger, FYVE/PHD-type (1);	.	.	.	.	T	0.39436	0.1078	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41466	-0.9507	9	0.39692	T	0.17	.	8.1641	0.31215	0.0:0.094:0.0:0.906	.	67	Q86UR5	RIMS1_HUMAN	R	67	ENSP00000430101:C67R;ENSP00000275037:C67R;ENSP00000264839:C67R;ENSP00000429959:C67R;ENSP00000430408:C67R;ENSP00000430502:C67R;ENSP00000430932:C67R;ENSP00000428417:C67R	ENSP00000264839:C67R	C	+	1	0	RIMS1	72735441	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.427000	0.34881	1.990000	0.58119	0.533000	0.62120	TGC	.	.		0.448	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
SNAP91	9892	hgsc.bcm.edu	37	6	84311120	84311120	+	Silent	SNP	T	T	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:84311120T>A	ENST00000439399.2	-	16	1510	c.1194A>T	c.(1192-1194)gcA>gcT	p.A398A	SNAP91_ENST00000520213.1_Intron|SNAP91_ENST00000428679.2_Silent_p.A398A|SNAP91_ENST00000521743.1_Silent_p.A398A|SNAP91_ENST00000437520.1_Intron|SNAP91_ENST00000195649.6_Silent_p.A398A|SNAP91_ENST00000369694.2_Silent_p.A398A|SNAP91_ENST00000521485.1_Silent_p.A398A|SNAP91_ENST00000520302.1_Silent_p.A396A	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	398	Ala-rich.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		CTGAAATCTGTGCTTCAGAGG	0.448																																					p.A398A		Atlas-SNP	.											.	SNAP91	199	.	0			c.A1194T						.						91.0	91.0	91.0					6																	84311120		1941	4131	6072	SO:0001819	synonymous_variant	9892	exon15			AATCTGTGCTTCA	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"""synaptosomal-associated protein, 91 kDa (mouse) homolog"", ""synaptosomal-associated protein, 91kDa homolog (mouse)"""			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.1194A>T	chr6.hg19:g.84311120T>A		260.0	0.0		177.0	109.0	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Silent	SNP	ENST00000439399.2	hg19	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.526100	0.27299	.	.	ENSG00000065609	ENST00000369691	.	.	.	5.58	1.72	0.24424	.	.	.	.	.	T	0.28433	0.0703	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.15065	-1.0450	4	.	.	.	-11.017	2.8386	0.05522	0.2468:0.0671:0.1286:0.5575	.	.	.	.	S	58	.	.	T	-	1	0	SNAP91	84367839	0.998000	0.40836	0.999000	0.59377	0.989000	0.77384	0.368000	0.20399	0.054000	0.16065	0.460000	0.39030	ACA	.	.		0.448	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1		
ZNF292	23036	hgsc.bcm.edu	37	6	87964908	87964908	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:87964908A>G	ENST00000369577.3	+	8	1604	c.1561A>G	c.(1561-1563)Ata>Gta	p.I521V	ZNF292_ENST00000339907.4_Missense_Mutation_p.I516V	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	521						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		GAAGAGAGAGATAAAACAGTT	0.403																																					p.I521V		Atlas-SNP	.											.	ZNF292	479	.	0			c.A1561G						.						114.0	105.0	108.0					6																	87964908		1876	4099	5975	SO:0001583	missense	23036	exon8			AGAGAGATAAAAC	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"""Zinc fingers, C2H2-type"""	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.1561A>G	chr6.hg19:g.87964908A>G	ENSP00000358590:p.Ile521Val	130.0	0.0		101.0	5.0	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	hg19	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.103979	0.37145	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.35421	1.31;1.31	5.87	5.87	0.94306	.	0.176797	0.64402	D	0.000013	T	0.36082	0.0954	L	0.50333	1.59	0.29927	N	0.822255	D	0.58268	0.982	P	0.55615	0.78	T	0.21415	-1.0246	10	0.44086	T	0.13	.	16.2631	0.82557	1.0:0.0:0.0:0.0	.	521	O60281	ZN292_HUMAN	V	521;516	ENSP00000358590:I521V;ENSP00000342847:I516V	ENSP00000342847:I516V	I	+	1	0	ZNF292	88021627	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.258000	0.65479	2.239000	0.73571	0.528000	0.53228	ATA	.	.		0.403	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021	
GABRR1	2569	hgsc.bcm.edu	37	6	89890099	89890099	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:89890099A>G	ENST00000454853.2	-	9	1168	c.1058T>C	c.(1057-1059)gTg>gCg	p.V353A	GABRR1_ENST00000435811.1_Missense_Mutation_p.V336A|GABRR1_ENST00000369451.3_Missense_Mutation_p.V266A	NM_001256704.1|NM_002042.4	NP_001243633.1|NP_002033.2	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 1	353					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|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)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(7)|lung(16)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	35		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	GAACACGAACACAAAGCTGAC	0.577																																					p.V353A		Atlas-SNP	.											.	GABRR1	63	.	0			c.T1058C						.						160.0	123.0	135.0					6																	89890099		2203	4300	6503	SO:0001583	missense	2569	exon9			ACGAACACAAAGC		CCDS5019.2, CCDS59028.1, CCDS59029.1	6q15	2012-06-22	2012-02-03		ENSG00000146276	ENSG00000146276		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4090	protein-coding gene	gene with protein product	"""GABA(A) receptor, rho 1"""	137161	"""gamma-aminobutyric acid (GABA) receptor, rho 1"""			1849271, 1315307	Standard	NM_002042		Approved		uc003pna.2	P24046	OTTHUMG00000015195	ENST00000454853.2:c.1058T>C	chr6.hg19:g.89890099A>G	ENSP00000412673:p.Val353Ala	122.0	0.0		74.0	4.0	NM_002042	A1L401|B4DJK8|B4DQT5|B7ZBQ7|Q9BX06	Missense_Mutation	SNP	ENST00000454853.2	hg19	CCDS5019.2	.	.	.	.	.	.	.	.	.	.	A	26.2	4.716499	0.89205	.	.	ENSG00000146276	ENST00000454853;ENST00000435811;ENST00000369451;ENST00000436331	D;D;D	0.86694	-2.16;-2.16;-2.16	5.07	5.07	0.68467	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.86690	0.5993	L	0.41236	1.265	0.52099	D	0.999948	P;D	0.59767	0.936;0.986	P;D	0.65140	0.737;0.932	D	0.86484	0.1793	9	.	.	.	-24.6553	14.8538	0.70319	1.0:0.0:0.0:0.0	.	336;353	P24046-2;P24046	.;GBRR1_HUMAN	A	353;336;266;266	ENSP00000412673:V353A;ENSP00000394687:V336A;ENSP00000358463:V266A	.	V	-	2	0	GABRR1	89946818	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.306000	0.78905	1.891000	0.54761	0.455000	0.32223	GTG	.	.		0.577	GABRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041479.2		
METTL24	728464	hgsc.bcm.edu	37	6	110644068	110644068	+	Missense_Mutation	SNP	C	C	A	rs545654177		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:110644068C>A	ENST00000338882.4	-	2	325	c.326G>T	c.(325-327)cGg>cTg	p.R109L	METTL24_ENST00000490043.1_5'UTR	NM_001123364.1	NP_001116836.1	Q5JXM2	MET24_HUMAN	methyltransferase like 24	109						extracellular region (GO:0005576)	methyltransferase activity (GO:0008168)	p.R109Q(1)									TATATGCCACCGGGGACCCTG	0.522																																					p.R109L		Atlas-SNP	.											C6orf186,colon,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G326T						.						55.0	53.0	54.0					6																	110644068		1568	3582	5150	SO:0001583	missense	728464	exon2			TGCCACCGGGGAC		CCDS43489.1	6q21	2012-03-08	2012-02-21	2012-02-21	ENSG00000053328	ENSG00000053328			21566	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 186"""	C6orf186			Standard	NM_001123364		Approved	dJ71D21.2	uc010kdu.1	Q5JXM2	OTTHUMG00000015359	ENST00000338882.4:c.326G>T	chr6.hg19:g.110644068C>A	ENSP00000344071:p.Arg109Leu	46.0	0.0		46.0	2.0	NM_001123364	Q6ZSU5	Missense_Mutation	SNP	ENST00000338882.4	hg19	CCDS43489.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.482511	0.63962	.	.	ENSG00000053328	ENST00000338882	T	0.52754	0.65	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.59891	0.2227	M	0.65498	2.005	0.58432	D	0.999995	D	0.76494	0.999	D	0.79784	0.993	T	0.62656	-0.6808	10	0.62326	D	0.03	-22.4033	14.7961	0.69878	0.0:1.0:0.0:0.0	.	109	Q5JXM2	CF186_HUMAN	L	109	ENSP00000344071:R109L	ENSP00000344071:R109L	R	-	2	0	C6orf186	110750761	1.000000	0.71417	1.000000	0.80357	0.142000	0.21351	4.903000	0.63272	2.563000	0.86464	0.650000	0.86243	CGG	.	.		0.522	METTL24-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041794.1	NM_001123364	
LAMA4	3910	hgsc.bcm.edu	37	6	112435867	112435867	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:112435867T>C	ENST00000230538.7	-	37	5602	c.5205A>G	c.(5203-5205)acA>acG	p.T1735T	LAMA4_ENST00000522006.1_Splice_Site_p.T1728T|LAMA4_ENST00000389463.4_Splice_Site_p.T1728T|LAMA4_ENST00000424408.2_Splice_Site_p.T1728T	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1735	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)		TTTTCTCACCTGTAATTCTGT	0.443																																					p.T1735T		Atlas-SNP	.											.	LAMA4	227	.	0			c.A5205G						.						114.0	103.0	107.0					6																	112435867		2203	4300	6503	SO:0001630	splice_region_variant	3910	exon37			CTCACCTGTAATT		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.5206+1A>G	chr6.hg19:g.112435867T>C		167.0	0.0		99.0	4.0	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	hg19	CCDS43491.1																																																																																			.	.		0.443	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	Silent
STX7	8417	hgsc.bcm.edu	37	6	132796761	132796761	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:132796761A>G	ENST00000367941.2	-	3	239	c.126T>C	c.(124-126)ccT>ccC	p.P42P	STX7_ENST00000448348.3_5'UTR|STX7_ENST00000367937.4_Silent_p.P42P	NM_003569.2	NP_003560.2	O15400	STX7_HUMAN	syntaxin 7	42					intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)|synaptic vesicle exocytosis (GO:0016079)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(1)|lung(5)	19	Breast(56;0.0615)			OV - Ovarian serous cystadenocarcinoma(155;0.00532)|GBM - Glioblastoma multiforme(226;0.0114)		GTGAATCTTGAGGTGTTCCAA	0.294																																					p.P42P		Atlas-SNP	.											.	STX7	25	.	0			c.T126C						.						74.0	70.0	72.0					6																	132796761		2201	4297	6498	SO:0001819	synonymous_variant	8417	exon3			ATCTTGAGGTGTT	U77942	CCDS5153.1	6q23.1	2008-02-05			ENSG00000079950	ENSG00000079950			11442	protein-coding gene	gene with protein product		603217				9358037	Standard	NM_003569		Approved		uc003qdg.2	O15400	OTTHUMG00000015577	ENST00000367941.2:c.126T>C	chr6.hg19:g.132796761A>G		63.0	0.0		62.0	4.0	NM_003569	E1P579|Q5SZW2|Q96ES9	Silent	SNP	ENST00000367941.2	hg19	CCDS5153.1																																																																																			.	.		0.294	STX7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042252.2		
ALDH8A1	64577	hgsc.bcm.edu	37	6	135239987	135239987	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:135239987T>C	ENST00000265605.2	-	7	1098	c.1030A>G	c.(1030-1032)Aga>Gga	p.R344G	ALDH8A1_ENST00000367847.2_Missense_Mutation_p.R294G|ALDH8A1_ENST00000367845.2_Missense_Mutation_p.R290G	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	344					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		GCAAGAGCTCTCTTGACGTAA	0.463																																					p.R344G		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.A1030G						.						102.0	108.0	106.0					6																	135239987		2203	4300	6503	SO:0001583	missense	64577	exon7			GAGCTCTCTTGAC	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"""Aldehyde dehydrogenases"""	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.1030A>G	chr6.hg19:g.135239987T>C	ENSP00000265605:p.Arg344Gly	124.0	0.0		106.0	6.0	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	hg19	CCDS5171.1	.	.	.	.	.	.	.	.	.	.	T	5.017	0.188873	0.09547	.	.	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847;ENST00000460753	T;T;T;T	0.76839	-1.05;1.54;-1.05;-1.05	5.57	5.57	0.84162	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.445184	0.27155	N	0.020664	T	0.50786	0.1636	N	0.25380	0.74	0.22457	N	0.999083	B;B;B	0.13145	0.002;0.006;0.007	B;B;B	0.09377	0.002;0.003;0.004	T	0.35226	-0.9797	10	0.28530	T	0.3	.	15.73	0.77794	0.0:0.0:0.0:1.0	.	294;290;344	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	G	344;290;294;29	ENSP00000265605:R344G;ENSP00000356819:R290G;ENSP00000356821:R294G;ENSP00000437161:R29G	ENSP00000265605:R344G	R	-	1	2	ALDH8A1	135281680	0.753000	0.28349	0.497000	0.27552	0.150000	0.21749	3.104000	0.50306	2.116000	0.64780	0.533000	0.62120	AGA	.	.		0.463	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2		
ALDH8A1	64577	hgsc.bcm.edu	37	6	135253949	135253949	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:135253949T>C	ENST00000265605.2	-	5	882	c.814A>G	c.(814-816)Att>Gtt	p.I272V	ALDH8A1_ENST00000367847.2_Missense_Mutation_p.I222V|ALDH8A1_ENST00000367845.2_Missense_Mutation_p.I272V	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	272					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		GTTGCCGGAATGCACTCATCC	0.582																																					p.I272V		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.A814G						.						94.0	94.0	94.0					6																	135253949		2203	4300	6503	SO:0001583	missense	64577	exon5			CCGGAATGCACTC	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"""Aldehyde dehydrogenases"""	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.814A>G	chr6.hg19:g.135253949T>C	ENSP00000265605:p.Ile272Val	112.0	0.0		77.0	4.0	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	hg19	CCDS5171.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.707381	0.00719	.	.	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847	T;T;T	0.73681	-0.77;-0.77;-0.77	5.3	-1.66	0.08265	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.144549	0.64402	N	0.000009	T	0.18130	0.0435	N	0.01624	-0.795	0.41054	D	0.98532	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.11329	0.003;0.003;0.006	T	0.41610	-0.9499	10	0.02654	T	1	.	12.3445	0.55114	0.0:0.2474:0.0:0.7526	.	222;272;272	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	V	272;272;222	ENSP00000265605:I272V;ENSP00000356819:I272V;ENSP00000356821:I222V	ENSP00000265605:I272V	I	-	1	0	ALDH8A1	135295642	0.002000	0.14202	0.013000	0.15412	0.001000	0.01503	-0.076000	0.11412	-0.583000	0.05921	-0.410000	0.06199	ATT	.	.		0.582	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2		
MTFR2	113115	hgsc.bcm.edu	37	6	136564084	136564084	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:136564084A>G	ENST00000420702.1	-	4	585	c.196T>C	c.(196-198)Tct>Cct	p.S66P	MTFR2_ENST00000451457.2_Missense_Mutation_p.S66P	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	66					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											CAATTATCAGAGTCTACAGAG	0.378																																					p.S66P		Atlas-SNP	.											.	.	.	.	0			c.T196C						.						87.0	87.0	87.0					6																	136564084		2203	4300	6503	SO:0001583	missense	113115	exon4			TATCAGAGTCTAC	BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410			21115	protein-coding gene	gene with protein product			"""DUF729 domain containing 1"", ""family with sequence similarity 54, member A"""	DUFD1, FAM54A			Standard	NM_138419		Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.196T>C	chr6.hg19:g.136564084A>G	ENSP00000395232:p.Ser66Pro	71.0	0.0		56.0	4.0	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Missense_Mutation	SNP	ENST00000420702.1	hg19	CCDS5176.1	.	.	.	.	.	.	.	.	.	.	A	9.562	1.118771	0.20877	.	.	ENSG00000146410	ENST00000451457;ENST00000420702;ENST00000418509	T;T;T	0.46819	0.86;0.86;0.86	5.62	-2.01	0.07410	.	0.962031	0.08693	N	0.907605	T	0.09992	0.0245	N	0.17564	0.495	0.09310	N	1	B	0.16166	0.016	B	0.17979	0.02	T	0.31586	-0.9938	10	0.27785	T	0.31	-1.7625	4.9444	0.13982	0.4544:0.2768:0.2688:0.0	.	66	Q6P444	FA54A_HUMAN	P	66;66;23	ENSP00000407010:S66P;ENSP00000395232:S66P;ENSP00000410861:S23P	ENSP00000410861:S23P	S	-	1	0	FAM54A	136605777	0.000000	0.05858	0.027000	0.17364	0.661000	0.39034	-0.044000	0.12023	-0.208000	0.10171	0.533000	0.62120	TCT	.	.		0.378	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419	
MAP3K5	4217	hgsc.bcm.edu	37	6	136935339	136935339	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:136935339C>A	ENST00000359015.4	-	16	2596	c.2236G>T	c.(2236-2238)Gag>Tag	p.E746*	MAP3K5_ENST00000355845.4_5'UTR	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	746	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		AAACCATTCTCACTGAAAGAG	0.393																																					p.E746X		Atlas-SNP	.											.	MAP3K5	136	.	0			c.G2236T						.						151.0	144.0	146.0					6																	136935339		2203	4300	6503	SO:0001587	stop_gained	4217	exon16			CATTCTCACTGAA	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.2236G>T	chr6.hg19:g.136935339C>A	ENSP00000351908:p.Glu746*	113.0	0.0		87.0	4.0	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Nonsense_Mutation	SNP	ENST00000359015.4	hg19	CCDS5179.1	.	.	.	.	.	.	.	.	.	.	C	43	10.477992	0.99412	.	.	ENSG00000197442	ENST00000359015;ENST00000367768	.	.	.	5.2	5.2	0.72013	.	0.095780	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	12.4507	0.55675	0.0:0.9222:0.0:0.0778	.	.	.	.	X	746;826	.	ENSP00000351908:E746X	E	-	1	0	MAP3K5	136977032	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.634000	0.61325	2.565000	0.86533	0.650000	0.86243	GAG	.	.		0.393	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1		
KIAA1244	57221	hgsc.bcm.edu	37	6	138629880	138629880	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:138629880A>G	ENST00000251691.4	+	24	4144	c.3978A>G	c.(3976-3978)aaA>aaG	p.K1326K		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CCTTAGGAAAAGGCCAAGCTC	0.443																																					p.K1326K		Atlas-SNP	.											.	KIAA1244	236	.	0			c.A3978G						.						142.0	139.0	140.0					6																	138629880		2203	4300	6503	SO:0001819	synonymous_variant	57221	exon24			AGGAAAAGGCCAA	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.3978A>G	chr6.hg19:g.138629880A>G		163.0	0.0		89.0	4.0	NM_020340		Silent	SNP	ENST00000251691.4	hg19	CCDS5189.2																																																																																			.	.		0.443	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
ZC2HC1B	153918	hgsc.bcm.edu	37	6	144207245	144207245	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:144207245A>G	ENST00000237275.6	+	3	271	c.167A>G	c.(166-168)cAg>cGg	p.Q56R	ZC2HC1B_ENST00000539295.1_5'UTR	NM_001013623.2	NP_001013645.1	Q5TFG8	ZC21B_HUMAN	zinc finger, C2HC-type containing 1B	56							metal ion binding (GO:0046872)			endometrium(1)	1						CAAAGATTACAGGGCACTGAC	0.403																																					p.Q56R		Atlas-SNP	.											.	ZC2HC1B	6	.	0			c.A167G						.						140.0	116.0	123.0					6																	144207245		692	1591	2283	SO:0001583	missense	153918	exon3			GATTACAGGGCAC	BC146950	CCDS47495.1	6q24.2	2013-01-10	2012-02-03	2012-02-03	ENSG00000118491	ENSG00000118491		"""Zinc fingers, C2HC-type containing"""	21174	protein-coding gene	gene with protein product			"""family with sequence similarity 164, member B"", ""chromosome 6 open reading frame 94"""	FAM164B, C6orf94			Standard	NM_001013623		Approved	dJ468K18.5	uc010khk.3	Q5TFG8	OTTHUMG00000015734	ENST00000237275.6:c.167A>G	chr6.hg19:g.144207245A>G	ENSP00000237275:p.Gln56Arg	154.0	0.0		111.0	5.0	NM_001013623	B2RUZ7|Q5TFG9	Missense_Mutation	SNP	ENST00000237275.6	hg19	CCDS47495.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.17|12.17	1.858654|1.858654	0.32791|0.32791	.|.	.|.	ENSG00000118491|ENSG00000118491	ENST00000237275|ENST00000416313	T|.	0.30981|.	1.51|.	5.41|5.41	4.25|4.25	0.50352|0.50352	.|.	0.212726|.	0.33199|.	N|.	0.005174|.	T|T	0.37046|0.37046	0.0989|0.0989	L|L	0.38838|0.38838	1.175|1.175	0.80722|0.80722	D|D	1|1	B|.	0.11235|.	0.004|.	B|.	0.10450|.	0.005|.	T|T	0.22906|0.22906	-1.0203|-1.0203	10|5	0.30078|.	T|.	0.28|.	-5.8352|-5.8352	9.0317|9.0317	0.36262|0.36262	0.915:0.0:0.085:0.0|0.915:0.0:0.085:0.0	.|.	56|.	Q5TFG8|.	F164B_HUMAN|.	R|G	56|47	ENSP00000237275:Q56R|.	ENSP00000237275:Q56R|.	Q|R	+|+	2|1	0|2	C6orf94|C6orf94	144248938|144248938	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.790000|0.790000	0.44656|0.44656	3.616000|3.616000	0.54174|0.54174	0.904000|0.904000	0.36572|0.36572	0.533000|0.533000	0.62120|0.62120	CAG|AGG	.	.		0.403	ZC2HC1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001013623	
IPCEF1	26034	hgsc.bcm.edu	37	6	154480993	154480993	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:154480993A>G	ENST00000265198.4	-	12	1439	c.1284T>C	c.(1282-1284)ccT>ccC	p.P428P	OPRM1_ENST00000337049.4_Intron|IPCEF1_ENST00000519344.1_Silent_p.P400P|IPCEF1_ENST00000422970.2_Silent_p.P429P|IPCEF1_ENST00000367220.4_Silent_p.P429P	NM_001130700.1|NM_015553.2	NP_001124172.1|NP_056368.1	Q8WWN9	ICEF1_HUMAN	interaction protein for cytohesin exchange factors 1	428					oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|positive regulation of GTP catabolic process (GO:0033126)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	oxygen transporter activity (GO:0005344)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	12						AGGGAGAAGAAGGTGATTTCT	0.458																																					p.P429P		Atlas-SNP	.											.	IPCEF1	45	.	0			c.T1287C						.						61.0	65.0	63.0					6																	154480993		2203	4300	6503	SO:0001819	synonymous_variant	26034	exon13			AGAAGAAGGTGAT	AB007863	CCDS5245.1, CCDS47509.1	6q25.2	2013-01-10			ENSG00000074706	ENSG00000074706		"""Pleckstrin homology (PH) domain containing"""	21204	protein-coding gene	gene with protein product	"""phosphoinositide binding protein PIP3-E"""					11804589, 19756519	Standard	NM_001130699		Approved	PIP3-E, KIAA0403	uc021zhc.1	Q8WWN9	OTTHUMG00000015872	ENST00000265198.4:c.1284T>C	chr6.hg19:g.154480993A>G		79.0	0.0		57.0	5.0	NM_001130699	A8K1K2|B7ZL78|B7ZL80|O43153|Q5HYL8	Silent	SNP	ENST00000265198.4	hg19	CCDS5245.1																																																																																			.	.		0.458	IPCEF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042789.2	NM_001130699	
NOX3	50508	hgsc.bcm.edu	37	6	155750089	155750089	+	Silent	SNP	T	T	C	rs545302024	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:155750089T>C	ENST00000159060.2	-	9	1086	c.984A>G	c.(982-984)ccA>ccG	p.P328P		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	328	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.			P -> S (in Ref. 3; AAG15435). {ECO:0000305}.	detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		AAGATATGGCTGGGCACTGCA	0.567																																					p.P328P		Atlas-SNP	.											NOX3,NS,carcinoma,0,1	NOX3	93	.	0			c.A984G						.						80.0	81.0	81.0					6																	155750089		2203	4300	6503	SO:0001819	synonymous_variant	50508	exon9			TATGGCTGGGCAC	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.984A>G	chr6.hg19:g.155750089T>C		114.0	0.0		79.0	4.0	NM_015718	Q9HBJ9	Silent	SNP	ENST00000159060.2	hg19	CCDS5250.1																																																																																			.	.		0.567	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		
IGF2R	3482	hgsc.bcm.edu	37	6	160469467	160469467	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:160469467A>G	ENST00000356956.1	+	18	2554	c.2406A>G	c.(2404-2406)gaA>gaG	p.E802E		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	802					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)	ACTCAGGGGAACATGTCACGT	0.453																																					p.E802E		Atlas-SNP	.											.	IGF2R	251	.	0			c.A2406G						.						135.0	114.0	121.0					6																	160469467		2203	4300	6503	SO:0001819	synonymous_variant	3482	exon18			AGGGGAACATGTC	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.2406A>G	chr6.hg19:g.160469467A>G		124.0	0.0		62.0	4.0	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	hg19	CCDS5273.1																																																																																			.	.		0.453	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
THBS2	7058	hgsc.bcm.edu	37	6	169626380	169626380	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:169626380T>C	ENST00000366787.3	-	17	2682	c.2433A>G	c.(2431-2433)gaA>gaG	p.E811E	XXyac-YX65C7_A.2_ENST00000444188.1_RNA|THBS2_ENST00000488355.1_5'Flank	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	811					cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		AATTGTCTCGTTCATTGAAGA	0.468																																					p.E811E	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											THBS2,NS,carcinoma,0,1	THBS2	230	.	0			c.A2433G						.						93.0	88.0	89.0					6																	169626380		2203	4300	6503	SO:0001819	synonymous_variant	7058	exon17			GTCTCGTTCATTG		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.2433A>G	chr6.hg19:g.169626380T>C		84.0	0.0		50.0	3.0	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	hg19	CCDS34574.1																																																																																			.	.		0.468	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
WDR27	253769	hgsc.bcm.edu	37	6	170002368	170002368	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr6:170002368T>C	ENST00000448612.1	-	23	2480	c.2371A>G	c.(2371-2373)Atc>Gtc	p.I791V	WDR27_ENST00000333572.6_Missense_Mutation_p.I791V|WDR27_ENST00000546525.1_5'UTR|WDR27_ENST00000423258.1_Missense_Mutation_p.I664V	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	761						nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		CTGAAAGCGATTCCACATGGA	0.473																																					p.I791V		Atlas-SNP	.											.	WDR27	129	.	0			c.A2371G						.						36.0	39.0	38.0					6																	170002368		1924	4135	6059	SO:0001583	missense	253769	exon23			AAGCGATTCCACA	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"""WD repeat domain containing"""	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.2371A>G	chr6.hg19:g.170002368T>C	ENSP00000416289:p.Ile791Val	57.0	0.0		72.0	5.0	NM_182552	A5PLM8|C9JGV0|Q5T066	Missense_Mutation	SNP	ENST00000448612.1	hg19	CCDS47520.2	.	.	.	.	.	.	.	.	.	.	T	0.063	-1.220356	0.01542	.	.	ENSG00000184465	ENST00000448612;ENST00000333572;ENST00000423258	T;T;T	0.38077	5.1;1.16;5.1	4.56	-5.92	0.02261	.	.	.	.	.	T	0.04092	0.0114	N	0.16016	0.355	0.09310	N	1	B;B;B	0.20887	0.004;0.007;0.049	B;B;B	0.20184	0.002;0.003;0.028	T	0.38222	-0.9671	9	0.02654	T	1	-0.852	8.4385	0.32801	0.0:0.5975:0.1369:0.2656	.	791;664;791	F2Z2U5;A2RRH5-2;C9JGV0	.;.;.	V	791;791;664	ENSP00000416289:I791V;ENSP00000330265:I791V;ENSP00000397869:I664V	ENSP00000330265:I791V	I	-	1	0	WDR27	169744293	0.044000	0.20184	0.000000	0.03702	0.003000	0.03518	-0.027000	0.12371	-1.084000	0.03092	-0.417000	0.06048	ATC	.	.		0.473	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552	
NUDT1	4521	hgsc.bcm.edu	37	7	2284331	2284331	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:2284331A>G	ENST00000397046.1	+	3	219	c.122A>G	c.(121-123)gAa>gGa	p.E41G	NUDT1_ENST00000397049.1_Missense_Mutation_p.E64G|FTSJ2_ENST00000242257.8_5'Flank|NUDT1_ENST00000397048.1_Missense_Mutation_p.E64G|FTSJ2_ENST00000440306.2_5'Flank|NUDT1_ENST00000339737.2_Missense_Mutation_p.E41G|NUDT1_ENST00000343985.4_Missense_Mutation_p.E64G|NUDT1_ENST00000356714.1_Missense_Mutation_p.E41G|FTSJ2_ENST00000486040.1_5'Flank	NM_198950.1	NP_945188.1	P36639	8ODP_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 1	82					ATP catabolic process (GO:0006200)|dATP catabolic process (GO:0046061)|dGTP catabolic process (GO:0006203)|DNA protection (GO:0042262)|DNA repair (GO:0006281)|GTP catabolic process (GO:0006184)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleotide catabolic process (GO:0006195)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity (GO:0035539)|8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity (GO:0008413)|ATP diphosphatase activity (GO:0047693)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|snoRNA binding (GO:0030515)			large_intestine(3)|lung(8)|urinary_tract(1)	12		Ovarian(82;0.0253)|Melanoma(862;0.155)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0822)|OV - Ovarian serous cystadenocarcinoma(56;2.8e-14)|BRCA - Breast invasive adenocarcinoma(126;0.15)		AAAGTGCAAGAAGGAGAGACC	0.622								Modulation of nucleotide pools																													p.E64G		Atlas-SNP	.											.	NUDT1	22	.	0			c.A191G						.						43.0	43.0	43.0					7																	2284331		2203	4300	6503	SO:0001583	missense	4521	exon3			TGCAAGAAGGAGA	D16581	CCDS5329.1, CCDS5330.1	7p22	2008-07-18			ENSG00000106268	ENSG00000106268		"""Nudix motif containing"""	8048	protein-coding gene	gene with protein product	"""mutT human homolog 1"", ""nudix motif 1"", ""8-oxo-7,8-dihydrodeoxyguanosine triphosphatase"", ""8-oxo-dGTPase"", ""7,8-dihydro-8-oxoguanine triphosphatase"", ""8-oxo-7,8-dihydroguanosine triphosphatase"", ""nucleoside diphosphate-linked moiety X-type motif 1"""	600312		MTH1		7713494, 8226881	Standard	NM_002452		Approved		uc003slp.1	P36639	OTTHUMG00000023072	ENST00000397046.1:c.122A>G	chr7.hg19:g.2284331A>G	ENSP00000380239:p.Glu41Gly	65.0	0.0		67.0	4.0	NM_198949	A4D205|Q6LES7|Q6P0Y6|Q7Z7N6|Q8IV95|Q9UBM0|Q9UBM9	Missense_Mutation	SNP	ENST00000397046.1	hg19	CCDS5330.1	.	.	.	.	.	.	.	.	.	.	A	10.82	1.457932	0.26161	.	.	ENSG00000106268	ENST00000356714;ENST00000397049;ENST00000397046;ENST00000397048;ENST00000343985;ENST00000339737	T;T;T;T;T;T	0.09163	3.01;3.01;3.01;3.01;3.01;3.01	3.8	1.22	0.21188	NUDIX hydrolase (1);NUDIX hydrolase domain (3);NUDIX hydrolase, conserved site (1);NUDIX hydrolase domain-like (1);	0.792616	0.11873	N	0.521203	T	0.07999	0.0200	N	0.25094	0.71	0.28263	N	0.924759	B	0.30361	0.277	B	0.35182	0.197	T	0.38200	-0.9672	10	0.34782	T	0.22	-4.6872	6.7625	0.23548	0.535:0.3732:0.0918:0.0	.	82	P36639	8ODP_HUMAN	G	41;64;41;64;64;41	ENSP00000349148:E41G;ENSP00000380242:E64G;ENSP00000380239:E41G;ENSP00000380241:E64G;ENSP00000339503:E64G;ENSP00000343439:E41G	ENSP00000343439:E41G	E	+	2	0	NUDT1	2250857	0.845000	0.29573	0.938000	0.37757	0.616000	0.37450	2.490000	0.45294	0.019000	0.15079	0.379000	0.24179	GAA	.	.		0.622	NUDT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206922.1	NM_002452	
CARD11	84433	hgsc.bcm.edu	37	7	2956991	2956991	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:2956991G>T	ENST00000396946.4	-	20	3039	c.2636C>A	c.(2635-2637)tCa>tAa	p.S879*		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	879					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		GTCGCTTGTTGAAAGCGCTTC	0.552			Mis		DLBCL																																p.S879X		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	CARD11	339	.	0			c.C2636A						.						39.0	52.0	47.0					7																	2956991		2203	4299	6502	SO:0001587	stop_gained	84433	exon20			CTTGTTGAAAGCG	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.2636C>A	chr7.hg19:g.2956991G>T	ENSP00000380150:p.Ser879*	60.0	0.0		57.0	4.0	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Nonsense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	G	39	7.837902	0.98516	.	.	ENSG00000198286	ENST00000396946	.	.	.	4.99	4.99	0.66335	.	0.371673	0.24640	N	0.036804	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.4471	11.9441	0.52918	0.0834:0.0:0.9166:0.0	.	.	.	.	X	879	.	ENSP00000380150:S879X	S	-	2	0	CARD11	2923517	0.944000	0.32072	0.008000	0.14137	0.456000	0.32438	5.617000	0.67716	2.308000	0.77769	0.561000	0.74099	TCA	.	.		0.552	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
AP5Z1	9907	hgsc.bcm.edu	37	7	4825066	4825066	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:4825066T>C	ENST00000348624.4	+	8	1046	c.952T>C	c.(952-954)Tcc>Ccc	p.S318P	AP5Z1_ENST00000401897.1_Missense_Mutation_p.S318P	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	318					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											GAAGGGGGACTCCGACCTGCA	0.622																																					p.S318P		Atlas-SNP	.											.	.	.	.	0			c.T952C						.						35.0	42.0	40.0					7																	4825066		2081	4194	6275	SO:0001583	missense	9907	exon8			GGGGACTCCGACC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.952T>C	chr7.hg19:g.4825066T>C	ENSP00000297562:p.Ser318Pro	61.0	0.0		55.0	4.0	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	hg19	CCDS47528.1	.	.	.	.	.	.	.	.	.	.	T	16.37	3.103961	0.56291	.	.	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.46063	0.88;0.88	5.48	-4.59	0.03400	.	0.346233	0.28453	N	0.015297	T	0.42988	0.1227	L	0.53249	1.67	0.09310	N	1	P	0.47106	0.89	P	0.46796	0.527	T	0.54990	-0.8210	10	0.48119	T	0.1	.	19.5099	0.95137	0.0:0.0:0.7208:0.2792	.	318	O43299	K0415_HUMAN	P	318	ENSP00000297562:S318P;ENSP00000384980:S318P	ENSP00000297562:S318P	S	+	1	0	KIAA0415	4791592	0.061000	0.20836	0.059000	0.19551	0.764000	0.43329	-0.153000	0.10144	-0.619000	0.05648	0.459000	0.35465	TCC	.	.		0.622	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
SNX13	23161	hgsc.bcm.edu	37	7	17915106	17915106	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:17915106C>T	ENST00000409389.1	-	7	833	c.661G>A	c.(661-663)Gaa>Aaa	p.E221K	SNX13_ENST00000428135.3_Missense_Mutation_p.E221K			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	221	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.E221*(1)		breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					AGAAAACCTTCTTCATCTTTG	0.363																																					p.E221K		Atlas-SNP	.											SNX13,colon,carcinoma,0,1	SNX13	113	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G661A						.						70.0	67.0	68.0					7																	17915106		1816	4085	5901	SO:0001583	missense	23161	exon7			AACCTTCTTCATC	AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"""Sorting nexins"""	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.661G>A	chr7.hg19:g.17915106C>T	ENSP00000386705:p.Glu221Lys	74.0	1.0		54.0	3.0	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Missense_Mutation	SNP	ENST00000409389.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.57	1.678735	0.29783	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044	T;T	0.17054	2.3;2.56	5.77	5.77	0.91146	Phox-associated domain (2);PX-associated, sorting nexin 13 (1);	0.044457	0.85682	D	0.000000	T	0.11836	0.0288	N	0.11789	0.175	0.80722	D	1	B;B;B;B	0.23377	0.053;0.084;0.049;0.068	B;B;B;B	0.22880	0.032;0.042;0.017;0.025	T	0.20974	-1.0259	10	0.13470	T	0.59	.	19.9808	0.97324	0.0:1.0:0.0:0.0	.	18;221;221;221	B3KN60;Q9Y5W8;B8ZZT9;Q9Y5W8-2	.;SNX13_HUMAN;.;.	K	221;221;269	ENSP00000386705:E221K;ENSP00000398789:E221K	ENSP00000242044:E269K	E	-	1	0	SNX13	17881631	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.085000	0.76875	2.714000	0.92807	0.655000	0.94253	GAA	.	.		0.363	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132	
DFNA5	1687	hgsc.bcm.edu	37	7	24756897	24756897	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:24756897A>G	ENST00000342947.3	-	5	1098	c.673T>C	c.(673-675)Tac>Cac	p.Y225H	DFNA5_ENST00000419307.1_Missense_Mutation_p.Y61H|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000409970.1_Missense_Mutation_p.Y61H|DFNA5_ENST00000545231.1_Missense_Mutation_p.Y61H|DFNA5_ENST00000409775.3_Missense_Mutation_p.Y225H	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	225					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						AGTTTCACGTATAACTCAATG	0.572																																					p.Y225H	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.T673C						.						155.0	113.0	127.0					7																	24756897		2203	4300	6503	SO:0001583	missense	1687	exon5			TCACGTATAACTC	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.673T>C	chr7.hg19:g.24756897A>G	ENSP00000339587:p.Tyr225His	61.0	0.0		43.0	4.0	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	hg19	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.505486	0.44558	.	.	ENSG00000105928	ENST00000342947;ENST00000419307;ENST00000545231;ENST00000409970;ENST00000409775	T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93	5.7	4.52	0.55395	.	0.492653	0.22491	N	0.059365	T	0.46852	0.1414	M	0.72894	2.215	0.23401	N	0.997759	D;D	0.76494	0.999;0.999	D;D	0.72338	0.977;0.977	T	0.36890	-0.9729	10	0.30854	T	0.27	-14.1664	11.9919	0.53180	0.8547:0.1453:0.0:0.0	.	225;225	A4FTY0;O60443	.;DFNA5_HUMAN	H	225;61;61;61;225	ENSP00000339587:Y225H;ENSP00000401332:Y61H;ENSP00000442661:Y61H;ENSP00000387119:Y61H;ENSP00000386670:Y225H	ENSP00000339587:Y225H	Y	-	1	0	DFNA5	24723422	0.338000	0.24775	0.119000	0.21687	0.295000	0.27426	1.755000	0.38379	0.954000	0.37851	0.533000	0.62120	TAC	.	.		0.572	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
CRHR2	1395	hgsc.bcm.edu	37	7	30704769	30704769	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:30704769T>C	ENST00000471646.1	-	5	877	c.460A>G	c.(460-462)Aac>Gac	p.N154D	CRHR2_ENST00000348438.4_Missense_Mutation_p.N181D|CRHR2_ENST00000506074.2_Missense_Mutation_p.N154D|CRHR2_ENST00000341843.4_Missense_Mutation_p.N140D	NM_001202482.1|NM_001202483.1|NM_001883.4	NP_001189411.1|NP_001189412.1|NP_001874.2	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	154					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GTGATGAGGTTCCAGTGAATC	0.562																																					p.N181D		Atlas-SNP	.											.	CRHR2	104	.	0			c.A541G						.						121.0	96.0	104.0					7																	30704769		2203	4300	6503	SO:0001583	missense	1395	exon6			TGAGGTTCCAGTG		CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000471646.1:c.460A>G	chr7.hg19:g.30704769T>C	ENSP00000418722:p.Asn154Asp	117.0	0.0		97.0	4.0	NM_001202475	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Missense_Mutation	SNP	ENST00000471646.1	hg19	CCDS5429.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.675266	0.88445	.	.	ENSG00000106113	ENST00000471646;ENST00000348438;ENST00000341843;ENST00000506074	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	4.28	4.28	0.50868	GPCR, family 2-like (1);	0.046573	0.85682	D	0.000000	T	0.66046	0.2750	M	0.92691	3.335	0.80722	D	1	D;D;D;D;D	0.76494	0.99;0.997;0.999;0.999;0.995	D;D;D;D;D	0.72075	0.941;0.976;0.976;0.976;0.976	T	0.74677	-0.3585	10	0.87932	D	0	.	12.0279	0.53382	0.0:0.0:0.0:1.0	.	153;154;181;140;154	B3SXT0;B3SXS6;Q13324-2;Q13324-3;Q13324	.;.;.;.;CRFR2_HUMAN	D	154;181;140;154	ENSP00000418722:N154D;ENSP00000340943:N181D;ENSP00000344304:N140D;ENSP00000426498:N154D	ENSP00000344304:N140D	N	-	1	0	CRHR2	30671294	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.776000	0.85560	2.146000	0.66826	0.533000	0.62120	AAC	.	.		0.562	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250448.3		
AVL9	23080	hgsc.bcm.edu	37	7	32612832	32612832	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:32612832A>G	ENST00000318709.4	+	12	1593	c.1372A>G	c.(1372-1374)Atc>Gtc	p.I458V	AVL9_ENST00000404479.1_Intron|AVL9_ENST00000409301.1_Missense_Mutation_p.I458V	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	458					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TCTGATCCAGATCCATGATCC	0.507																																					p.I458V		Atlas-SNP	.											.	AVL9	66	.	0			c.A1372G						.						83.0	65.0	71.0					7																	32612832		2203	4300	6503	SO:0001583	missense	23080	exon12			ATCCAGATCCATG	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.1372A>G	chr7.hg19:g.32612832A>G	ENSP00000315568:p.Ile458Val	98.0	0.0		102.0	5.0	NM_015060	Q92573	Missense_Mutation	SNP	ENST00000318709.4	hg19	CCDS34613.1	.	.	.	.	.	.	.	.	.	.	A	9.602	1.128856	0.21041	.	.	ENSG00000105778	ENST00000318709;ENST00000409301;ENST00000329714;ENST00000446718	T;T;T	0.42131	0.98;0.98;0.98	5.52	4.37	0.52481	.	0.108992	0.64402	N	0.000008	T	0.29458	0.0734	L	0.38531	1.155	0.80722	D	1	B;B	0.12630	0.003;0.006	B;B	0.20184	0.009;0.028	T	0.07009	-1.0795	10	0.16420	T	0.52	-10.2239	7.8191	0.29278	0.7763:0.0:0.2237:0.0	.	458;458	Q8NBF6-2;Q8NBF6	.;AVL9_HUMAN	V	458;458;458;389	ENSP00000315568:I458V;ENSP00000387011:I458V;ENSP00000395134:I389V	ENSP00000315568:I458V	I	+	1	0	AVL9	32579357	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.308000	0.59129	0.924000	0.37069	0.533000	0.62120	ATC	.	.		0.507	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060	
VPS41	27072	hgsc.bcm.edu	37	7	38765881	38765881	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:38765881C>T	ENST00000310301.4	-	29	2584	c.2530G>A	c.(2530-2532)Gga>Aga	p.G844R	VPS41_ENST00000395969.2_Missense_Mutation_p.G819R	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	844					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						CTTCCTGGTCCACGGTTCTTA	0.363																																					p.G844R		Atlas-SNP	.											.	VPS41	102	.	0			c.G2530A						.						137.0	123.0	128.0					7																	38765881		2203	4300	6503	SO:0001583	missense	27072	exon29			CTGGTCCACGGTT	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.2530G>A	chr7.hg19:g.38765881C>T	ENSP00000309457:p.Gly844Arg	110.0	0.0		93.0	4.0	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	hg19	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.304227	0.60305	.	.	ENSG00000006715	ENST00000310301;ENST00000395969	T;T	0.17370	2.28;2.28	5.51	5.51	0.81932	.	0.049153	0.85682	D	0.000000	T	0.13628	0.0330	N	0.25144	0.715	0.80722	D	1	B;B;B	0.23058	0.046;0.079;0.079	B;B;B	0.18263	0.017;0.021;0.021	T	0.11690	-1.0577	10	0.18276	T	0.48	-24.2966	19.0496	0.93038	0.0:1.0:0.0:0.0	.	844;819;844	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	R	844;819	ENSP00000309457:G844R;ENSP00000379297:G819R	ENSP00000309457:G844R	G	-	1	0	VPS41	38732406	1.000000	0.71417	0.993000	0.49108	0.994000	0.84299	6.463000	0.73530	2.590000	0.87494	0.650000	0.86243	GGA	.	.		0.363	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
C7orf25	79020	hgsc.bcm.edu	37	7	42950513	42950513	+	5'UTR	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:42950513T>C	ENST00000350427.4	-	0	262				C7orf25_ENST00000447342.1_5'UTR|PSMA2_ENST00000442788.1_3'UTR|C7orf25_ENST00000438029.1_5'UTR|C7orf25_ENST00000431882.2_Missense_Mutation_p.N54S			Q9BPX7	CG025_HUMAN	chromosome 7 open reading frame 25											endometrium(6)|kidney(1)|large_intestine(7)|lung(2)|skin(1)	17						GTCAGCATTATTCCTTTCCTA	0.388																																					p.N54S		Atlas-SNP	.											.	C7orf25	36	.	0			c.A161G						.						91.0	89.0	90.0					7																	42950513		2202	4300	6502	SO:0001623	5_prime_UTR_variant	79020	exon2			GCATTATTCCTTT	BC001845	CCDS5466.1, CCDS47576.1	7p14.1	2011-11-24			ENSG00000136197	ENSG00000136197			21703	protein-coding gene	gene with protein product							Standard	NM_024054		Approved	MGC2821	uc003thx.4	Q9BPX7	OTTHUMG00000128869	ENST00000350427.4:c.-14A>G	chr7.hg19:g.42950513T>C		103.0	0.0		70.0	4.0	NM_001099858	A4D1V2|J3KR36|Q9H779	Missense_Mutation	SNP	ENST00000350427.4	hg19	CCDS5466.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.457279	0.43634	.	.	ENSG00000136197	ENST00000431882;ENST00000421724	T	0.39592	1.07	5.42	5.42	0.78866	.	.	.	.	.	T	0.24774	0.0601	N	0.08118	0	0.80722	D	1	B	0.18741	0.03	B	0.15870	0.014	T	0.07829	-1.0752	9	0.20519	T	0.43	.	15.4811	0.75528	0.0:0.0:0.0:1.0	.	54	B4DQM3	.	S	54;10	ENSP00000416290:N54S	ENSP00000395817:N10S	N	-	2	0	C7orf25	42917038	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	3.455000	0.52993	2.064000	0.61679	0.459000	0.35465	AAT	.	.		0.388	C7orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250814.2	NM_024054	
H2AFV	94239	hgsc.bcm.edu	37	7	44875219	44875219	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:44875219T>C	ENST00000308153.4	-	4	325	c.234A>G	c.(232-234)aaA>aaG	p.K78K	H2AFV_ENST00000350771.3_Silent_p.K52K|H2AFV_ENST00000437072.1_Silent_p.K40K|H2AFV_ENST00000349299.3_Silent_p.K40K|H2AFV_ENST00000381124.5_Intron|H2AFV_ENST00000521529.1_Intron|H2AFV_ENST00000222690.6_Silent_p.K78K|H2AFV_ENST00000446531.1_Silent_p.K78K	NM_012412.4	NP_036544.1	Q71UI9	H2AV_HUMAN	H2A histone family, member V	78						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	9						TACGCTTTACTTTGAGATCCT	0.458																																					p.K78K		Atlas-SNP	.											.	H2AFV	14	.	0			c.A234G						.						113.0	94.0	100.0					7																	44875219		2203	4300	6503	SO:0001819	synonymous_variant	94239	exon4			CTTTACTTTGAGA	AF081192	CCDS5495.1, CCDS5496.1, CCDS5497.1, CCDS5498.1, CCDS47581.1	7p13	2011-01-27		2004-03-26	ENSG00000105968	ENSG00000105968		"""Histones / Replication-independent"""	20664	protein-coding gene	gene with protein product				H2AV			Standard	NM_012412		Approved	MGC10170, MGC10831, MGC1947	uc003tma.2	Q71UI9	OTTHUMG00000129217	ENST00000308153.4:c.234A>G	chr7.hg19:g.44875219T>C		132.0	0.0		82.0	6.0	NM_012412	A6NFA8|A6NKY0|A6NN01|A8MQC5|Q59GV8|Q6PK98	Silent	SNP	ENST00000308153.4	hg19	CCDS5496.1																																																																																			.	.		0.458	H2AFV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251305.1	NM_012412	
CCM2	83605	hgsc.bcm.edu	37	7	45077891	45077891	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:45077891G>T	ENST00000258781.6	+	2	219	c.70G>T	c.(70-72)Ggt>Tgt	p.G24C	CCM2_ENST00000475551.1_Missense_Mutation_p.G18C|CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000381112.3_Missense_Mutation_p.G45C|CCM2_ENST00000544363.1_Missense_Mutation_p.G24C|CCM2_ENST00000474617.1_Missense_Mutation_p.G18C|CCM2_ENST00000541586.1_Intron	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	24					blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						ATTCCTAAAAGGTGAAAAGAG	0.468																																					p.G45C		Atlas-SNP	.											.	CCM2	42	.	0			c.G133T						.						89.0	88.0	88.0					7																	45077891		2203	4300	6503	SO:0001583	missense	83605	exon2			CTAAAAGGTGAAA	BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"""malcavernin"""	607929	"""chromosome 7 open reading frame 22"""	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.70G>T	chr7.hg19:g.45077891G>T	ENSP00000258781:p.Gly24Cys	93.0	0.0		71.0	4.0	NM_001029835	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Missense_Mutation	SNP	ENST00000258781.6	hg19	CCDS5500.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.625189	0.66901	.	.	ENSG00000136280	ENST00000258781;ENST00000544363;ENST00000543541;ENST00000475551;ENST00000381112;ENST00000474617	T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.72391	0.3454	M	0.67953	2.075	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.991;1.0;1.0;1.0	T	0.74090	-0.3777	10	0.87932	D	0	-18.6522	18.3739	0.90428	0.0:0.0:1.0:0.0	.	45;45;24;24	B7Z5A6;E9PDJ3;F5H0E1;Q9BSQ5	.;.;.;CCM2_HUMAN	C	24;24;24;18;45;18	ENSP00000258781:G24C;ENSP00000438035:G24C;ENSP00000417180:G18C;ENSP00000370503:G45C;ENSP00000419474:G18C	ENSP00000258781:G24C	G	+	1	0	CCM2	45044416	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.277000	0.95755	2.696000	0.92011	0.655000	0.94253	GGT	.	.		0.468	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443	
COBL	23242	hgsc.bcm.edu	37	7	51085259	51085259	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:51085259A>G	ENST00000265136.7	-	13	3940	c.3775T>C	c.(3775-3777)Ttg>Ctg	p.L1259L	COBL_ENST00000395542.2_Silent_p.L1341L|RP4-724E13.2_ENST00000420449.1_RNA|RP4-724E13.2_ENST00000582616.1_RNA	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1259					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					CACACGAGCAAGGGCACCTGC	0.498																																					p.L1259L	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.T3775C						.						105.0	99.0	101.0					7																	51085259		2203	4300	6503	SO:0001819	synonymous_variant	23242	exon13			CGAGCAAGGGCAC	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.3775T>C	chr7.hg19:g.51085259A>G		125.0	0.0		98.0	4.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	hg19	CCDS34637.1																																																																																			.	.		0.498	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
COBL	23242	hgsc.bcm.edu	37	7	51096495	51096495	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:51096495T>C	ENST00000265136.7	-	10	2463	c.2298A>G	c.(2296-2298)aaA>aaG	p.K766K	COBL_ENST00000395542.2_Silent_p.K848K	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	766					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					ACTCTCTGACTTTCCCAATGG	0.587																																					p.K766K	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.A2298G						.						50.0	50.0	50.0					7																	51096495		2203	4300	6503	SO:0001819	synonymous_variant	23242	exon10			TCTGACTTTCCCA	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.2298A>G	chr7.hg19:g.51096495T>C		150.0	0.0		86.0	5.0	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	hg19	CCDS34637.1	.	.	.	.	.	.	.	.	.	.	T	0.505	-0.868926	0.02570	.	.	ENSG00000106078	ENST00000457306	.	.	.	5.83	-0.929	0.10444	.	.	.	.	.	.	.	.	.	.	.	0.19945	N	0.99994	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.2731	0.15636	0.0:0.2763:0.262:0.4617	.	.	.	.	.	-1	.	.	.	-	.	.	COBL	51063989	0.430000	0.25538	0.000000	0.03702	0.011000	0.07611	-0.022000	0.12480	-0.387000	0.07809	0.533000	0.62120	.	.	.		0.587	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
ZNF716	441234	hgsc.bcm.edu	37	7	57522850	57522851	+	Missense_Mutation	DNP	AA	AA	TT			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:57522850_57522851AA>TT	ENST00000420713.1	+	3	350_351	c.238_239AA>TT	c.(238-240)AAt>TTt	p.N80F		NM_001159279.1	NP_001152751.1	A6NP11	ZN716_HUMAN	zinc finger protein 716	80	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|lung(20)|ovary(2)	24						TATAAAGAGAAATGAGATGGTA	0.406																																					p.N80Y|p.N80I		Atlas-SNP	.											.	ZNF716	207	.	0			c.A238T|c.A239T						.																																			SO:0001583	missense	441234	exon3			AAGAGAAATGAGA|AGAGAAATGAGAT	AK131575	CCDS55112.1	7p11.1	2013-01-08			ENSG00000182111	ENSG00000182111		"""Zinc fingers, C2H2-type"", ""-"""	32458	protein-coding gene	gene with protein product							Standard	NM_001159279		Approved	FLJ46189	uc011kdi.1	A6NP11	OTTHUMG00000156689	Exception_encountered	chr7.hg19:g.57522850_57522851delinsTT	ENSP00000394248:p.Asn80Phe	41.0	0.0		34.0	9.0	NM_001159279		Missense_Mutation	SNP	ENST00000420713.1	hg19	CCDS55112.1																																																																																			.	.		0.406	ZNF716-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345309.1	NM_001159279	
ZNF273	10793	hgsc.bcm.edu	37	7	64389279	64389279	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:64389279C>T	ENST00000476120.1	+	4	1644	c.1573C>T	c.(1573-1575)Cgg>Tgg	p.R525W	ZNF273_ENST00000527278.1_3'UTR|ZNF273_ENST00000319636.5_Missense_Mutation_p.R460W	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	525					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				AGCTTTTAACCGGTCCTCAAA	0.388																																					p.R525W	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)	Atlas-SNP	.											.	ZNF273	45	.	0			c.C1573T						.						60.0	66.0	64.0					7																	64389279		2203	4300	6503	SO:0001583	missense	10793	exon4			TTTAACCGGTCCT	X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"""Zinc fingers, C2H2-type"", ""-"""	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.1573C>T	chr7.hg19:g.64389279C>T	ENSP00000418719:p.Arg525Trp	113.0	0.0		127.0	6.0	NM_021148	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	hg19	CCDS5528.2	.	.	.	.	.	.	.	.	.	.	.	8.866	0.948193	0.18356	.	.	ENSG00000198039	ENST00000476120;ENST00000319636	T;T	0.36520	1.25;1.25	1.16	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25082	0.0609	L	0.48642	1.525	0.09310	N	1	B	0.27316	0.175	B	0.20384	0.029	T	0.19745	-1.0296	9	0.26408	T	0.33	.	4.1332	0.10159	0.401:0.599:0.0:0.0	.	525	Q14593	ZN273_HUMAN	W	525;460	ENSP00000418719:R525W;ENSP00000324518:R460W	ENSP00000324518:R460W	R	+	1	2	ZNF273	64026714	0.000000	0.05858	0.771000	0.31576	0.771000	0.43674	-0.164000	0.09983	0.202000	0.20498	0.205000	0.17691	CGG	.	.		0.388	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1		
ZNF92	168374	hgsc.bcm.edu	37	7	64864692	64864692	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:64864692T>C	ENST00000328747.7	+	4	1864	c.1665T>C	c.(1663-1665)caT>caC	p.H555H	ZNF92_ENST00000357512.2_Silent_p.H523H|ZNF92_ENST00000431504.1_Silent_p.H479H|ZNF92_ENST00000450302.2_Silent_p.H486H	NM_152626.2	NP_689839.1	Q03936	ZNF92_HUMAN	zinc finger protein 92	555					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)			breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				TTATTACACATCAGATAATTT	0.348																																					p.H555H		Atlas-SNP	.											.	ZNF92	68	.	0			c.T1665C						.						42.0	49.0	47.0					7																	64864692		2203	4298	6501	SO:0001819	synonymous_variant	168374	exon4			TACACATCAGATA	M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757		"""Zinc fingers, C2H2-type"", ""-"""	13168	protein-coding gene	gene with protein product		603974	"""zinc finger protein 92 (HTF12)"""			8467795	Standard	NM_001287533		Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000328747.7:c.1665T>C	chr7.hg19:g.64864692T>C		106.0	0.0		82.0	4.0	NM_152626	A6NNF9|Q8N492|Q8NB35	Silent	SNP	ENST00000328747.7	hg19	CCDS34646.1																																																																																			.	.		0.348	ZNF92-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344589.2	NM_152626	
HIP1	3092	hgsc.bcm.edu	37	7	75184733	75184733	+	Silent	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:75184733G>A	ENST00000336926.6	-	19	1976	c.1950C>T	c.(1948-1950)tgC>tgT	p.C650C	HIP1_ENST00000434438.2_Silent_p.C650C	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	650					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						CAGACCCAGCGCAGCTGATGA	0.542			T	PDGFRB	CMML																																p.C650C		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	HIP1,NS,carcinoma,0,1	HIP1	91	.	0			c.C1950T						.						87.0	70.0	76.0					7																	75184733		2203	4300	6503	SO:0001819	synonymous_variant	3092	exon19			CCCAGCGCAGCTG	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.1950C>T	chr7.hg19:g.75184733G>A		146.0	0.0		100.0	4.0	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	hg19	CCDS34669.1																																																																																			.	.		0.542	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338	
CCDC146	57639	hgsc.bcm.edu	37	7	76883831	76883831	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:76883831A>G	ENST00000285871.4	+	5	585	c.458A>G	c.(457-459)gAa>gGa	p.E153G	AC073635.5_ENST00000476561.2_RNA|CCDC146_ENST00000431197.1_5'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	153										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				AGCTTAAAGGAAGAAAAAATC	0.294																																					p.E153G		Atlas-SNP	.											.	CCDC146	87	.	0			c.A458G						.						46.0	49.0	48.0					7																	76883831		2200	4295	6495	SO:0001583	missense	57639	exon5			TAAAGGAAGAAAA	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.458A>G	chr7.hg19:g.76883831A>G	ENSP00000285871:p.Glu153Gly	52.0	0.0		40.0	4.0	NM_020879	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	hg19	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	A	17.55	3.417321	0.62622	.	.	ENSG00000135205	ENST00000415750;ENST00000285871	D	0.83914	-1.78	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.90359	0.6983	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90074	0.4165	10	0.41790	T	0.15	-21.6388	13.899	0.63790	1.0:0.0:0.0:0.0	.	153	Q8IYE0	CC146_HUMAN	G	153	ENSP00000285871:E153G	ENSP00000285871:E153G	E	+	2	0	AC007000.1	76721767	1.000000	0.71417	0.997000	0.53966	0.522000	0.34438	5.832000	0.69337	2.227000	0.72691	0.455000	0.32223	GAA	.	.		0.294	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
AKAP9	10142	hgsc.bcm.edu	37	7	91706167	91706167	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:91706167A>G	ENST00000359028.2	+	30	6873		c.e30-1		AKAP9_ENST00000356239.3_Splice_Site|AKAP9_ENST00000358100.2_Splice_Site			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9						G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TTGTTATTAAAGATTACAAAC	0.254			T	BRAF	papillary thyroid																																.		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.6613-2A>G						.						20.0	20.0	20.0					7																	91706167		2150	4238	6388	SO:0001630	splice_region_variant	10142	exon29			TATTAAAGATTAC	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.6649-1A>G	chr7.hg19:g.91706167A>G		171.0	0.0		121.0	5.0	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Splice_Site	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	A	20.5	4.005307	0.74932	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0786	0.80985	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AKAP9	91544103	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	7.422000	0.80217	2.254000	0.74563	0.460000	0.39030	.	.	.		0.254	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	Intron
COL1A2	1278	hgsc.bcm.edu	37	7	94057035	94057035	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:94057035C>A	ENST00000297268.6	+	49	3835	c.3364C>A	c.(3364-3366)Cct>Act	p.P1122T		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1122				Missing (in Ref. 17; CAA23761). {ECO:0000305}.	blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GGCTGACCAGCCTCGCTCAGC	0.557										HNSCC(75;0.22)																											p.P1122T		Atlas-SNP	.											.	COL1A2	240	.	0			c.C3364A						.						100.0	99.0	99.0					7																	94057035		2203	4300	6503	SO:0001583	missense	1278	exon49			GACCAGCCTCGCT	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3364C>A	chr7.hg19:g.94057035C>A	ENSP00000297268:p.Pro1122Thr	86.0	0.0		95.0	4.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.848173	0.51164	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.89485	-2.52	5.71	5.71	0.89125	.	0.055529	0.64402	D	0.000001	D	0.92338	0.7569	L	0.55103	1.725	0.38795	D	0.955079	D	0.89917	1.0	D	0.80764	0.994	D	0.89134	0.3512	10	0.15499	T	0.54	.	17.7362	0.88394	0.0:1.0:0.0:0.0	.	1122	P08123	CO1A2_HUMAN	T	1122;1123	ENSP00000297268:P1122T	ENSP00000297268:P1122T	P	+	1	0	COL1A2	93894971	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.698000	0.54771	2.873000	0.98535	0.561000	0.74099	CCT	.	.		0.557	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
TRRAP	8295	hgsc.bcm.edu	37	7	98609873	98609873	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:98609873C>T	ENST00000359863.4	+	72	11684	c.11475C>T	c.(11473-11475)ctC>ctT	p.L3825L	AC004893.11_ENST00000360902.1_RNA|TRRAP_ENST00000355540.3_Silent_p.L3796L|TRRAP_ENST00000446306.3_Silent_p.L3814L	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	3825	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TGCACAACCTCGCCCAGTTCG	0.652																																					p.L3825L		Atlas-SNP	.											.	TRRAP	863	.	0			c.C11475T						.						53.0	48.0	50.0					7																	98609873		2203	4300	6503	SO:0001819	synonymous_variant	8295	exon72			CAACCTCGCCCAG	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.11475C>T	chr7.hg19:g.98609873C>T		81.0	0.0		63.0	12.0	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	hg19	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	C	9.306	1.054218	0.19907	.	.	ENSG00000196367	ENST00000456197	.	.	.	5.16	-4.29	0.03721	.	.	.	.	.	T	0.53769	0.1817	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53809	-0.8386	4	.	.	.	.	10.3402	0.43873	0.0:0.2236:0.3968:0.3796	.	.	.	.	L	3554	.	.	S	+	2	0	TRRAP	98447809	0.022000	0.18835	0.967000	0.41034	0.993000	0.82548	-0.981000	0.03766	-0.770000	0.04614	-0.345000	0.07892	TCG	.	.		0.652	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
STAG3	10734	hgsc.bcm.edu	37	7	99800175	99800175	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:99800175A>G	ENST00000426455.1	+	25	3069	c.2662A>G	c.(2662-2664)Atg>Gtg	p.M888V	STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000543273.1_RNA|STAG3_ENST00000394018.2_Missense_Mutation_p.M830V|STAG3_ENST00000317296.5_Missense_Mutation_p.M888V|GATS_ENST00000436886.2_3'UTR	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	888					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGTGCTGGAGATGGATGCAGC	0.517																																					p.M888V		Atlas-SNP	.											.	STAG3	121	.	0			c.A2662G						.						163.0	170.0	168.0					7																	99800175		2203	4300	6503	SO:0001583	missense	10734	exon25			CTGGAGATGGATG	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.2662A>G	chr7.hg19:g.99800175A>G	ENSP00000400359:p.Met888Val	88.0	0.0		57.0	4.0	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	hg19	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	.	13.88	2.369405	0.42003	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000317296	T;T;T	0.20738	2.05;2.05;2.05	5.18	2.92	0.33932	.	0.343528	0.25143	N	0.032816	T	0.18383	0.0441	L	0.53561	1.675	0.80722	D	1	B;B;B	0.14438	0.001;0.01;0.004	B;B;B	0.12156	0.007;0.004;0.005	T	0.04509	-1.0946	10	0.45353	T	0.12	-8.28	6.2811	0.21007	0.6573:0.2074:0.0:0.1354	.	830;888;888	B4DZ10;D6W5U7;Q9UJ98	.;.;STAG3_HUMAN	V	888;830;888	ENSP00000400359:M888V;ENSP00000377586:M830V;ENSP00000319318:M888V	ENSP00000319318:M888V	M	+	1	0	STAG3	99638111	0.487000	0.25988	0.982000	0.44146	0.953000	0.61014	0.453000	0.21811	0.495000	0.27882	0.460000	0.39030	ATG	.	.		0.517	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447	
CUX1	1523	hgsc.bcm.edu	37	7	101839938	101839938	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:101839938A>G	ENST00000292535.7	+	15	1285	c.1247A>G	c.(1246-1248)gAc>gGc	p.D416G	CUX1_ENST00000560541.1_Intron|CUX1_ENST00000546411.2_Intron|CUX1_ENST00000425244.2_Intron|SNORA48_ENST00000517015.1_RNA|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000549414.2_Missense_Mutation_p.D416G|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000360264.3_Missense_Mutation_p.D427G|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000556210.1_Intron|CUX1_ENST00000550008.2_Missense_Mutation_p.D416G|CUX1_ENST00000437600.4_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	416					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						AAAGGGAAAGACCAGCCTGAA	0.542																																					p.D427G		Atlas-SNP	.											.	CUX1	253	.	0			c.A1280G						.						38.0	48.0	44.0					7																	101839938		2198	4297	6495	SO:0001583	missense	1523	exon15			GGAAAGACCAGCC	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.1247A>G	chr7.hg19:g.101839938A>G	ENSP00000292535:p.Asp416Gly	132.0	0.0		96.0	4.0	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	A	19.90	3.913591	0.72983	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008	T;T;T;T	0.61274	0.12;0.14;0.13;0.17	5.78	5.78	0.91487	.	0.057469	0.64402	D	0.000002	T	0.61726	0.2370	N	0.16743	0.435	0.80722	D	1	D;D	0.69078	0.996;0.997	P;D	0.66196	0.877;0.942	T	0.67810	-0.5574	10	0.72032	D	0.01	-29.1043	16.1054	0.81216	1.0:0.0:0.0:0.0	.	416;427	P39880;P39880-3	CUX1_HUMAN;.	G	427;416;416;416	ENSP00000353401:D427G;ENSP00000292535:D416G;ENSP00000446630:D416G;ENSP00000447373:D416G	ENSP00000292535:D416G	D	+	2	0	CUX1	101626658	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.521000	0.90569	2.198000	0.70561	0.459000	0.35465	GAC	.	.		0.542	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913	
CFTR	1080	hgsc.bcm.edu	37	7	117232660	117232660	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:117232660T>C	ENST00000003084.6	+	14	2571	c.2439T>C	c.(2437-2439)tcT>tcC	p.S813S	CFTR_ENST00000454343.1_Silent_p.S752S	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	813					cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	GAAGGTTATCTCAAGAAACTG	0.418									Cystic Fibrosis																												p.S813S		Atlas-SNP	.											.	CFTR	171	.	0			c.T2439C						.						56.0	57.0	57.0					7																	117232660		2203	4300	6503	SO:0001819	synonymous_variant	1080	exon14	Familial Cancer Database	CF	GTTATCTCAAGAA	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"""Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators"", ""ATP binding cassette transporters / subfamily C"""	1884	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family C, member 7"""	602421	"""cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"""	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.2439T>C	chr7.hg19:g.117232660T>C		83.0	0.0		61.0	4.0	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Silent	SNP	ENST00000003084.6	hg19	CCDS5773.1																																																																																			.	.		0.418	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121652375	121652375	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:121652375T>C	ENST00000393386.2	+	12	3686	c.3275T>C	c.(3274-3276)aTt>aCt	p.I1092T	PTPRZ1_ENST00000483028.1_Intron|PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1092					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						TCTGTTTCCATTTCTAGCACC	0.388																																					p.I1092T		Atlas-SNP	.											PTPRZ1_ENST00000393386,NS,carcinoma,0,2	PTPRZ1	605	.	0			c.T3275C						.						114.0	113.0	113.0					7																	121652375		2203	4300	6503	SO:0001583	missense	5803	exon12			TTTCCATTTCTAG	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.3275T>C	chr7.hg19:g.121652375T>C	ENSP00000377047:p.Ile1092Thr	139.0	0.0		92.0	4.0	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	T	7.681	0.689039	0.14973	.	.	ENSG00000106278	ENST00000393386	T	0.44881	0.91	5.32	-2.34	0.06704	.	1.440510	0.03998	N	0.296006	T	0.20981	0.0505	N	0.08118	0	0.20074	N	0.999934	B	0.02656	0.0	B	0.04013	0.001	T	0.15407	-1.0438	10	0.41790	T	0.15	.	3.5483	0.07836	0.1308:0.0764:0.4062:0.3866	.	1092	P23471	PTPRZ_HUMAN	T	1092	ENSP00000377047:I1092T	ENSP00000377047:I1092T	I	+	2	0	PTPRZ1	121439611	0.277000	0.24220	0.022000	0.16811	0.981000	0.71138	0.486000	0.22340	-0.270000	0.09285	0.454000	0.30748	ATT	.	.		0.388	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
RNF148	378925	hgsc.bcm.edu	37	7	122342235	122342235	+	Silent	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:122342235G>A	ENST00000434824.1	-	1	786	c.570C>T	c.(568-570)taC>taT	p.Y190Y	CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000313070.7_Intron|RNF148_ENST00000447240.1_Intron	NM_198085.1	NP_932351.1	Q8N7C7	RN148_HUMAN	ring finger protein 148	190						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|lung(7)	16						GATACATGATGTAATGGCTCA	0.443																																					p.Y190Y		Atlas-SNP	.											.	RNF148	71	.	0			c.C570T						.						193.0	191.0	192.0					7																	122342235		2056	4213	6269	SO:0001819	synonymous_variant	378925	exon1			CATGATGTAATGG	BC029264	CCDS47692.1	7q31.33	2013-01-09			ENSG00000235631	ENSG00000235631		"""RING-type (C3HC4) zinc fingers"""	22411	protein-coding gene	gene with protein product						8744354	Standard	NM_198085		Approved	MGC35222	uc003vkk.1	Q8N7C7	OTTHUMG00000157099	ENST00000434824.1:c.570C>T	chr7.hg19:g.122342235G>A		97.0	0.0		84.0	4.0	NM_198085	A4D0X4|Q8N308	Silent	SNP	ENST00000434824.1	hg19	CCDS47692.1																																																																																			.	.		0.443	RNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347424.1	NM_198085	
CREB3L2	64764	hgsc.bcm.edu	37	7	137567210	137567210	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:137567210A>G	ENST00000330387.6	-	11	1786	c.1435T>C	c.(1435-1437)Tcg>Ccg	p.S479P		NM_194071.3	NP_919047.2	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like 2	479					cartilage development (GO:0051216)|chondrocyte differentiation (GO:0002062)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of transcription, DNA-templated (GO:0045893)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cAMP response element binding (GO:0035497)|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)|transcription regulatory region DNA binding (GO:0044212)		FUS/CREB3L2(158)	breast(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						GTCTCATTCGAGATAATGAAA	0.577			T	FUS	fibromyxoid sarcoma																																p.S479P		Atlas-SNP	.		Dom	yes		7	7q34	64764	cAMP responsive element binding protein 3-like 2		M	.	CREB3L2	62	.	0			c.T1435C						.						81.0	75.0	77.0					7																	137567210		2203	4300	6503	SO:0001583	missense	64764	exon11			CATTCGAGATAAT	AJ549092	CCDS34760.1, CCDS59083.1	7q34	2013-01-10			ENSG00000182158	ENSG00000182158		"""basic leucine zipper proteins"""	23720	protein-coding gene	gene with protein product		608834					Standard	NM_194071		Approved	BBF2H7, TCAG_1951439	uc003vtw.3	Q70SY1	OTTHUMG00000155744	ENST00000330387.6:c.1435T>C	chr7.hg19:g.137567210A>G	ENSP00000329140:p.Ser479Pro	115.0	0.0		122.0	5.0	NM_194071	Q6P454|Q6ZMR6	Missense_Mutation	SNP	ENST00000330387.6	hg19	CCDS34760.1	.	.	.	.	.	.	.	.	.	.	A	16.82	3.229194	0.58777	.	.	ENSG00000182158	ENST00000330387	T	0.59772	0.24	5.59	1.58	0.23477	.	0.683518	0.14898	N	0.291978	T	0.41971	0.1182	L	0.36672	1.1	0.80722	D	1	P	0.38978	0.652	B	0.35813	0.211	T	0.14309	-1.0477	10	0.37606	T	0.19	-16.7484	7.5023	0.27524	0.4328:0.4449:0.0:0.1223	.	479	Q70SY1	CR3L2_HUMAN	P	479	ENSP00000329140:S479P	ENSP00000329140:S479P	S	-	1	0	CREB3L2	137217750	1.000000	0.71417	0.298000	0.25002	0.996000	0.88848	1.881000	0.39638	0.373000	0.24621	0.454000	0.30748	TCG	.	.		0.577	CREB3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341462.1	NM_194071	
OR9A4	130075	hgsc.bcm.edu	37	7	141619595	141619595	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:141619595G>T	ENST00000548136.1	+	1	979	c.920G>T	c.(919-921)cGc>cTc	p.R307L	MGAM_ENST00000497554.1_Intron	NM_001001656.1	NP_001001656.1	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A, member 4	307						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|large_intestine(9)|lung(7)|prostate(1)|skin(2)	22	Melanoma(164;0.0171)					GGGGTGAAACGCTGCTGTCAA	0.428																																					p.R307L		Atlas-SNP	.											.	OR9A4	58	.	0			c.G920T						.						93.0	94.0	94.0					7																	141619595		2045	4228	6273	SO:0001583	missense	130075	exon1			TGAAACGCTGCTG		CCDS43661.1	7q34	2012-10-03			ENSG00000258083	ENSG00000258083		"""GPCR / Class A : Olfactory receptors"""	15095	protein-coding gene	gene with protein product							Standard	NM_001001656		Approved		uc003vwu.1	Q8NGU2	OTTHUMG00000158370	ENST00000548136.1:c.920G>T	chr7.hg19:g.141619595G>T	ENSP00000448789:p.Arg307Leu	69.0	0.0		61.0	24.0	NM_001001656	B9EGV6|Q6IFI4	Missense_Mutation	SNP	ENST00000548136.1	hg19	CCDS43661.1	.	.	.	.	.	.	.	.	.	.	G	11.35	1.612135	0.28712	.	.	ENSG00000258083	ENST00000548136	T	0.38560	1.13	3.71	-2.07	0.07276	.	.	.	.	.	T	0.34221	0.0890	L	0.42008	1.315	0.09310	N	1	B	0.19200	0.034	B	0.22601	0.04	T	0.40572	-0.9556	9	0.87932	D	0	-0.0715	10.694	0.45888	0.2205:0.0:0.7795:0.0	.	307	Q8NGU2	OR9A4_HUMAN	L	307	ENSP00000448789:R307L	ENSP00000386148:R307L	R	+	2	0	OR9A4	141266064	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.804000	0.04535	-0.394000	0.07727	-0.423000	0.05987	CGC	.	.		0.428	OR9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350806.3	NM_001001656	
FAM131B	9715	hgsc.bcm.edu	37	7	143054115	143054115	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:143054115T>C	ENST00000409408.1	-	6	2235	c.527A>G	c.(526-528)gAt>gGt	p.D176G	FAM131B_ENST00000409222.3_Splice_Site_p.D176G|FAM131B_ENST00000409578.1_Splice_Site_p.D192G|FAM131B_ENST00000409346.1_Splice_Site_p.D176G|FAM131B_ENST00000443739.2_Splice_Site_p.D204G			Q86XD5	F131B_HUMAN	family with sequence similarity 131, member B	176										breast(1)|endometrium(4)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24	Melanoma(164;0.205)					AGCCAGGGCATCTGGAAAAAG	0.542																																					p.D204G		Atlas-SNP	.											.	FAM131B	104	.	0			c.A611G						.						35.0	31.0	33.0					7																	143054115		2203	4300	6503	SO:0001630	splice_region_variant	9715	exon7			AGGGCATCTGGAA	BC045611	CCDS5882.1, CCDS47734.1	7q34	2007-03-20			ENSG00000159784	ENSG00000159784			22202	protein-coding gene	gene with protein product							Standard	NM_014690		Approved	KIAA0773	uc010lpa.3	Q86XD5	OTTHUMG00000152697	ENST00000409408.1:c.527-1A>G	chr7.hg19:g.143054115T>C		74.0	0.0		74.0	4.0	NM_001031690	A4D2H6|A6NDW3|A8K605|B8ZZN2|D3DXE3|J3KQX2|Q7L0D6|Q86T97	Missense_Mutation	SNP	ENST00000409408.1	hg19	CCDS5882.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.197677	0.58126	.	.	ENSG00000159784	ENST00000443739;ENST00000409578;ENST00000409346;ENST00000452076;ENST00000409408;ENST00000409222	T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87	5.46	5.46	0.80206	.	0.199172	0.53938	D	0.000058	T	0.33059	0.0850	L	0.59436	1.845	0.52099	D	0.999945	B;P	0.45531	0.16;0.86	B;P	0.44561	0.117;0.453	T	0.12400	-1.0549	10	0.66056	D	0.02	.	15.5417	0.76057	0.0:0.0:0.0:1.0	.	192;176	Q86XD5-2;Q86XD5	.;F131B_HUMAN	G	204;192;176;180;176;176	ENSP00000410603:D204G;ENSP00000386568:D192G;ENSP00000386984:D176G;ENSP00000387017:D176G;ENSP00000387147:D176G	ENSP00000387147:D176G	D	-	2	0	FAM131B	142764237	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	2.713000	0.47194	2.072000	0.62099	0.533000	0.62120	GAT	.	.		0.542	FAM131B-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328057.1	NM_014690	Missense_Mutation
ZNF777	27153	hgsc.bcm.edu	37	7	149133833	149133833	+	Missense_Mutation	SNP	C	C	T	rs375051872		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:149133833C>T	ENST00000247930.4	-	5	1495	c.1172G>A	c.(1171-1173)gGa>gAa	p.G391E		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	391	Glu-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)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			TTCCACCTGTCCCATCAGGGG	0.597																																					p.G391E		Atlas-SNP	.											.	ZNF777	63	.	0			c.G1172A						.	C	GLU/GLY	1,3871		0,1,1935	68.0	70.0	70.0		1172	5.7	1.0	7		70	1,8249		0,1,4124	no	missense	ZNF777	NM_015694.2	98	0,2,6059	TT,TC,CC		0.0121,0.0258,0.0165	possibly-damaging	391/832	149133833	2,12120	1936	4125	6061	SO:0001583	missense	27153	exon5			ACCTGTCCCATCA	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"""Zinc fingers, C2H2-type"", ""-"""	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.1172G>A	chr7.hg19:g.149133833C>T	ENSP00000247930:p.Gly391Glu	94.0	0.0		90.0	5.0	NM_015694	Q8N2R2|Q8N659	Missense_Mutation	SNP	ENST00000247930.4	hg19	CCDS43675.1	.	.	.	.	.	.	.	.	.	.	C	19.07	3.756411	0.69648	2.58E-4	1.21E-4	ENSG00000196453	ENST00000247930;ENST00000314683	T	0.05996	3.36	5.66	5.66	0.87406	.	0.000000	0.53938	D	0.000055	T	0.13286	0.0322	L	0.29908	0.895	0.35148	D	0.769547	D	0.76494	0.999	D	0.76575	0.988	T	0.25745	-1.0123	10	0.23302	T	0.38	-16.2994	12.218	0.54416	0.1701:0.8299:0.0:0.0	.	391	Q9ULD5-2	.	E	391;134	ENSP00000247930:G391E	ENSP00000247930:G391E	G	-	2	0	ZNF777	148764766	0.329000	0.24696	0.977000	0.42913	0.959000	0.62525	1.119000	0.31258	2.662000	0.90505	0.555000	0.69702	GGA	.	.		0.597	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694	
ABCF2	10061	hgsc.bcm.edu	37	7	150912710	150912710	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr7:150912710C>A	ENST00000287844.2	-	13	1619	c.1510G>T	c.(1510-1512)Ggt>Tgt	p.G504C	ABCF2_ENST00000473874.1_5'Flank|ABCF2_ENST00000222388.2_Missense_Mutation_p.G504C	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	504	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCAGTGAGACCGTATCGCCCA	0.517																																					p.G504C		Atlas-SNP	.											.	ABCF2	54	.	0			c.G1510T						.						320.0	281.0	294.0					7																	150912710		2203	4300	6503	SO:0001583	missense	10061	exon13			TGAGACCGTATCG	AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"""ATP binding cassette transporters / subfamily F"""	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.1510G>T	chr7.hg19:g.150912710C>A	ENSP00000287844:p.Gly504Cys	122.0	0.0		99.0	4.0	NM_005692	O60864|Q75MJ0|Q75MJ1|Q96TE8	Missense_Mutation	SNP	ENST00000287844.2	hg19	CCDS5923.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.314606	0.81358	.	.	ENSG00000033050	ENST00000222388;ENST00000287844	D;D	0.94931	-3.56;-3.56	5.76	5.76	0.90799	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.98526	0.9508	H	0.97918	4.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99466	1.0944	10	0.87932	D	0	-10.3108	18.9739	0.92728	0.0:1.0:0.0:0.0	.	504;504	Q9UG63;Q75MJ1	ABCF2_HUMAN;.	C	504	ENSP00000222388:G504C;ENSP00000287844:G504C	ENSP00000222388:G504C	G	-	1	0	ABCF2	150543643	1.000000	0.71417	0.945000	0.38365	0.487000	0.33371	7.237000	0.78164	2.706000	0.92434	0.655000	0.94253	GGT	.	.		0.517	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
XKR6	286046	hgsc.bcm.edu	37	8	10756400	10756400	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:10756400A>G	ENST00000416569.2	-	3	1014	c.988T>C	c.(988-990)Tcc>Ccc	p.S330P	XKR6_ENST00000304437.2_Missense_Mutation_p.S51P	NM_173683.3	NP_775954.2	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related family, member 6	330						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(8)|ovary(2)|prostate(1)|skin(3)	31				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		CAAGCCAGGGACATCAGGGAA	0.572																																					p.S330P		Atlas-SNP	.											.	XKR6	85	.	0			c.T988C						.						93.0	83.0	87.0					8																	10756400		2203	4300	6503	SO:0001583	missense	286046	exon3			CCAGGGACATCAG	BC024146	CCDS5978.2	8p23.1	2009-05-27	2006-01-12	2005-07-28	ENSG00000171044	ENSG00000171044			27806	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 7"", ""chromosome 8 open reading frame 21"", ""X Kell blood group precursor-related family, member 6"", ""chromosome 8 open reading frame 5"""	C8orf7, C8orf21, C8orf5			Standard	NM_173683		Approved		uc003wtk.1	Q5GH73	OTTHUMG00000129351	ENST00000416569.2:c.988T>C	chr8.hg19:g.10756400A>G	ENSP00000416707:p.Ser330Pro	111.0	0.0		43.0	6.0	NM_173683	Q8TBA0	Missense_Mutation	SNP	ENST00000416569.2	hg19	CCDS5978.2	.	.	.	.	.	.	.	.	.	.	A	17.65	3.441667	0.63067	.	.	ENSG00000171044	ENST00000304437;ENST00000416569	T;T	0.75367	-0.93;-0.93	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.88603	0.6481	M	0.91354	3.2	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.91037	0.4868	10	0.72032	D	0.01	-24.4852	14.297	0.66321	1.0:0.0:0.0:0.0	.	330	Q5GH73	XKR6_HUMAN	P	51;330	ENSP00000307120:S51P;ENSP00000416707:S330P	ENSP00000307120:S51P	S	-	1	0	XKR6	10793810	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	1.964000	0.57103	0.459000	0.35465	TCC	.	.		0.572	XKR6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383958.1	NM_173683	
XPO7	23039	hgsc.bcm.edu	37	8	21848326	21848326	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:21848326A>G	ENST00000252512.9	+	18	2037	c.1937A>G	c.(1936-1938)gAg>gGg	p.E646G	XPO7_ENST00000434536.1_Missense_Mutation_p.E655G|XPO7_ENST00000433566.4_Missense_Mutation_p.E647G	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	646					mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		CAATAGAGCGAGCACTTTTCA	0.423																																					p.E646G		Atlas-SNP	.											.	XPO7	79	.	0			c.A1937G						.						157.0	151.0	153.0					8																	21848326		1862	4095	5957	SO:0001583	missense	23039	exon18			AGAGCGAGCACTT	AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227		"""Exportins"""	14108	protein-coding gene	gene with protein product		606140	"""RAN binding protein 16"""	RANBP16		11024021, 9872452	Standard	NM_015024		Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.1937A>G	chr8.hg19:g.21848326A>G	ENSP00000252512:p.Glu646Gly	88.0	0.0		21.0	4.0	NM_015024	O94846|Q6PJK9|Q8NEK7	Missense_Mutation	SNP	ENST00000252512.9	hg19	CCDS47818.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.843186	0.91197	.	.	ENSG00000130227	ENST00000434536;ENST00000252512;ENST00000433566	T;T;T	0.68624	-0.34;-0.34;-0.34	5.94	5.94	0.96194	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73984	0.3657	M	0.83774	2.66	0.80722	D	1	P;P;P	0.48640	0.749;0.913;0.913	B;P;P	0.45343	0.206;0.477;0.477	T	0.78006	-0.2373	10	0.51188	T	0.08	-19.812	16.0637	0.80856	1.0:0.0:0.0:0.0	.	647;655;646	E7ESC6;E9PEN8;Q9UIA9	.;.;XPO7_HUMAN	G	655;646;647	ENSP00000404853:E655G;ENSP00000252512:E646G;ENSP00000410249:E647G	ENSP00000252512:E646G	E	+	2	0	XPO7	21904272	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.313000	0.96297	2.274000	0.75844	0.528000	0.53228	GAG	.	.		0.423	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024	
HR	55806	hgsc.bcm.edu	37	8	21984816	21984816	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:21984816T>C	ENST00000381418.4	-	3	2619	c.1139A>G	c.(1138-1140)aAg>aGg	p.K380R	HR_ENST00000312841.8_Missense_Mutation_p.K380R	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	380					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CCATGTCTTCTTCAGCTTGGT	0.662																																					p.K380R		Atlas-SNP	.											.	HR	71	.	0			c.A1139G						.						121.0	136.0	131.0					8																	21984816		2203	4300	6503	SO:0001583	missense	55806	exon3			GTCTTCTTCAGCT	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.1139A>G	chr8.hg19:g.21984816T>C	ENSP00000370826:p.Lys380Arg	156.0	0.0		75.0	4.0	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	hg19	CCDS6022.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.836857	0.91117	.	.	ENSG00000168453	ENST00000381418;ENST00000312841	D;D	0.81739	-1.53;-1.52	6.04	6.04	0.98038	.	0.000000	0.64402	D	0.000011	D	0.84479	0.5481	L	0.36672	1.1	0.34520	D	0.708092	D;D	0.71674	0.998;0.997	D;D	0.80764	0.994;0.985	D	0.88893	0.3347	10	0.59425	D	0.04	-28.9319	12.9803	0.58559	0.0:0.0:0.0:1.0	.	380;380	O43593-2;O43593	.;HAIR_HUMAN	R	380	ENSP00000370826:K380R;ENSP00000326765:K380R	ENSP00000326765:K380R	K	-	2	0	HR	22040761	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	4.925000	0.63425	2.317000	0.78254	0.460000	0.39030	AAG	.	.		0.662	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
DOCK5	80005	hgsc.bcm.edu	37	8	25191685	25191685	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:25191685A>G	ENST00000276440.7	+	21	2209	c.2165A>G	c.(2164-2166)aAg>aGg	p.K722R		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	722					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		TACATTTACAAGCACTTCAGC	0.363																																					p.K722R	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.A2165G						.						147.0	143.0	145.0					8																	25191685		2203	4300	6503	SO:0001583	missense	80005	exon21			TTTACAAGCACTT		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.2165A>G	chr8.hg19:g.25191685A>G	ENSP00000276440:p.Lys722Arg	373.0	0.0		100.0	4.0	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	hg19	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.897626	0.91962	.	.	ENSG00000147459	ENST00000276440	T	0.20463	2.07	6.04	6.04	0.98038	Armadillo-type fold (1);	0.100947	0.64402	D	0.000003	T	0.32436	0.0829	M	0.72118	2.19	0.80722	D	1	P;P;P	0.47253	0.645;0.892;0.803	B;P;B	0.44732	0.313;0.459;0.313	T	0.08452	-1.0721	10	0.59425	D	0.04	.	16.5763	0.84648	1.0:0.0:0.0:0.0	.	712;497;722	D3DSS6;Q68DL4;Q9H7D0	.;.;DOCK5_HUMAN	R	722	ENSP00000276440:K722R	ENSP00000276440:K722R	K	+	2	0	DOCK5	25247602	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.339000	0.96797	2.317000	0.78254	0.459000	0.35465	AAG	.	.		0.363	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
PPP2R2A	5520	hgsc.bcm.edu	37	8	26227714	26227714	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:26227714A>G	ENST00000380737.3	+	10	1458	c.1129A>G	c.(1129-1131)Ata>Gta	p.I377V	PPP2R2A_ENST00000315985.7_Missense_Mutation_p.I387V	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	377					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		AAAGCGAGACATAACCCTAGA	0.413																																					p.I387V		Atlas-SNP	.											.	PPP2R2A	44	.	0			c.A1159G						.						80.0	75.0	77.0					8																	26227714		2203	4300	6503	SO:0001583	missense	5520	exon10			CGAGACATAACCC	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9304	protein-coding gene	gene with protein product	"""PP2A subunit B isoform alpha"""	604941	"""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"""			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.1129A>G	chr8.hg19:g.26227714A>G	ENSP00000370113:p.Ile377Val	200.0	0.0		108.0	5.0	NM_001177591	B2RBU8|B4E1T7|P50409|Q00007	Missense_Mutation	SNP	ENST00000380737.3	hg19	CCDS34867.1	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.634009	0.00806	.	.	ENSG00000221914	ENST00000380737;ENST00000524169;ENST00000315985	T;T;T	0.39592	1.65;1.07;1.65	5.25	5.25	0.73442	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.147313	0.44097	U	0.000491	T	0.18467	0.0443	N	0.02685	-0.53	0.38222	D	0.940789	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.16305	-1.0407	10	0.02654	T	1	-20.2723	15.6084	0.76692	1.0:0.0:0.0:0.0	.	387;377;378	B4E1T7;P63151;Q6ZP32	.;2ABA_HUMAN;.	V	377;156;387	ENSP00000370113:I377V;ENSP00000430320:I156V;ENSP00000325074:I387V	ENSP00000325074:I387V	I	+	1	0	PPP2R2A	26283631	0.932000	0.31603	1.000000	0.80357	0.997000	0.91878	1.432000	0.34936	2.326000	0.78906	0.533000	0.62120	ATA	.	.		0.413	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717	
ELP3	55140	hgsc.bcm.edu	37	8	28016144	28016144	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:28016144A>G	ENST00000256398.8	+	12	1628	c.1251A>G	c.(1249-1251)ccA>ccG	p.P417P	ELP3_ENST00000524103.1_Silent_p.P345P|ELP3_ENST00000537665.1_Silent_p.P298P|ELP3_ENST00000380353.4_Silent_p.P325P|ELP3_ENST00000521015.1_Silent_p.P403P|ELP3_ENST00000542181.1_Silent_p.P288P	NM_001284220.1|NM_001284226.1|NM_018091.5	NP_001271149.1|NP_001271155.1|NP_060561.3	Q9H9T3	ELP3_HUMAN	elongator acetyltransferase complex subunit 3	417	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	histone acetyltransferase activity (GO:0004402)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|phosphorylase kinase regulator activity (GO:0008607)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		AAGTACGGCCATACCAGGTTA	0.493																																					p.P417P		Atlas-SNP	.											.	ELP3	36	.	0			c.A1251G						.						115.0	99.0	105.0					8																	28016144		2203	4300	6503	SO:0001819	synonymous_variant	55140	exon12			ACGGCCATACCAG		CCDS6065.1, CCDS64860.1, CCDS64861.1, CCDS75717.1, CCDS75718.1	8p21.1	2012-08-14	2012-08-08		ENSG00000134014	ENSG00000134014		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Elongator acetyltransferase complex subunits"""	20696	protein-coding gene	gene with protein product		612722	"""elongation protein 3 homolog (S. cerevisiae)"""			11714725	Standard	NM_018091		Approved	FLJ10422, KAT9	uc003xgo.4	Q9H9T3	OTTHUMG00000102124	ENST00000256398.8:c.1251A>G	chr8.hg19:g.28016144A>G		147.0	0.0		44.0	4.0	NM_018091	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Silent	SNP	ENST00000256398.8	hg19	CCDS6065.1																																																																																			.	.		0.493	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091	
HMBOX1	79618	hgsc.bcm.edu	37	8	28904937	28904937	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:28904937A>G	ENST00000397358.3	+	9	1701	c.997A>G	c.(997-999)Aga>Gga	p.R333G	HMBOX1_ENST00000558662.1_Missense_Mutation_p.R333G|HMBOX1_ENST00000287701.10_Missense_Mutation_p.R333G|RNA5SP260_ENST00000363849.1_RNA|HMBOX1_ENST00000524238.1_Missense_Mutation_p.R333G|HMBOX1_ENST00000519047.1_Missense_Mutation_p.R333G|HMBOX1_ENST00000355231.5_Missense_Mutation_p.R333G|HMBOX1_ENST00000523613.1_Missense_Mutation_p.R333G|HMBOX1_ENST00000517386.1_3'UTR|HMBOX1_ENST00000444075.1_Missense_Mutation_p.R333G	NM_024567.3	NP_078843.2	Q6NT76	HMBX1_HUMAN	homeobox containing 1	333					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)	DNA binding (GO:0003677)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	11		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)		GTTTGCTAACAGAAGGAAGGA	0.368																																					p.R333G		Atlas-SNP	.											HMBOX1,NS,carcinoma,0,1	HMBOX1	34	.	0			c.A997G						.						109.0	109.0	109.0					8																	28904937		2203	4300	6503	SO:0001583	missense	79618	exon9			GCTAACAGAAGGA	AY522342	CCDS6071.1	8p12	2013-05-23			ENSG00000147421	ENSG00000147421		"""Homeoboxes / HNF class"""	26137	protein-coding gene	gene with protein product	"""homeobox telomere-binding protein 1"""					16825764	Standard	NM_024567		Approved	HNF1LA, PBHNF, FLJ21616, HOT1	uc003xhd.4	Q6NT76	OTTHUMG00000172138	ENST00000397358.3:c.997A>G	chr8.hg19:g.28904937A>G	ENSP00000380516:p.Arg333Gly	142.0	0.0		69.0	3.0	NM_024567	A4K385|A8K3R8|B4DHY5|D3DSU0|Q3Y6P1|Q96GS5|Q9H701	Missense_Mutation	SNP	ENST00000397358.3	hg19	CCDS6071.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.043030	0.75732	.	.	ENSG00000147421	ENST00000287701;ENST00000444075;ENST00000519047;ENST00000397358;ENST00000524238;ENST00000517340;ENST00000355231	D;D;D;D;D	0.97529	-4.42;-4.42;-4.42;-4.42;-4.42	5.06	3.88	0.44766	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.98820	0.9602	H	0.96720	3.87	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.991;1.0	D;D;D;D;D;D	0.91635	0.998;0.999;0.997;0.998;0.987;0.998	D	0.98440	1.0586	10	0.42905	T	0.14	.	11.6787	0.51444	0.846:0.154:0.0:0.0	.	333;333;333;333;333;333	Q6NT76-5;D3DSU2;Q6NT76-2;Q6NT76-3;Q6NT76;E5RGZ2	.;.;.;.;HMBX1_HUMAN;.	G	333	ENSP00000287701:R333G;ENSP00000401769:R333G;ENSP00000430059:R333G;ENSP00000380516:R333G;ENSP00000430110:R333G	ENSP00000287701:R333G	R	+	1	2	HMBOX1	28960856	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.183000	0.50918	0.755000	0.32990	0.477000	0.44152	AGA	.	.		0.368	HMBOX1-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255267.4	NM_024567	
MBOAT4	619373	hgsc.bcm.edu	37	8	29989847	29989847	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:29989847T>C	ENST00000320542.3	-	3	1004	c.920A>G	c.(919-921)aAc>aGc	p.N307S	LEPROTL1_ENST00000523116.1_Intron|LEPROTL1_ENST00000442880.2_Intron	NM_001100916.1	NP_001094386.1	Q96T53	MBOA4_HUMAN	membrane bound O-acyltransferase domain containing 4	307					cellular protein metabolic process (GO:0044267)|peptidyl-serine octanoylation (GO:0018191)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	serine O-acyltransferase activity (GO:0016412)			endometrium(1)	1						TGTGCTTTGGTTCCACTTTCT	0.552																																					p.N307S		Atlas-SNP	.											.	MBOAT4	31	.	0			c.A920G						.						174.0	154.0	160.0					8																	29989847		692	1591	2283	SO:0001583	missense	619373	exon3			CTTTGGTTCCACT	AF359269	CCDS47835.1	8p12	2008-08-04	2006-06-29	2006-06-29	ENSG00000177669	ENSG00000177669			32311	protein-coding gene	gene with protein product	"""ghrelin O-acyltransferase"""	611940	"""O-acyltransferase (membrane bound) domain containing 4"""	OACT4		18443287	Standard	NM_001100916		Approved	FKSG89, GOAT	uc010lvg.3	Q96T53	OTTHUMG00000163824	ENST00000320542.3:c.920A>G	chr8.hg19:g.29989847T>C	ENSP00000314196:p.Asn307Ser	263.0	0.0		100.0	4.0	NM_001100916	B1Q003	Missense_Mutation	SNP	ENST00000320542.3	hg19	CCDS47835.1	.	.	.	.	.	.	.	.	.	.	T	19.43	3.825907	0.71143	.	.	ENSG00000177669	ENST00000320542	D	0.83335	-1.71	5.16	5.16	0.70880	.	0.000000	0.64402	D	0.000001	D	0.89894	0.6847	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89947	0.4077	9	.	.	.	.	13.0026	0.58685	0.0:0.0:0.0:1.0	.	307	Q96T53	MBOA4_HUMAN	S	307	ENSP00000314196:N307S	.	N	-	2	0	MBOAT4	30109389	1.000000	0.71417	0.999000	0.59377	0.693000	0.40251	6.373000	0.73128	2.177000	0.69029	0.455000	0.32223	AAC	.	.		0.552	MBOAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375795.1		
KAT6A	7994	hgsc.bcm.edu	37	8	41791422	41791422	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:41791422T>C	ENST00000396930.3	-	18	4859	c.4316A>G	c.(4315-4317)cAt>cGt	p.H1439R	KAT6A_ENST00000265713.2_Missense_Mutation_p.H1439R|KAT6A_ENST00000406337.1_Missense_Mutation_p.H1439R	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1439					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GGCGCCCTCATGCTCACTGCT	0.502																																					p.H1439R		Atlas-SNP	.											.	.	.	.	0			c.A4316G						.						118.0	110.0	113.0					8																	41791422		2203	4300	6503	SO:0001583	missense	7994	exon18			CCCTCATGCTCAC	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.4316A>G	chr8.hg19:g.41791422T>C	ENSP00000380136:p.His1439Arg	109.0	0.0		61.0	5.0	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	T	11.87	1.767305	0.31320	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930	T;T;T	0.59083	0.29;0.29;0.29	5.96	5.96	0.96718	.	0.131092	0.53938	D	0.000054	T	0.35480	0.0933	N	0.08118	0	0.53688	D	0.999974	B	0.22414	0.069	B	0.21546	0.035	T	0.33701	-0.9858	10	0.02654	T	1	-13.3592	16.4311	0.83844	0.0:0.0:0.0:1.0	.	1439	Q92794	KAT6A_HUMAN	R	1439	ENSP00000265713:H1439R;ENSP00000385888:H1439R;ENSP00000380136:H1439R	ENSP00000265713:H1439R	H	-	2	0	KAT6A	41910579	1.000000	0.71417	0.867000	0.34043	0.502000	0.33828	5.650000	0.67944	2.277000	0.76020	0.528000	0.53228	CAT	.	.		0.502	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
KAT6A	7994	hgsc.bcm.edu	37	8	41794799	41794799	+	Missense_Mutation	SNP	T	T	A	rs201760077|rs3837198	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:41794799T>A	ENST00000396930.3	-	17	3870	c.3327A>T	c.(3325-3327)gaA>gaT	p.E1109D	KAT6A_ENST00000265713.2_Missense_Mutation_p.E1109D|KAT6A_ENST00000406337.1_Missense_Mutation_p.E1109D	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1109					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										ACTCTTCATCTTCTTCTTCAT	0.403																																					p.E1109D		Atlas-SNP	.											.	.	.	.	0			c.A3327T						.						114.0	110.0	112.0					8																	41794799		2203	4300	6503	SO:0001583	missense	7994	exon17			TTCATCTTCTTCT	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.3327A>T	chr8.hg19:g.41794799T>A	ENSP00000380136:p.Glu1109Asp	100.0	0.0		31.0	4.0	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490030	0.26686	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000418721	T;T;T	0.60299	0.2;0.2;0.2	5.41	-10.8	0.00216	.	0.572288	0.16272	N	0.221734	T	0.25975	0.0633	L	0.29908	0.895	0.24514	N	0.994196	B	0.02656	0.0	B	0.01281	0.0	T	0.29366	-1.0014	10	0.13853	T	0.58	-1.715	0.3601	0.00363	0.3421:0.1983:0.2542:0.2054	.	1109	Q92794	KAT6A_HUMAN	D	1109;1109;1109;689	ENSP00000265713:E1109D;ENSP00000385888:E1109D;ENSP00000380136:E1109D	ENSP00000265713:E1109D	E	-	3	2	KAT6A	41913956	0.002000	0.14202	0.062000	0.19696	0.839000	0.47603	-1.778000	0.01778	-3.256000	0.00203	-1.412000	0.01120	GAA	.	.		0.403	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
KCNB2	9312	hgsc.bcm.edu	37	8	73480279	73480279	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:73480279C>T	ENST00000523207.1	+	2	898	c.310C>T	c.(310-312)Cgg>Tgg	p.R104W		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	104					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.R104W(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	AAATTTCTACCGGACCGGGAA	0.463																																					p.R104W		Atlas-SNP	.											KCNB2,NS,carcinoma,0,1	KCNB2	228	.	1	Substitution - Missense(1)	lung(1)	c.C310T						.						76.0	80.0	78.0					8																	73480279		2203	4300	6503	SO:0001583	missense	9312	exon2			TTCTACCGGACCG	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.310C>T	chr8.hg19:g.73480279C>T	ENSP00000430846:p.Arg104Trp	178.0	1.0		302.0	21.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.728234	0.69074	.	.	ENSG00000182674	ENST00000523207	T	0.80824	-1.42	6.17	4.22	0.49857	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.32918	U	0.005494	D	0.91768	0.7396	H	0.96398	3.815	0.50467	D	0.999875	D	0.89917	1.0	D	0.97110	1.0	D	0.92664	0.6144	10	0.87932	D	0	.	9.3834	0.38327	0.2288:0.6924:0.0:0.0788	.	104	Q92953	KCNB2_HUMAN	W	104	ENSP00000430846:R104W	ENSP00000430846:R104W	R	+	1	2	KCNB2	73642833	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	2.559000	0.45888	1.630000	0.50440	0.655000	0.94253	CGG	.	.		0.463	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
ZFHX4	79776	hgsc.bcm.edu	37	8	77616406	77616406	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:77616406A>G	ENST00000521891.2	+	2	531	c.83A>G	c.(82-84)gAt>gGt	p.D28G	ZFHX4_ENST00000050961.6_Missense_Mutation_p.D28G|ZFHX4_ENST00000455469.2_Missense_Mutation_p.D28G|ZFHX4_ENST00000518282.1_Missense_Mutation_p.D28G|ZFHX4_ENST00000517683.1_Intron	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	28					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ACACAACTTGATAATGAGGTG	0.498										HNSCC(33;0.089)																											p.D28G		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A83G						.						60.0	61.0	61.0					8																	77616406		1995	4194	6189	SO:0001583	missense	79776	exon2			AACTTGATAATGA		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.83A>G	chr8.hg19:g.77616406A>G	ENSP00000430497:p.Asp28Gly	182.0	0.0		281.0	27.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	16.51	3.142703	0.57044	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000520307;ENST00000523885;ENST00000517585;ENST00000523809;ENST00000518282	T;T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.53	5.53	0.82687	.	0.000000	0.45867	U	0.000325	T	0.29355	0.0731	N	0.19112	0.55	0.58432	D	0.999998	D;D;D;P	0.61697	0.982;0.972;0.99;0.89	B;P;P;B	0.48840	0.388;0.453;0.592;0.419	T	0.05419	-1.0886	10	0.54805	T	0.06	.	15.827	0.78718	1.0:0.0:0.0:0.0	.	28;28;28;28	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	G	28	ENSP00000430497:D28G;ENSP00000399605:D28G;ENSP00000050961:D28G;ENSP00000428525:D28G;ENSP00000429495:D28G;ENSP00000427775:D28G;ENSP00000427739:D28G;ENSP00000430848:D28G	ENSP00000050961:D28G	D	+	2	0	ZFHX4	77778961	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.585000	0.67497	2.324000	0.78689	0.533000	0.62120	GAT	.	.		0.498	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
STMN2	11075	hgsc.bcm.edu	37	8	80553709	80553709	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:80553709T>C	ENST00000220876.7	+	3	594	c.212T>C	c.(211-213)tTa>tCa	p.L71S	STMN2_ENST00000518491.1_Missense_Mutation_p.L60S|STMN2_ENST00000518111.1_Missense_Mutation_p.L71S	NM_001199214.1|NM_007029.3	NP_001186143.1|NP_008960.2	Q93045	STMN2_HUMAN	stathmin 2	71	Regulatory/phosphorylation domain. {ECO:0000255}.|SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				cellular response to nerve growth factor stimulus (GO:1990090)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|positive regulation of microtubule depolymerization (GO:0031117)|positive regulation of neuron projection development (GO:0010976)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)			CCACGAACTTTAGCTTCTCCA	0.463																																					p.L71S		Atlas-SNP	.											.	STMN2	23	.	0			c.T212C						.						70.0	67.0	68.0					8																	80553709		1889	4123	6012	SO:0001583	missense	11075	exon3			GAACTTTAGCTTC		CCDS43748.1, CCDS56542.1	8q21.13	2014-04-01	2014-04-01	2001-07-13	ENSG00000104435	ENSG00000104435			10577	protein-coding gene	gene with protein product		600621	"""stathmin-like 2"""	SCGN10		8622778, 12140291	Standard	NM_007029		Approved	SCG10	uc022awk.1	Q93045	OTTHUMG00000164610	ENST00000220876.7:c.212T>C	chr8.hg19:g.80553709T>C	ENSP00000220876:p.Leu71Ser	122.0	0.0		246.0	35.0	NM_007029	A8K9M2|G3V110|O14952|Q6PK68	Missense_Mutation	SNP	ENST00000220876.7	hg19	CCDS43748.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.455924	0.26161	.	.	ENSG00000104435	ENST00000220876;ENST00000518111;ENST00000518491	.	.	.	5.49	5.49	0.81192	.	0.540325	0.19802	N	0.105739	T	0.54208	0.1844	L	0.27053	0.805	0.35621	D	0.809458	D;D	0.59767	0.986;0.96	P;P	0.60473	0.875;0.761	T	0.62756	-0.6787	9	0.42905	T	0.14	-3.7681	10.0198	0.42035	0.0:0.0755:0.0:0.9245	.	71;71	B7Z4K3;Q93045	.;STMN2_HUMAN	S	71;71;60	.	ENSP00000220876:L71S	L	+	2	0	STMN2	80716264	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.698000	0.84413	2.073000	0.62155	0.383000	0.25322	TTA	.	.		0.463	STMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379261.2	NM_007029	
REXO1L1P	254958	hgsc.bcm.edu	37	8	86573858	86573858	+	Silent	SNP	G	G	A	rs145542023		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:86573858G>A	ENST00000379010.2	-	1	1868	c.1869C>T	c.(1867-1869)gcC>gcT	p.A623A		NM_172239.4	NP_758439.4														endometrium(1)|lung(4)	5						CCAGGTAGTCGGCCGCGAGAT	0.637																																					p.A623A		Atlas-SNP	.											REXO1L1_ENST00000379010,NS,carcinoma,0,2	REXO1L1	28	.	0			c.C1869T						.						2.0	2.0	2.0					8																	86573858		897	2027	2924	SO:0001819	synonymous_variant	254958	exon1			GTAGTCGGCCGCG																												ENST00000379010.2:c.1869C>T	chr8.hg19:g.86573858G>A		13.0	1.0		35.0	2.0	NM_172239		Silent	SNP	ENST00000379010.2	hg19																																																																																				.	.		0.637	REXO1L1-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000381106.1		
SLC7A13	157724	hgsc.bcm.edu	37	8	87226642	87226642	+	Silent	SNP	C	C	T	rs202114931|rs56993779	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:87226642C>T	ENST00000297524.3	-	4	1516	c.1413G>A	c.(1411-1413)taG>taA	p.*471*	CTD-3118D11.3_ENST00000523112.1_RNA|SLC7A13_ENST00000419776.2_3'UTR	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	0						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						CTTCCGACATCTATTCCTCAG	0.303																																					p.X471X		Atlas-SNP	.											SLC7A13,NS,carcinoma,0,2	SLC7A13	97	.	0			c.G1413A						.						42.0	42.0	42.0					8																	87226642		2196	4256	6452	SO:0001819	synonymous_variant	157724	exon4			CGACATCTATTCC	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.1413G>A	chr8.hg19:g.87226642C>T		8.0	0.0		16.0	5.0	NM_138817	Q05C37|Q08AH9|Q96N84	Silent	SNP	ENST00000297524.3	hg19	CCDS34917.1																																																																																			.	.		0.303	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
CNBD1	168975	hgsc.bcm.edu	37	8	88218281	88218281	+	Silent	SNP	A	A	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:88218281A>C	ENST00000518476.1	+	5	543	c.492A>C	c.(490-492)ccA>ccC	p.P164P	CNBD1_ENST00000522427.1_3'UTR	NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	164										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						AAACAATTCCAGATTTAACCT	0.373																																					p.P164P		Atlas-SNP	.											.	CNBD1	206	.	0			c.A492C						.						56.0	55.0	55.0					8																	88218281		1845	4076	5921	SO:0001819	synonymous_variant	168975	exon5			AATTCCAGATTTA	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.492A>C	chr8.hg19:g.88218281A>C		63.0	0.0		113.0	5.0	NM_173538		Silent	SNP	ENST00000518476.1	hg19	CCDS55259.1																																																																																			.	.		0.373	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538	
MFSD3	113655	hgsc.bcm.edu	37	8	145737638	145737638	+	IGR	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:145737638T>C	ENST00000301327.4	+	0	1548				CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000532237.1_5'UTR|RECQL4_ENST00000428558.2_Missense_Mutation_p.D1042G	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	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)			AGCGGTCAAGTCCCCCGGGCT	0.647																																					p.D1042G		Atlas-SNP	.											.	RECQL4	75	.	0			c.A3125G						.						35.0	40.0	38.0					8																	145737638		2065	4206	6271	SO:0001628	intergenic_variant	9401	exon19			GTCAAGTCCCCCG		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177		chr8.hg19:g.145737638T>C		57.0	0.0		115.0	6.0	NM_004260		Missense_Mutation	SNP	ENST00000301327.4	hg19	CCDS6431.1																																																																																			.	.		0.647	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431	
LRRC24	441381	hgsc.bcm.edu	37	8	145748134	145748134	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr8:145748134C>T	ENST00000529415.2	-	5	1384	c.1267G>A	c.(1267-1269)Gcc>Acc	p.A423T	LRRC14_ENST00000292524.1_3'UTR|LRRC14_ENST00000528528.1_3'UTR|LRRC24_ENST00000533758.1_Missense_Mutation_p.A420T			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	423						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)			CAGATCATGGCGACCAGGAGC	0.711																																					p.A423T		Atlas-SNP	.											.	LRRC24	11	.	0			c.G1267A						.						6.0	6.0	6.0					8																	145748134		2132	4224	6356	SO:0001583	missense	441381	exon5			TCATGGCGACCAG	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.1267G>A	chr8.hg19:g.145748134C>T	ENSP00000434849:p.Ala423Thr	16.0	0.0		34.0	7.0	NM_001024678		Missense_Mutation	SNP	ENST00000529415.2	hg19	CCDS34969.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.732977	0.30684	.	.	ENSG00000254402	ENST00000529415;ENST00000533758	T;T	0.55930	0.63;0.49	4.73	1.28	0.21552	.	0.865932	0.10420	N	0.676868	T	0.36744	0.0978	N	0.24115	0.695	0.18873	N	0.999986	B;B	0.19706	0.038;0.022	B;B	0.18871	0.023;0.01	T	0.25012	-1.0144	10	0.35671	T	0.21	.	9.3443	0.38098	0.0:0.7528:0.0:0.2472	.	420;423	G3V1D8;Q50LG9	.;LRC24_HUMAN	T	423;420	ENSP00000434849:A423T;ENSP00000435653:A420T	ENSP00000434849:A423T	A	-	1	0	LRRC24	145718942	0.001000	0.12720	0.928000	0.36995	0.845000	0.48019	0.014000	0.13333	0.427000	0.26145	0.561000	0.74099	GCC	.	.		0.711	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678	
UHRF2	115426	hgsc.bcm.edu	37	9	6481676	6481676	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:6481676A>G	ENST00000276893.5	+	7	1362	c.1194A>G	c.(1192-1194)gaA>gaG	p.E398E		NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	398					cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		ATTCCAGTGAAGTTGTAAAGG	0.368																																					p.E398E		Atlas-SNP	.											.	UHRF2	50	.	0			c.A1194G						.						89.0	98.0	95.0					9																	6481676		2203	4299	6502	SO:0001819	synonymous_variant	115426	exon7			CAGTGAAGTTGTA	AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	12557	protein-coding gene	gene with protein product	"""Np95-like ring finger protein"""	615211	"""ubiquitin-like with PHD and ring finger domains 2"""			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.1194A>G	chr9.hg19:g.6481676A>G		120.0	0.0		95.0	4.0	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Silent	SNP	ENST00000276893.5	hg19	CCDS6469.1																																																																																			.	.		0.368	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306	
UHRF2	115426	hgsc.bcm.edu	37	9	6493855	6493855	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:6493855A>G	ENST00000276893.5	+	10	1695	c.1527A>G	c.(1525-1527)ggA>ggG	p.G509G	UHRF2_ENST00000485617.2_3'UTR	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	509	Methyl-CpG binding and interaction with HDAC1.|YDG. {ECO:0000255|PROSITE- ProRule:PRU00358}.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|positive regulation of cell cycle arrest (GO:0071158)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)	17		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		CATACACTGGAAGCGGTGGTA	0.363																																					p.G509G		Atlas-SNP	.											.	UHRF2	50	.	0			c.A1527G						.						88.0	80.0	83.0					9																	6493855		2203	4300	6503	SO:0001819	synonymous_variant	115426	exon10			CACTGGAAGCGGT	AF274049	CCDS6469.1	9p24.1	2013-01-28	2012-02-23		ENSG00000147854	ENSG00000147854		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	12557	protein-coding gene	gene with protein product	"""Np95-like ring finger protein"""	615211	"""ubiquitin-like with PHD and ring finger domains 2"""			12176013	Standard	NM_152896		Approved	RNF107, NIRF, URF2, MGC33463	uc003zjy.3	Q96PU4	OTTHUMG00000019521	ENST00000276893.5:c.1527A>G	chr9.hg19:g.6493855A>G		120.0	0.0		74.0	4.0	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Silent	SNP	ENST00000276893.5	hg19	CCDS6469.1																																																																																			.	.		0.363	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306	
MPDZ	8777	hgsc.bcm.edu	37	9	13188853	13188853	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:13188853T>C	ENST00000319217.7	-	17	2541	c.2294A>G	c.(2293-2295)gAg>gGg	p.E765G	MPDZ_ENST00000546205.1_Missense_Mutation_p.E765G|MPDZ_ENST00000381015.4_Missense_Mutation_p.E765G|MPDZ_ENST00000536827.1_Missense_Mutation_p.E765G|MPDZ_ENST00000381022.2_Missense_Mutation_p.E765G|MPDZ_ENST00000541718.1_Missense_Mutation_p.E765G|MPDZ_ENST00000447879.1_Missense_Mutation_p.E765G	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	765	PDZ 5. {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)		TACAGCTTCCTCAAGACTGCT	0.468																																					p.E765G		Atlas-SNP	.											.	MPDZ	324	.	0			c.A2294G						.						240.0	238.0	238.0					9																	13188853		1990	4161	6151	SO:0001583	missense	8777	exon17			GCTTCCTCAAGAC	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.2294A>G	chr9.hg19:g.13188853T>C	ENSP00000320006:p.Glu765Gly	141.0	0.0		97.0	4.0	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	hg19		.	.	.	.	.	.	.	.	.	.	T	29.4	5.005993	0.93287	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42;1.42;1.42	5.9	5.9	0.94986	.	0.000000	0.48286	D	0.000196	T	0.54029	0.1833	M	0.62209	1.925	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.53034	-0.8495	10	0.51188	T	0.08	.	16.3283	0.82996	0.0:0.0:0.0:1.0	.	765;765;765	B7ZMI4;O75970-3;O75970-2	.;.;.	G	765;765;765;765;765;765;715;765	ENSP00000320006:E765G;ENSP00000439807:E765G;ENSP00000370410:E765G;ENSP00000444151:E765G;ENSP00000415208:E765G;ENSP00000370403:E765G;ENSP00000446358:E765G	ENSP00000320006:E765G	E	-	2	0	MPDZ	13178853	1.000000	0.71417	0.988000	0.46212	0.991000	0.79684	4.784000	0.62411	2.257000	0.74773	0.533000	0.62120	GAG	.	.		0.468	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
DENND4C	55667	hgsc.bcm.edu	37	9	19350716	19350716	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:19350716A>G	ENST00000380432.2	+	19	3512	c.3479A>G	c.(3478-3480)gAc>gGc	p.D1160G	DENND4C_ENST00000602925.1_Missense_Mutation_p.D1396G|DENND4C_ENST00000434457.2_Missense_Mutation_p.D1445G			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1160					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						ACTAATAGAGACTACAGCTTC	0.393																																					p.D1396G		Atlas-SNP	.											.	DENND4C	120	.	0			c.A4187G						.						63.0	62.0	62.0					9																	19350716		2203	4300	6503	SO:0001583	missense	55667	exon23			ATAGAGACTACAG	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.3479A>G	chr9.hg19:g.19350716A>G	ENSP00000369797:p.Asp1160Gly	94.0	0.0		70.0	5.0	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	hg19		.	.	.	.	.	.	.	.	.	.	A	10.87	1.473271	0.26423	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024;ENST00000380424	T;T	0.58506	0.33;0.33	5.61	5.61	0.85477	.	0.282354	0.28338	N	0.015720	T	0.42404	0.1201	L	0.27053	0.805	0.33684	D	0.612536	B;B;B;B	0.15930	0.015;0.004;0.007;0.001	B;B;B;B	0.18871	0.023;0.006;0.016;0.002	T	0.50972	-0.8764	10	0.22706	T	0.39	-18.6985	10.1977	0.43065	0.9259:0.0:0.0741:0.0	.	490;1160;342;1160	B7Z660;Q5VZ89-5;Q5VZ89-3;Q5VZ89	.;.;.;DEN4C_HUMAN	G	1160;633;342;490;633;342;157;31	ENSP00000305795:D633G;ENSP00000443804:D490G	ENSP00000305795:D633G	D	+	2	0	DENND4C	19340716	1.000000	0.71417	1.000000	0.80357	0.711000	0.40976	3.871000	0.56077	2.125000	0.65367	0.533000	0.62120	GAC	.	.		0.393	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
TEK	7010	hgsc.bcm.edu	37	9	27213566	27213566	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:27213566G>A	ENST00000380036.4	+	18	3404	c.2962G>A	c.(2962-2964)Ggt>Agt	p.G988S	TEK_ENST00000406359.4_Missense_Mutation_p.G945S|TEK_ENST00000519097.1_Missense_Mutation_p.G840S	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	988	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	ATTGTCCCGAGGTCAAGAGGT	0.428																																					p.G988S		Atlas-SNP	.											.	TEK	250	.	0			c.G2962A						.						124.0	122.0	123.0					9																	27213566		2203	4300	6503	SO:0001583	missense	7010	exon18			TCCCGAGGTCAAG	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.2962G>A	chr9.hg19:g.27213566G>A	ENSP00000369375:p.Gly988Ser	92.0	0.0		72.0	4.0	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	hg19	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	G	35	5.585865	0.96578	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359	D;D;D	0.81739	-1.53;-1.53;-1.53	5.65	5.65	0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	D	0.000072	T	0.80199	0.4579	N	0.04636	-0.2	0.80722	D	1	D;D;D	0.89917	1.0;0.991;1.0	D;D;D	0.97110	1.0;0.97;1.0	D	0.83567	0.0110	10	0.41790	T	0.15	.	19.7221	0.96147	0.0:0.0:1.0:0.0	.	840;1021;988	E7EWI2;Q59HG2;Q02763	.;.;TIE2_HUMAN	S	840;988;945	ENSP00000430686:G840S;ENSP00000369375:G988S;ENSP00000383977:G945S	ENSP00000369375:G988S	G	+	1	0	TEK	27203566	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.679000	0.91253	0.655000	0.94253	GGT	.	.		0.428	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
C9orf72	203228	hgsc.bcm.edu	37	9	27556627	27556627	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:27556627T>C	ENST00000380003.3	-	8	1086	c.1023A>G	c.(1021-1023)agA>agG	p.R341R	C9orf72_ENST00000488117.1_5'UTR	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN	chromosome 9 open reading frame 72	341					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634)	Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		CTGAAGTGGCTCTCCAGAAGG	0.448																																					p.R341R		Atlas-SNP	.											.	C9orf72	48	.	0			c.A1023G						.						154.0	141.0	145.0					9																	27556627		2203	4300	6503	SO:0001819	synonymous_variant	203228	exon8			AGTGGCTCTCCAG	AL832467	CCDS6522.1, CCDS6523.1	9p21.1	2014-09-17			ENSG00000147894	ENSG00000147894			28337	protein-coding gene	gene with protein product		614260				21944778, 24549040	Standard	NM_145005		Approved	MGC23980	uc003zqq.3	Q96LT7	OTTHUMG00000019716	ENST00000380003.3:c.1023A>G	chr9.hg19:g.27556627T>C		208.0	0.0		119.0	5.0	NM_018325	A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Silent	SNP	ENST00000380003.3	hg19	CCDS6522.1																																																																																			.	.		0.448	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325	
GALT	2592	hgsc.bcm.edu	37	9	34649497	34649497	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:34649497T>C	ENST00000378842.3	+	10	1037	c.995T>C	c.(994-996)gTc>gCc	p.V332A	GALT_ENST00000556278.1_Intron|IL11RA_ENST00000555003.1_5'Flank|GALT_ENST00000450095.2_Missense_Mutation_p.V223A|GALT_ENST00000488412.2_3'UTR|IL11RA_ENST00000441545.2_5'Flank	NM_000155.3	NP_000146.2	P07902	GALT_HUMAN	galactose-1-phosphate uridylyltransferase	332					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|galactose metabolic process (GO:0006012)|small molecule metabolic process (GO:0044281)|UDP-glucose catabolic process (GO:0006258)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	UDP-glucose:hexose-1-phosphate uridylyltransferase activity (GO:0008108)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(2)|lung(5)|upper_aerodigestive_tract(1)	16	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		TCTGCCACTGTCCGGAAATTC	0.582									Galactosemia																												p.V332A		Atlas-SNP	.											.	GALT	29	.	0			c.T995C						.						119.0	112.0	114.0					9																	34649497		2203	4300	6503	SO:0001583	missense	2592	exon10	Familial Cancer Database	Galactose-1-Phosphate Uridyltransferase Deficiency	CCACTGTCCGGAA	M60091	CCDS6565.1, CCDS59122.1	9p13	2013-01-08			ENSG00000213930	ENSG00000213930	2.7.7.12		4135	protein-coding gene	gene with protein product		606999					Standard	NM_000155		Approved		uc003zve.4	P07902	OTTHUMG00000019836	ENST00000378842.3:c.995T>C	chr9.hg19:g.34649497T>C	ENSP00000368119:p.Val332Ala	117.0	0.0		92.0	4.0	NM_000155	B4E097|E7ET32|Q14355|Q14356|Q14357|Q14358|Q14359|Q14360|Q14361|Q14363|Q14364|Q14365|Q14369|Q14370|Q14371|Q14372|Q14373|Q14374|Q14375|Q14377|Q14378|Q14380|Q14381|Q14382|Q14383|Q14384|Q14385|Q14386|Q14387|Q14389|Q16766|Q53XK1|Q5VZ81|Q96BY1	Missense_Mutation	SNP	ENST00000378842.3	hg19	CCDS6565.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.855412	0.91355	.	.	ENSG00000213930	ENST00000450095;ENST00000378842	D;D	0.99503	-6.03;-6.03	5.2	5.2	0.72013	Histidine triad motif (1);Galactose-1-phosphate uridyl transferase, C-terminal (1);Histidine triad-like motif (1);	0.235140	0.34435	U	0.003979	D	0.99687	0.9882	H	0.96889	3.9	0.53688	D	0.999975	D;D	0.89917	1.0;1.0	D;D	0.83275	0.983;0.996	D	0.97401	0.9996	10	0.87932	D	0	-8.4733	13.888	0.63721	0.0:0.0:0.0:1.0	.	223;332	E7ET32;P07902	.;GALT_HUMAN	A	223;332	ENSP00000401956:V223A;ENSP00000368119:V332A	ENSP00000368119:V332A	V	+	2	0	GALT	34639497	0.995000	0.38212	0.993000	0.49108	0.971000	0.66376	7.562000	0.82300	1.967000	0.57214	0.454000	0.30748	GTC	.	.		0.582	GALT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052231.1	NM_000155	
IL11RA	3590	hgsc.bcm.edu	37	9	34656848	34656848	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:34656848T>C	ENST00000555003.1	+	4	1630	c.274T>C	c.(274-276)Tac>Cac	p.Y92H	IL11RA_ENST00000478802.2_3'UTR|GALT_ENST00000556278.1_Missense_Mutation_p.Y236H|IL11RA_ENST00000318041.9_Missense_Mutation_p.Y92H|IL11RA_ENST00000378817.4_Missense_Mutation_p.Y92H|IL11RA_ENST00000602473.1_Missense_Mutation_p.Y92H|IL11RA_ENST00000441545.2_Missense_Mutation_p.Y92H			Q14626	I11RA_HUMAN	interleukin 11 receptor, alpha	92	Ig-like C2-type.				developmental process (GO:0032502)|embryo implantation (GO:0007566)|head development (GO:0060322)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.174)	Oprelvekin(DB00038)	TGAGGGCACCTACATCTGCCA	0.612																																					p.Y92H		Atlas-SNP	.											.	IL11RA	34	.	0			c.T274C						.						68.0	60.0	63.0					9																	34656848		2203	4300	6503	SO:0001583	missense	3590	exon4			GGCACCTACATCT	Z38102	CCDS6567.1	9p13	2014-05-22			ENSG00000137070	ENSG00000137070		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5967	protein-coding gene	gene with protein product		600939				7670098	Standard	NM_001142784		Approved		uc011loq.3	Q14626	OTTHUMG00000019837	ENST00000555003.1:c.274T>C	chr9.hg19:g.34656848T>C	ENSP00000450565:p.Tyr92His	131.0	0.0		75.0	4.0	NM_001142784	Q16542|Q5VZ80|Q7KYJ7	Missense_Mutation	SNP	ENST00000555003.1	hg19	CCDS6567.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.936705	0.73557	.	.	ENSG00000258728;ENSG00000137070;ENSG00000137070;ENSG00000137070;ENSG00000137070;ENSG00000137070;ENSG00000137070;ENSG00000137070	ENST00000556278;ENST00000555003;ENST00000441545;ENST00000556792;ENST00000378817;ENST00000318041;ENST00000556531;ENST00000555981	T;T;T;T;T;T;D;T	0.94758	-0.08;-0.08;-0.08;-0.08;-0.08;-0.08;-3.51;-0.08	5.34	5.34	0.76211	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	D	0.95962	0.8685	L	0.58101	1.795	0.51482	D	0.999927	D	0.89917	1.0	D	0.79108	0.992	D	0.95621	0.8681	10	0.52906	T	0.07	-14.6428	11.6292	0.51164	0.0:0.0:0.0:1.0	.	92	Q14626	I11RA_HUMAN	H	236;92;92;92;92;92;92;92	ENSP00000451792:Y236H;ENSP00000450565:Y92H;ENSP00000394391:Y92H;ENSP00000450543:Y92H;ENSP00000368094:Y92H;ENSP00000326500:Y92H;ENSP00000451447:Y92H;ENSP00000450640:Y92H	ENSP00000326500:Y92H	Y	+	1	0	RP11-195F19.29;IL11RA	34646848	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.056000	0.57448	2.242000	0.73789	0.533000	0.62120	TAC	.	.		0.612	IL11RA-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410625.1	NM_001142784	
UNC13B	10497	hgsc.bcm.edu	37	9	35389938	35389938	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:35389938A>G	ENST00000378495.3	+	24	3165	c.2943A>G	c.(2941-2943)gaA>gaG	p.E981E	UNC13B_ENST00000396787.1_Silent_p.E993E|UNC13B_ENST00000378496.4_Silent_p.E981E	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	981					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			TCATAGAGGAAGATAAGAATT	0.493																																					p.E981E		Atlas-SNP	.											.	UNC13B	153	.	0			c.A2943G						.						230.0	217.0	221.0					9																	35389938		2203	4300	6503	SO:0001819	synonymous_variant	10497	exon24			AGAGGAAGATAAG	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"""unc-13-like (C. elegans)"""	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.2943A>G	chr9.hg19:g.35389938A>G		167.0	0.0		109.0	5.0	NM_006377	Q5VYM8	Silent	SNP	ENST00000378495.3	hg19	CCDS6579.1																																																																																			.	.		0.493	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	
GNE	10020	hgsc.bcm.edu	37	9	36222836	36222836	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:36222836G>A	ENST00000539815.1	-	8	1611	c.1571C>T	c.(1570-1572)gCg>gTg	p.A524V	GNE_ENST00000377902.5_Missense_Mutation_p.A524V|GNE_ENST00000539208.1_Missense_Mutation_p.A414V|GNE_ENST00000396594.3_Missense_Mutation_p.A555V|GNE_ENST00000543356.2_Missense_Mutation_p.A519V|GNE_ENST00000447283.2_Intron			Q9Y223	GLCNE_HUMAN	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	524	N-acetylmannosamine kinase.		A -> V (in IBM2). {ECO:0000269|PubMed:12409274}.		carbohydrate phosphorylation (GO:0046835)|cell adhesion (GO:0007155)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate metabolic process (GO:0006054)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|metal ion binding (GO:0046872)|N-acylmannosamine kinase activity (GO:0009384)|UDP-N-acetylglucosamine 2-epimerase activity (GO:0008761)			endometrium(8)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			STAD - Stomach adenocarcinoma(86;0.228)			TTTCCTTTCCGCCAGGGCAGC	0.512																																					p.A555V	GBM(184;106 2118 20004 35750 50727)	Atlas-SNP	.											.	GNE	141	.	0			c.C1664T	GRCh37	CM024159	GNE	M		.						153.0	150.0	151.0					9																	36222836		2203	4300	6503	SO:0001583	missense	10020	exon9			CTTTCCGCCAGGG	AF051852	CCDS6602.1, CCDS47965.1, CCDS55308.1, CCDS55309.1, CCDS55310.1	9p13.1	2008-02-05	2003-12-01		ENSG00000159921	ENSG00000159921			23657	protein-coding gene	gene with protein product		603824	"""UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase"""	IBM2		9305887, 9305888	Standard	NM_005476		Approved	Uae1	uc010mli.3	Q9Y223	OTTHUMG00000019899	ENST00000539815.1:c.1571C>T	chr9.hg19:g.36222836G>A	ENSP00000439155:p.Ala524Val	159.0	0.0		96.0	4.0	NM_001128227	A6PZH2|A6PZH3|A7UNU7|B2R6E1|B7Z372|B7Z428|D3DRP7|F5H499|H0YFA7|Q0VA94	Missense_Mutation	SNP	ENST00000539815.1	hg19	CCDS6602.1	.	.	.	.	.	.	.	.	.	.	G	34	5.334432	0.95758	.	.	ENSG00000159921	ENST00000377902;ENST00000396594;ENST00000339267;ENST00000539815;ENST00000543356;ENST00000539208	D;D;D;D	0.99232	-5.6;-5.6;-5.6;-5.6	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.99573	0.9846	H	0.94582	3.555	0.80722	D	1	D;D;D;D	0.89917	0.998;0.999;1.0;0.999	P;P;P;D	0.65773	0.856;0.898;0.898;0.938	D	0.98294	1.0515	10	0.87932	D	0	-21.442	17.9148	0.88945	0.0:0.0:1.0:0.0	.	414;483;555;524	F5H499;Q9Y223-3;Q9Y223-2;Q9Y223	.;.;.;GLCNE_HUMAN	V	524;555;519;524;496;414	ENSP00000367134:A524V;ENSP00000379839:A555V;ENSP00000439155:A524V;ENSP00000445117:A414V	ENSP00000340770:A519V	A	-	2	0	GNE	36212836	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.162000	0.94745	2.823000	0.97156	0.591000	0.81541	GCG	.	.		0.512	GNE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052412.4	NM_005476	
FBXO10	26267	hgsc.bcm.edu	37	9	37525156	37525156	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:37525156A>G	ENST00000432825.2	-	6	1768	c.1720T>C	c.(1720-1722)Ttc>Ctc	p.F574L	FBXO10_ENST00000541829.1_Missense_Mutation_p.F99L|RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000543968.1_5'UTR	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	574					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		CGGCCCTTGAAGATGTGGTTC	0.547																																					p.F574L		Atlas-SNP	.											.	FBXO10	75	.	0			c.T1720C						.						34.0	34.0	34.0					9																	37525156		1953	4142	6095	SO:0001583	missense	26267	exon6			CCTTGAAGATGTG	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"""F-boxes /  ""other"""""	13589	protein-coding gene	gene with protein product		609092	"""F-box only protein 10"""			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.1720T>C	chr9.hg19:g.37525156A>G	ENSP00000403802:p.Phe574Leu	88.0	0.0		78.0	4.0	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	hg19	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.987150	0.93106	.	.	ENSG00000147912	ENST00000432825;ENST00000541829	T;T	0.79454	-1.22;-1.27	4.96	4.96	0.65561	Pectin lyase fold/virulence factor (1);Carbohydrate-binding/sugar hydrolysis domain (1);	0.052247	0.85682	D	0.000000	D	0.83069	0.5174	M	0.68593	2.085	0.58432	D	0.999999	D;P;D	0.57257	0.979;0.507;0.972	P;B;P	0.57846	0.828;0.208;0.801	T	0.81531	-0.0890	10	0.27785	T	0.31	-21.0908	13.6457	0.62279	1.0:0.0:0.0:0.0	.	453;99;574	Q59F51;Q08AL4;Q9UK96	.;.;FBX10_HUMAN	L	574;99	ENSP00000403802:F574L;ENSP00000441307:F99L	ENSP00000403802:F574L	F	-	1	0	FBXO10	37515156	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.873000	0.92357	1.858000	0.53909	0.533000	0.62120	TTC	.	.		0.547	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3		
TJP2	9414	hgsc.bcm.edu	37	9	71845029	71845029	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:71845029G>A	ENST00000377245.4	+	11	1760	c.1552G>A	c.(1552-1554)Gga>Aga	p.G518R	TJP2_ENST00000453658.2_Missense_Mutation_p.G495R|TJP2_ENST00000535702.1_Missense_Mutation_p.G522R|TJP2_ENST00000539225.1_Missense_Mutation_p.G549R|TJP2_ENST00000265384.7_Missense_Mutation_p.G518R|TJP2_ENST00000348208.4_Missense_Mutation_p.G518R	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	518	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						GTTCAAGAAGGGAGACAGCGT	0.483																																					p.G549R		Atlas-SNP	.											.	TJP2	120	.	0			c.G1645A						.						78.0	79.0	79.0					9																	71845029		2203	4300	6503	SO:0001583	missense	9414	exon11			AAGAAGGGAGACA	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.1552G>A	chr9.hg19:g.71845029G>A	ENSP00000366453:p.Gly518Arg	123.0	0.0		80.0	4.0	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	hg19	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.749259	0.89753	.	.	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	T;T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43;0.43	5.86	5.86	0.93980	PDZ/DHR/GLGF (3);	0.000000	0.85682	D	0.000000	T	0.74245	0.3691	M	0.83774	2.66	0.80722	D	1	D;D;D;D;D	0.89917	0.977;0.989;1.0;0.999;0.997	P;D;D;D;D	0.79784	0.847;0.962;0.966;0.993;0.973	T	0.76849	-0.2807	10	0.87932	D	0	.	14.699	0.69142	0.069:0.0:0.9309:0.0	.	549;522;518;518;518	F5H301;F5H886;Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;.;.;ZO2_HUMAN;.	R	495;518;518;518;522;549	ENSP00000392178:G495R;ENSP00000366453:G518R;ENSP00000345893:G518R;ENSP00000265384:G518R;ENSP00000442090:G522R;ENSP00000438262:G549R	ENSP00000265384:G518R	G	+	1	0	TJP2	71034849	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.975000	0.88055	2.937000	0.99478	0.650000	0.86243	GGA	.	.		0.483	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
PTAR1	375743	hgsc.bcm.edu	37	9	72356709	72356709	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:72356709T>C	ENST00000340434.4	-	3	325	c.322A>G	c.(322-324)Agg>Ggg	p.R108G	PTAR1_ENST00000377200.5_Intron	NM_001099666.1	NP_001093136.1	Q7Z6K3	PTAR1_HUMAN	protein prenyltransferase alpha subunit repeat containing 1	108					protein prenylation (GO:0018342)		protein prenyltransferase activity (GO:0008318)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)	5						ATGACATACCTCACGTTCCAT	0.333																																					p.R108G		Atlas-SNP	.											.	PTAR1	46	.	0			c.A322G						.						82.0	76.0	77.0					9																	72356709		1875	4118	5993	SO:0001630	splice_region_variant	375743	exon3			CATACCTCACGTT	BC053622	CCDS47978.1	9q21.13	2008-10-01			ENSG00000188647	ENSG00000188647		"""Prenyltransferase alpha subunit repeat containing"""	30449	protein-coding gene	gene with protein product						12477932	Standard	NM_001099666		Approved		uc004ahj.4	Q7Z6K3	OTTHUMG00000019982	ENST00000340434.4:c.323+1A>G	chr9.hg19:g.72356709T>C		133.0	0.0		99.0	4.0	NM_001099666	Q5T7V5|Q5T7V6	Missense_Mutation	SNP	ENST00000340434.4	hg19	CCDS47978.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.270626	0.80469	.	.	ENSG00000188647	ENST00000340434	T	0.70749	-0.51	5.74	5.74	0.90152	Protein prenyltransferase (1);	.	.	.	.	T	0.77103	0.4081	M	0.70595	2.14	0.80722	D	1	D	0.58620	0.983	P	0.49683	0.619	T	0.80845	-0.1200	9	0.87932	D	0	.	16.0405	0.80679	0.0:0.0:0.0:1.0	.	108	Q7Z6K3	PTAR1_HUMAN	G	108	ENSP00000344299:R108G	ENSP00000344299:R108G	R	-	1	2	PTAR1	71546529	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.519000	0.60517	2.187000	0.69744	0.519000	0.50382	AGG	.	.		0.333	PTAR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052582.4	NM_001099666	Missense_Mutation
C9orf57	138240	hgsc.bcm.edu	37	9	74674293	74674293	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:74674293A>G	ENST00000377024.3	-	2	116	c.21T>C	c.(19-21)agT>agC	p.S7S	C9orf57_ENST00000424431.2_Intron	NM_001128618.1	NP_001122090.1	Q5W0N0	CI057_HUMAN	chromosome 9 open reading frame 57	7						integral component of membrane (GO:0016021)				endometrium(1)	1						GACACGTCCCACTGATTTCTG	0.348																																					p.S7S		Atlas-SNP	.											.	C9orf57	16	.	0			c.T21C						.						105.0	88.0	93.0					9																	74674293		692	1591	2283	SO:0001819	synonymous_variant	138240	exon2			CGTCCCACTGATT	BC036255	CCDS47980.1	9q21.2	2012-03-15			ENSG00000204669	ENSG00000204669			27037	protein-coding gene	gene with protein product						12477932	Standard	NM_001128618		Approved		uc004aip.3	Q5W0N0	OTTHUMG00000020003	ENST00000377024.3:c.21T>C	chr9.hg19:g.74674293A>G		108.0	0.0		86.0	4.0	NM_001128618	A1L456	Silent	SNP	ENST00000377024.3	hg19	CCDS47980.1																																																																																			.	.		0.348	C9orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052631.1	NM_001128618	
PRUNE2	158471	hgsc.bcm.edu	37	9	79461504	79461504	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:79461504A>G	ENST00000376718.3	-	4	558	c.435T>C	c.(433-435)tcT>tcC	p.S145S	PRUNE2_ENST00000376713.3_Silent_p.S145S|PRUNE2_ENST00000428286.1_5'UTR	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	145					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						GCACGAGAGAAGAGGAAGACT	0.468																																					p.S145S		Atlas-SNP	.											.	PRUNE2	331	.	0			c.T435C						.						106.0	103.0	104.0					9																	79461504		2203	4300	6503	SO:0001819	synonymous_variant	158471	exon4			GAGAGAAGAGGAA	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.435T>C	chr9.hg19:g.79461504A>G		114.0	0.0		80.0	5.0	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	hg19	CCDS47982.1																																																																																			.	.		0.468	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
VPS13A	23230	hgsc.bcm.edu	37	9	79960046	79960046	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:79960046A>G	ENST00000360280.3	+	52	7537	c.7277A>G	c.(7276-7278)cAa>cGa	p.Q2426R	VPS13A_ENST00000376636.3_Missense_Mutation_p.Q2387R|VPS13A_ENST00000376634.4_Missense_Mutation_p.Q2426R|VPS13A_ENST00000357409.5_Missense_Mutation_p.Q2426R	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2426					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						GAACTTGTTCAATACAATCAA	0.313																																					p.Q2426R		Atlas-SNP	.											.	VPS13A	735	.	0			c.A7277G						.						126.0	127.0	127.0					9																	79960046		2203	4298	6501	SO:0001583	missense	23230	exon52			TTGTTCAATACAA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.7277A>G	chr9.hg19:g.79960046A>G	ENSP00000353422:p.Gln2426Arg	104.0	0.0		88.0	4.0	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	A	2.662	-0.279511	0.05642	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.26	5.26	0.73747	Vacuolar protein sorting-associated protein (1);	0.670270	0.14937	N	0.289778	T	0.17746	0.0426	N	0.12182	0.205	0.80722	D	1	B;B;B;B	0.10296	0.001;0.003;0.002;0.002	B;B;B;B	0.11329	0.003;0.006;0.006;0.004	T	0.09357	-1.0678	10	0.19590	T	0.45	.	10.9338	0.47233	0.843:0.157:0.0:0.0	.	2387;2426;2426;2426	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	R	2426;2387;2426;2426	ENSP00000365821:Q2426R;ENSP00000365823:Q2387R;ENSP00000353422:Q2426R;ENSP00000349985:Q2426R	ENSP00000349985:Q2426R	Q	+	2	0	VPS13A	79149866	1.000000	0.71417	0.761000	0.31378	0.032000	0.12392	5.624000	0.67764	1.980000	0.57719	0.477000	0.44152	CAA	.	.		0.313	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
GKAP1	80318	hgsc.bcm.edu	37	9	86395306	86395306	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:86395306T>A	ENST00000376371.2	-	7	976	c.576A>T	c.(574-576)aaA>aaT	p.K192N	GKAP1_ENST00000376365.3_Missense_Mutation_p.K192N	NM_025211.3	NP_079487.2	Q5VSY0	GKAP1_HUMAN	G kinase anchoring protein 1	192					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)				endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)	14						CCTCAGTCTTTTTACTAATGT	0.249																																					p.K192N		Atlas-SNP	.											.	GKAP1	27	.	0			c.A576T						.						48.0	53.0	51.0					9																	86395306		2199	4285	6484	SO:0001583	missense	80318	exon7			AGTCTTTTTACTA	BC014476	CCDS35049.1, CCDS47988.1	9q22.1	2008-02-05			ENSG00000165113	ENSG00000165113			17496	protein-coding gene	gene with protein product	"""cGMP-dependent protein kinase anchoring protein 42kDa"""	611356					Standard	NM_025211		Approved	GKAP42, FKSG21	uc004amy.3	Q5VSY0	OTTHUMG00000020106	ENST00000376371.2:c.576A>T	chr9.hg19:g.86395306T>A	ENSP00000365550:p.Lys192Asn	280.0	0.0		243.0	17.0	NM_025211	Q96LI0|Q9BYI1|Q9BYI2|Q9H225	Missense_Mutation	SNP	ENST00000376371.2	hg19	CCDS35049.1	.	.	.	.	.	.	.	.	.	.	T	16.48	3.136019	0.56936	.	.	ENSG00000165113	ENST00000376371;ENST00000376365	.	.	.	5.19	4.05	0.47172	.	0.090473	0.85682	D	0.000000	T	0.66137	0.2759	L	0.49350	1.555	0.48087	D	0.999588	D;P	0.89917	1.0;0.661	D;B	0.85130	0.997;0.287	T	0.61422	-0.7066	9	0.26408	T	0.33	-16.4182	9.3504	0.38133	0.0:0.083:0.0:0.917	.	192;192	Q5VSY0-2;Q5VSY0	.;GKAP1_HUMAN	N	192	.	ENSP00000365544:K192N	K	-	3	2	GKAP1	85585126	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.837000	0.39201	0.923000	0.37045	0.460000	0.39030	AAA	.	.		0.249	GKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052839.2	NM_025211	
NUTM2F	54754	hgsc.bcm.edu	37	9	97080944	97080944	+	Missense_Mutation	SNP	G	G	C	rs150455117	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:97080944G>C	ENST00000253262.4	-	7	2094	c.2074C>G	c.(2074-2076)Cct>Gct	p.P692A	NUTM2F_ENST00000335456.7_Intron|NUTM2F_ENST00000341207.4_Missense_Mutation_p.P677A	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	692																	TTGCTGGCAGGAGAAGGTGAT	0.607																																					p.P692A		Atlas-SNP	.											.	FAM22F	72	.	0			c.C2074G						.						21.0	19.0	20.0					9																	97080944		1843	4069	5912	SO:0001583	missense	54754	exon7			TGGCAGGAGAAGG		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member F"""	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.2074C>G	chr9.hg19:g.97080944G>C	ENSP00000253262:p.Pro692Ala	390.0	0.0		312.0	21.0	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Missense_Mutation	SNP	ENST00000253262.4	hg19	CCDS47994.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.581686	0.00879	.	.	ENSG00000130950	ENST00000253262;ENST00000341207;ENST00000375347	T;T	0.14640	2.49;2.52	1.52	-3.04	0.05412	Nuclear Testis protein, C-terminal (1);	2.077270	0.02242	N	0.065820	T	0.12561	0.0305	L	0.56769	1.78	0.09310	N	1	B	0.13594	0.008	B	0.16289	0.015	T	0.30621	-0.9972	10	0.09084	T	0.74	.	5.0244	0.14378	0.1751:0.5512:0.2738:0.0	.	692	A1L443	FA22F_HUMAN	A	692;677;526	ENSP00000253262:P692A;ENSP00000343865:P677A	ENSP00000253262:P692A	P	-	1	0	FAM22F	96120765	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.495000	0.06443	-1.287000	0.02381	-0.518000	0.04402	CCT	.	.		0.607	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561	
ZNF782	158431	hgsc.bcm.edu	37	9	99580298	99580298	+	Silent	SNP	T	T	C	rs561032098	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:99580298T>C	ENST00000481138.1	-	6	2668	c.2007A>G	c.(2005-2007)acA>acG	p.T669T	ZNF782_ENST00000535338.1_Silent_p.T537T|ZNF782_ENST00000466833.1_5'Flank	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	669					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				GTTTCTCCCCTGTGTGAGTTC	0.423																																					p.T669T		Atlas-SNP	.											.	ZNF782	64	.	0			c.A2007G						.						103.0	104.0	104.0					9																	99580298		2203	4300	6503	SO:0001819	synonymous_variant	158431	exon6			CTCCCCTGTGTGA	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.2007A>G	chr9.hg19:g.99580298T>C		246.0	0.0		175.0	8.0	NM_001001662	B2RNR0	Silent	SNP	ENST00000481138.1	hg19	CCDS35075.1	.	.	.	.	.	.	.	.	.	.	t	7.390	0.630621	0.14322	.	.	ENSG00000196597	ENST00000289032	.	.	.	2.64	0.104	0.14531	.	.	.	.	.	T	0.51822	0.1697	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39165	-0.9627	4	.	.	.	.	6.321	0.21217	0.43:0.0:0.0:0.57	.	.	.	.	G	658	.	.	R	-	1	2	ZNF782	98620119	0.062000	0.20869	0.999000	0.59377	0.992000	0.81027	-0.986000	0.03747	0.000000	0.14550	0.533000	0.62120	AGG	.	.		0.423	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662	
CCDC180	100499483	hgsc.bcm.edu	37	9	100074426	100074426	+	Silent	SNP	C	C	A	rs377165805		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:100074426C>A	ENST00000357054.1	+	18	1776	c.841C>A	c.(841-843)Cga>Aga	p.R281R	CCDC180_ENST00000529487.1_Silent_p.R142R|CCDC180_ENST00000375202.2_Silent_p.R142R|CCDC180_ENST00000460482.2_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000411667.2_Silent_p.R142R|CCDC180_ENST00000395220.1_Silent_p.R281R			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	281						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											GGAAAAAGCCCGAGAGAGTGA	0.557																																					p.R142R		Atlas-SNP	.											.	.	.	.	0			c.C424A						.						120.0	122.0	121.0					9																	100074426		2203	4300	6503	SO:0001819	synonymous_variant	0	exon4			AAAGCCCGAGAGA	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.841C>A	chr9.hg19:g.100074426C>A		95.0	0.0		73.0	4.0	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	hg19																																																																																				.	.		0.557	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
IKBKAP	8518	hgsc.bcm.edu	37	9	111656321	111656321	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:111656321A>G	ENST00000374647.5	-	26	3069	c.2762T>C	c.(2761-2763)cTt>cCt	p.L921P	IKBKAP_ENST00000537196.1_Missense_Mutation_p.L572P	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	921					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						AAGTGTATTAAGAAATGGAAG	0.294																																					p.L921P		Atlas-SNP	.											.	IKBKAP	122	.	0			c.T2762C						.						83.0	80.0	81.0					9																	111656321		2203	4300	6503	SO:0001583	missense	8518	exon26			GTATTAAGAAATG	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.2762T>C	chr9.hg19:g.111656321A>G	ENSP00000363779:p.Leu921Pro	118.0	0.0		69.0	4.0	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	hg19	CCDS6773.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.390549	0.82902	.	.	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.59502	0.26;0.26	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.82323	0.5012	H	0.94385	3.53	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87135	0.2199	10	0.87932	D	0	-18.042	14.3095	0.66407	1.0:0.0:0.0:0.0	.	921	O95163	ELP1_HUMAN	P	921;572	ENSP00000363779:L921P;ENSP00000439367:L572P	ENSP00000363779:L921P	L	-	2	0	IKBKAP	110696142	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.073000	0.93992	2.270000	0.75569	0.477000	0.44152	CTT	.	.		0.294	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
SVEP1	79987	hgsc.bcm.edu	37	9	113169046	113169046	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:113169046T>C	ENST00000401783.2	-	38	9170	c.8834A>G	c.(8833-8835)aAa>aGa	p.K2945R	SVEP1_ENST00000297826.5_Missense_Mutation_p.K871R|SVEP1_ENST00000374469.1_Missense_Mutation_p.K2922R	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2945	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GTTGACTGGTTTACAGAGAGG	0.478																																					p.K2945R		Atlas-SNP	.											.	SVEP1	326	.	0			c.A8834G						.						187.0	183.0	184.0					9																	113169046		1959	4153	6112	SO:0001583	missense	79987	exon38			ACTGGTTTACAGA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.8834A>G	chr9.hg19:g.113169046T>C	ENSP00000384917:p.Lys2945Arg	118.0	0.0		97.0	4.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	T	12.45	1.940874	0.34283	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.24151	1.87;1.87;1.87	5.57	4.4	0.53042	Complement control module (2);Sushi/SCR/CCP (1);	0.155382	0.56097	D	0.000027	T	0.19046	0.0457	L	0.42487	1.325	0.80722	D	1	P	0.38922	0.651	B	0.33521	0.165	T	0.03017	-1.1082	10	0.17369	T	0.5	.	11.7457	0.51819	0.1323:0.0:0.0:0.8677	.	2945	Q4LDE5	SVEP1_HUMAN	R	2945;2922;871	ENSP00000384917:K2945R;ENSP00000363593:K2922R;ENSP00000297826:K871R	ENSP00000297826:K871R	K	-	2	0	SVEP1	112208867	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	3.891000	0.56227	0.907000	0.36646	0.482000	0.46254	AAA	.	.		0.478	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SLC31A1	1317	hgsc.bcm.edu	37	9	116018546	116018546	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:116018546A>G	ENST00000374212.4	+	2	270	c.118A>G	c.(118-120)Atg>Gtg	p.M40V	CDC26_ENST00000490408.1_Intron|SLC31A1_ENST00000374210.6_Missense_Mutation_p.M40V	NM_001859.3	NP_001850.1	O15431	COPT1_HUMAN	solute carrier family 31 (copper transporter), member 1	40					cellular copper ion homeostasis (GO:0006878)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	copper ion transmembrane transporter activity (GO:0005375)|copper uptake transmembrane transporter activity (GO:0015088)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7					Bortezomib(DB00188)|Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	AGACAGCAGCATGATGATGAT	0.483																																					p.M40V	Ovarian(135;1049 1799 4519 17564 28677)	Atlas-SNP	.											.	SLC31A1	12	.	0			c.A118G						.						115.0	84.0	95.0					9																	116018546		2203	4300	6503	SO:0001583	missense	1317	exon2			AGCAGCATGATGA	U83460	CCDS6789.1	9q32	2013-07-17	2013-07-17		ENSG00000136868	ENSG00000136868		"""Solute carriers"""	11016	protein-coding gene	gene with protein product	copper transport 1 homolog (S. cerevisiae)	603085		COPT1		9207117	Standard	NM_001859		Approved	hCTR1, CTR1	uc004bgu.3	O15431	OTTHUMG00000020519	ENST00000374212.4:c.118A>G	chr9.hg19:g.116018546A>G	ENSP00000363329:p.Met40Val	203.0	0.0		166.0	7.0	NM_001859	A8K8Z6|Q53GR5|Q5T1M4	Missense_Mutation	SNP	ENST00000374212.4	hg19	CCDS6789.1	.	.	.	.	.	.	.	.	.	.	A	8.096	0.775624	0.16051	.	.	ENSG00000136868	ENST00000374212;ENST00000374210	T;T	0.66280	-0.16;-0.2	5.54	4.35	0.52113	.	0.234155	0.44285	D	0.000466	T	0.37758	0.1015	N	0.08118	0	0.80722	D	1	B;B	0.25667	0.131;0.009	B;B	0.22386	0.039;0.01	T	0.25916	-1.0118	10	0.30078	T	0.28	-12.7871	8.8623	0.35265	0.8342:0.0:0.0:0.1658	.	40;40	Q5T1M3;O15431	.;COPT1_HUMAN	V	40	ENSP00000363329:M40V;ENSP00000363327:M40V	ENSP00000363327:M40V	M	+	1	0	SLC31A1	115058367	0.999000	0.42202	0.999000	0.59377	0.947000	0.59692	1.699000	0.37804	2.095000	0.63458	0.460000	0.39030	ATG	.	.		0.483	SLC31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053715.1	NM_001859	
WDR31	114987	hgsc.bcm.edu	37	9	116079110	116079110	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:116079110A>G	ENST00000374193.4	-	11	1269	c.1023T>C	c.(1021-1023)tgT>tgC	p.C341C	WDR31_ENST00000461942.1_5'UTR|WDR31_ENST00000374195.3_Silent_p.C216C|WDR31_ENST00000341761.4_Silent_p.C340C	NM_001012361.2|NM_145241.3	NP_001012361.1|NP_660284.1	Q8NA23	WDR31_HUMAN	WD repeat domain 31	341										NS(1)|large_intestine(1)|lung(2)|prostate(2)	6						TAAAACTTGCACACAATAAGG	0.527																																					p.C341C		Atlas-SNP	.											.	WDR31	23	.	0			c.T1023C						.						141.0	128.0	132.0					9																	116079110		2203	4300	6503	SO:0001819	synonymous_variant	114987	exon11			ACTTGCACACAAT	BC012352	CCDS6792.1, CCDS35110.1	9q33.1	2013-01-09			ENSG00000148225	ENSG00000148225		"""WD repeat domain containing"""	21421	protein-coding gene	gene with protein product	"""similar to spermatid WD-repeat protein"""						Standard	NM_145241		Approved	FLJ35921	uc004bhb.3	Q8NA23	OTTHUMG00000020525	ENST00000374193.4:c.1023T>C	chr9.hg19:g.116079110A>G		90.0	0.0		56.0	4.0	NM_001012361	Q5W0T9|Q96EG8	Silent	SNP	ENST00000374193.4	hg19	CCDS35110.1																																																																																			.	.		0.527	WDR31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053734.2	NM_145241	
TNC	3371	hgsc.bcm.edu	37	9	117852928	117852928	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:117852928T>C	ENST00000350763.4	-	2	781	c.370A>G	c.(370-372)Agc>Ggc	p.S124G	TNC_ENST00000535648.1_Missense_Mutation_p.S124G|TNC_ENST00000423613.2_Missense_Mutation_p.S124G|TNC_ENST00000537320.1_Missense_Mutation_p.S124G|TNC_ENST00000340094.3_Missense_Mutation_p.S124G|TNC_ENST00000341037.4_Missense_Mutation_p.S124G|TNC_ENST00000346706.3_Missense_Mutation_p.S124G|TNC_ENST00000345230.3_Missense_Mutation_p.S124G|TNC_ENST00000542877.1_Missense_Mutation_p.S124G	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	124					bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						TCCAGTCTGCTCAGCAGCTCC	0.592																																					p.S124G		Atlas-SNP	.											TNC,NS,carcinoma,0,1	TNC	282	.	0			c.A370G						.						139.0	150.0	146.0					9																	117852928		2203	4300	6503	SO:0001583	missense	3371	exon2			GTCTGCTCAGCAG		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.370A>G	chr9.hg19:g.117852928T>C	ENSP00000265131:p.Ser124Gly	95.0	1.0		94.0	4.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.931316	0.92389	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34	5.94	5.94	0.96194	.	0.244211	0.53938	D	0.000056	T	0.45256	0.1333	M	0.65975	2.015	0.48975	D	0.999735	P;P	0.51791	0.948;0.85	B;P	0.46208	0.441;0.507	T	0.48822	-0.9001	10	0.62326	D	0.03	.	15.5674	0.76303	0.0:0.0:0.0:1.0	.	124;124	E9PC84;P24821	.;TENA_HUMAN	G	124	ENSP00000344400:S124G;ENSP00000438152:S124G;ENSP00000344555:S124G;ENSP00000345861:S124G;ENSP00000265131:S124G;ENSP00000339553:S124G;ENSP00000411406:S124G;ENSP00000443478:S124G;ENSP00000442242:S124G	ENSP00000344400:S124G	S	-	1	0	TNC	116892749	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	6.152000	0.71812	2.261000	0.74972	0.533000	0.62120	AGC	.	.		0.592	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
CDK5RAP2	55755	hgsc.bcm.edu	37	9	123156882	123156882	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:123156882T>A	ENST00000349780.4	-	36	5665	c.5486A>T	c.(5485-5487)cAt>cTt	p.H1829L	CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.H1750L|CDK5RAP2_ENST00000480467.1_5'UTR|CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.H1788L|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.H1797L	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1829	Interaction with PCNT and AKAP9.				brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						CAATTTTTTATGTAGTTTGGT	0.348																																					p.H1829L		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.A5486T						.						146.0	133.0	138.0					9																	123156882		2203	4300	6503	SO:0001583	missense	55755	exon36			TTTTTATGTAGTT	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.5486A>T	chr9.hg19:g.123156882T>A	ENSP00000343818:p.His1829Leu	319.0	0.0		252.0	35.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	hg19	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	T	12.67	2.008474	0.35415	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000416449;ENST00000425647;ENST00000345313	T;T;T;T;T;T	0.23348	3.89;3.81;3.9;3.81;2.22;1.91	5.39	3.04	0.35103	.	0.578085	0.16911	N	0.194491	T	0.36082	0.0954	M	0.67953	2.075	0.30138	N	0.804181	P;B;P;P;P	0.47762	0.589;0.279;0.9;0.483;0.763	B;B;P;B;B	0.53185	0.114;0.124;0.72;0.058;0.229	T	0.33523	-0.9865	10	0.72032	D	0.01	.	5.7886	0.18347	0.0:0.2872:0.0:0.7128	.	839;1797;1750;1829;1223	Q5JTU8;Q96SN8-2;Q96SN8-4;Q96SN8;B1AMJ5	.;.;.;CK5P2_HUMAN;.	L	1797;1788;1829;1750;1223;839;1601	ENSP00000354065:H1797L;ENSP00000352258:H1788L;ENSP00000343818:H1829L;ENSP00000353317:H1750L;ENSP00000400395:H1223L;ENSP00000409941:H839L	ENSP00000341695:H1601L	H	-	2	0	CDK5RAP2	122196703	0.734000	0.28142	0.490000	0.27465	0.491000	0.33493	0.229000	0.17833	0.869000	0.35703	0.533000	0.62120	CAT	.	.		0.348	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
RC3H2	54542	hgsc.bcm.edu	37	9	125642094	125642094	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:125642094T>C	ENST00000373670.1	-	7	1752	c.1152A>G	c.(1150-1152)gtA>gtG	p.V384V	RC3H2_ENST00000335387.5_Silent_p.V384V|RC3H2_ENST00000423239.2_Silent_p.V384V|SNORD90_ENST00000391145.1_RNA|RC3H2_ENST00000357244.2_Silent_p.V384V|RC3H2_ENST00000373665.2_Silent_p.V384V			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	384					B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						GGCCATGAACTACTGTTTTAA	0.438																																					p.V384V		Atlas-SNP	.											.	RC3H2	150	.	0			c.A1152G						.						69.0	69.0	69.0					9																	125642094		1872	4098	5970	SO:0001819	synonymous_variant	54542	exon8			ATGAACTACTGTT	AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCCH-type domain containing"""	21461	protein-coding gene	gene with protein product		615231	"""membrane associated DNA binding protein"", ""ring finger and CCCH-type zinc finger domains 2"""	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.1152A>G	chr9.hg19:g.125642094T>C		78.0	0.0		68.0	5.0	NM_018835	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Silent	SNP	ENST00000373670.1	hg19	CCDS43874.1																																																																																			.	.		0.438	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835	
ODF2	4957	hgsc.bcm.edu	37	9	131231625	131231625	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:131231625A>G	ENST00000434106.3	+	5	776	c.413A>G	c.(412-414)aAg>aGg	p.K138R	ODF2_ENST00000604420.1_Missense_Mutation_p.K138R|ODF2_ENST00000372807.5_Missense_Mutation_p.K133R|RP11-339B21.9_ENST00000420801.1_RNA|ODF2_ENST00000372791.3_Missense_Mutation_p.K119R|ODF2_ENST00000448249.3_Intron|ODF2_ENST00000372814.3_Missense_Mutation_p.K182R|ODF2_ENST00000393527.3_Missense_Mutation_p.K114R|ODF2_ENST00000546203.1_Missense_Mutation_p.K119R|ODF2_ENST00000444119.2_Missense_Mutation_p.K114R|ODF2_ENST00000535026.1_Intron|ODF2_ENST00000393533.2_Missense_Mutation_p.K138R|ODF2_ENST00000351030.3_Missense_Mutation_p.K133R	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	138					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						GGTTGTCTGAAGTCTGAGGTG	0.498																																					p.K202R		Atlas-SNP	.											.	ODF2	227	.	0			c.A605G						.						152.0	142.0	145.0					9																	131231625		2203	4300	6503	SO:0001583	missense	4957	exon5			GTCTGAAGTCTGA	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.413A>G	chr9.hg19:g.131231625A>G	ENSP00000403453:p.Lys138Arg	89.0	0.0		63.0	4.0	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	hg19	CCDS56588.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.370217	0.82573	.	.	ENSG00000136811	ENST00000393533;ENST00000372814;ENST00000351030;ENST00000372796;ENST00000303890;ENST00000444119;ENST00000434106;ENST00000546203;ENST00000446274;ENST00000372791	T;T;T;T;T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	5.97	5.97	0.96955	.	0.042327	0.85682	D	0.000000	T	0.81607	0.4858	L	0.59436	1.845	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	0.996;0.999;0.998;0.998;0.998;0.996;0.999;0.984	T	0.81957	-0.0695	10	0.51188	T	0.08	-29.8851	15.2656	0.73657	1.0:0.0:0.0:0.0	.	119;133;72;138;133;119;138;114	Q5BJF6-8;Q5BJF6-4;Q5BJF6-2;B4DX73;B1AND4;Q5BJF6-5;Q5BJF6;Q5BJF6-3	.;.;.;.;.;.;ODFP2_HUMAN;.	R	138;182;133;138;114;114;138;119;119;119	ENSP00000377166:K138R;ENSP00000361901:K182R;ENSP00000342581:K133R;ENSP00000361882:K138R;ENSP00000307781:K114R;ENSP00000394506:K114R;ENSP00000403453:K138R;ENSP00000437579:K119R;ENSP00000415290:K119R;ENSP00000361877:K119R	ENSP00000307781:K114R	K	+	2	0	ODF2	130271446	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	6.649000	0.74364	2.285000	0.76669	0.477000	0.44152	AAG	.	.		0.498	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
PHYHD1	254295	hgsc.bcm.edu	37	9	131689459	131689459	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:131689459A>G	ENST00000372592.3	+	4	1109	c.176A>G	c.(175-177)gAg>gGg	p.E59G	PHYHD1_ENST00000353176.5_Missense_Mutation_p.E59G|PHYHD1_ENST00000308941.5_Missense_Mutation_p.E59G|PHYHD1_ENST00000421063.2_Missense_Mutation_p.E59G	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	59							dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						CAGGAAGAGGAGCAGCTTCGA	0.582											OREG0019526	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E59G		Atlas-SNP	.											.	PHYHD1	29	.	0			c.A176G						.						137.0	118.0	124.0					9																	131689459		2203	4300	6503	SO:0001583	missense	254295	exon2			AAGAGGAGCAGCT	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.176A>G	chr9.hg19:g.131689459A>G	ENSP00000361673:p.Glu59Gly	102.0	0.0	1589	70.0	4.0	NM_001100877	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Missense_Mutation	SNP	ENST00000372592.3	hg19	CCDS43885.1	.	.	.	.	.	.	.	.	.	.	A	15.58	2.876179	0.51801	.	.	ENSG00000175287	ENST00000372592;ENST00000428610;ENST00000308941;ENST00000419552;ENST00000353176;ENST00000426694;ENST00000421063	D;D;D	0.89810	-2.54;-2.57;-2.57	5.32	5.32	0.75619	.	0.100735	0.64402	D	0.000003	D	0.90868	0.7131	M	0.73598	2.24	0.58432	D	0.999999	P;P;D	0.54397	0.734;0.605;0.966	B;B;P	0.49887	0.373;0.412;0.625	D	0.91285	0.5054	10	0.51188	T	0.08	-23.6398	14.0941	0.65008	1.0:0.0:0.0:0.0	.	59;59;59	Q5SRE7-2;Q5SRE7;Q5SRE7-3	.;PHYD1_HUMAN;.	G	59	ENSP00000361673:E59G;ENSP00000340945:E59G;ENSP00000409928:E59G	ENSP00000309515:E59G	E	+	2	0	PHYHD1	130729280	1.000000	0.71417	0.998000	0.56505	0.324000	0.28378	3.925000	0.56484	2.002000	0.58637	0.533000	0.62120	GAG	.	.		0.582	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933	
PTGES	9536	hgsc.bcm.edu	37	9	132502117	132502117	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:132502117T>C	ENST00000340607.4	-	3	266	c.232A>G	c.(232-234)Acc>Gcc	p.T78A	PTGES_ENST00000481476.1_5'UTR	NM_004878.4	NP_004869.1	O14684	PTGES_HUMAN	prostaglandin E synthase	78					acute inflammatory response (GO:0002526)|arachidonic acid metabolic process (GO:0019369)|chronic inflammatory response (GO:0002544)|cyclooxygenase pathway (GO:0019371)|negative regulation of cell proliferation (GO:0008285)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|response to calcium ion (GO:0051592)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)	glutathione binding (GO:0043295)|prostaglandin-E synthase activity (GO:0050220)			lung(1)|skin(1)	2		Ovarian(14;0.00556)				GGGTAGATGGTCTCCATGTCG	0.572																																					p.T78A		Atlas-SNP	.											.	PTGES	7	.	0			c.A232G						.						69.0	44.0	52.0					9																	132502117		2192	4292	6484	SO:0001583	missense	9536	exon3			AGATGGTCTCCAT	AF010316	CCDS6927.1	9q34.3	2008-07-21			ENSG00000148344	ENSG00000148344			9599	protein-coding gene	gene with protein product	"""microsomal glutathione S-transferase 1-like 1"", ""tumor protein p53 inducible protein 12"", ""p53-induced gene 12"", ""microsomal prostaglandin E synthase-1"", ""glutathione S-transferase 1-like 1"", ""MGST1-like 1"""	605172		MGST1L1		9305847, 10091672	Standard	NM_004878		Approved	MGST-IV, PIG12, MGST1-L1, TP53I12	uc004byi.3	O14684	OTTHUMG00000020791	ENST00000340607.4:c.232A>G	chr9.hg19:g.132502117T>C	ENSP00000342385:p.Thr78Ala	118.0	0.0		90.0	4.0	NM_004878	O14900|Q5SZC0	Missense_Mutation	SNP	ENST00000340607.4	hg19	CCDS6927.1	.	.	.	.	.	.	.	.	.	.	T	18.56	3.650502	0.67472	.	.	ENSG00000148344	ENST00000340607	T	0.57273	0.41	4.6	4.6	0.57074	Membrane associated eicosanoid/glutathione metabolism-like domain (1);	0.138330	0.64402	D	0.000005	T	0.48095	0.1481	L	0.33485	1.01	0.47949	D	0.999557	B	0.23650	0.089	B	0.35114	0.196	T	0.52909	-0.8512	10	0.87932	D	0	-50.199	13.6096	0.62068	0.0:0.0:0.0:1.0	.	78	O14684	PTGES_HUMAN	A	78	ENSP00000342385:T78A	ENSP00000342385:T78A	T	-	1	0	PTGES	131541938	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.762000	0.85270	2.048000	0.60808	0.459000	0.35465	ACC	.	.		0.572	PTGES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054599.2	NM_004878	
TOR1B	27348	hgsc.bcm.edu	37	9	132571282	132571282	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:132571282T>C	ENST00000259339.2	+	4	800	c.740T>C	c.(739-741)cTg>cCg	p.L247P		NM_014506.1	NP_055321.1	O14657	TOR1B_HUMAN	torsin family 1, member B (torsin B)	247					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum organization (GO:0007029)|nuclear membrane organization (GO:0071763)|protein homooligomerization (GO:0051260)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)	12		Ovarian(14;0.0586)				GAACCTGTACTGTCTGTCGGA	0.502																																					p.L247P		Atlas-SNP	.											.	TOR1B	20	.	0			c.T740C						.						84.0	88.0	86.0					9																	132571282		2203	4300	6503	SO:0001583	missense	27348	exon4			CTGTACTGTCTGT	AF007872	CCDS6929.1	9q34	2008-07-21			ENSG00000136816	ENSG00000136816			11995	protein-coding gene	gene with protein product		608050				9288096, 10644435	Standard	NM_014506		Approved	DQ1, MGC4386	uc004byk.1	O14657	OTTHUMG00000020795	ENST00000259339.2:c.740T>C	chr9.hg19:g.132571282T>C	ENSP00000259339:p.Leu247Pro	95.0	0.0		78.0	4.0	NM_014506		Missense_Mutation	SNP	ENST00000259339.2	hg19	CCDS6929.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.336735	0.81801	.	.	ENSG00000136816	ENST00000259339;ENST00000437263	T	0.58210	0.35	4.72	4.72	0.59763	.	0.140502	0.48286	D	0.000199	T	0.76528	0.4000	M	0.91406	3.205	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.82438	-0.0457	10	0.72032	D	0.01	-30.1219	13.5395	0.61666	0.0:0.0:0.0:1.0	.	247	O14657	TOR1B_HUMAN	P	247;216	ENSP00000259339:L247P	ENSP00000259339:L247P	L	+	2	0	TOR1B	131611103	0.954000	0.32549	0.974000	0.42286	0.971000	0.66376	7.327000	0.79147	1.979000	0.57680	0.528000	0.53228	CTG	.	.		0.502	TOR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054615.1	NM_014506	
TSC1	7248	hgsc.bcm.edu	37	9	135771990	135771990	+	Missense_Mutation	SNP	T	T	C	rs397514812		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:135771990T>C	ENST00000298552.3	-	23	3348	c.3127A>G	c.(3127-3129)Agc>Ggc	p.S1043G	TSC1_ENST00000545250.1_Missense_Mutation_p.S992G|TSC1_ENST00000440111.2_Missense_Mutation_p.S1043G	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	1043	Poly-Ser.		Missing (in TSC1; unknown pathological significance; no effect on expression; no effect on subcellular localization; no effect on inhibition of TORC1 signaling). {ECO:0000269|PubMed:22161988}.		activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		GAAAGCTCgctgctgctgctg	0.642			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																												p.S1043G		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"""E, O"""	TSC1,colon,carcinoma,0,2	TSC1	167	.	1	Unknown(1)	bone(1)	c.A3127G						.						23.0	26.0	25.0					9																	135771990		2203	4299	6502	SO:0001583	missense	7248	exon23	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GCTCGCTGCTGCT	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.3127A>G	chr9.hg19:g.135771990T>C	ENSP00000298552:p.Ser1043Gly	55.0	1.0		34.0	3.0	NM_000368	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	hg19	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	T	9.298	1.052277	0.19827	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250	D;D;T	0.82255	-1.59;-1.59;-1.4	3.95	3.95	0.45737	.	0.297282	0.36665	N	0.002471	D	0.86818	0.6024	M	0.64997	1.995	0.80722	D	1	D;P	0.58268	0.982;0.905	D;B	0.67548	0.952;0.423	D	0.83606	0.0131	10	0.18710	T	0.47	-4.8503	10.7727	0.46332	0.0:0.0:0.0:1.0	.	992;1043	B7Z897;Q92574	.;TSC1_HUMAN	G	1043;1043;992	ENSP00000298552:S1043G;ENSP00000394524:S1043G;ENSP00000444017:S992G	ENSP00000298552:S1043G	S	-	1	0	TSC1	134761811	1.000000	0.71417	0.961000	0.40146	0.822000	0.46500	2.796000	0.47869	1.405000	0.46838	0.338000	0.21704	AGC	.	.		0.642	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		
GLT6D1	360203	hgsc.bcm.edu	37	9	138516329	138516329	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:138516329C>T	ENST00000371763.1	-	5	698	c.445G>A	c.(445-447)Gtg>Atg	p.V149M		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	149					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		TTCACATGCACCAGGGGGCCA	0.557																																					p.V149M		Atlas-SNP	.											.	GLT6D1	56	.	0			c.G445A						.						41.0	43.0	42.0					9																	138516329		1993	4157	6150	SO:0001583	missense	360203	exon5			CATGCACCAGGGG	AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"""Glycosyltransferase family 6 domain containing"""	23671	protein-coding gene	gene with protein product		613699	"""galactosyltransferase family 6 domain containing 1"""	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.445G>A	chr9.hg19:g.138516329C>T	ENSP00000360829:p.Val149Met	80.0	0.0		47.0	4.0	NM_182974		Missense_Mutation	SNP	ENST00000371763.1	hg19	CCDS43900.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.971199	0.00457	.	.	ENSG00000204007	ENST00000371763	T	0.01178	5.22	3.43	-6.86	0.01676	.	1.441670	0.03843	N	0.271043	T	0.00384	0.0012	N	0.00729	-1.24	0.09310	N	1	B	0.22909	0.077	B	0.19148	0.024	T	0.42292	-0.9460	10	0.07175	T	0.84	-1.1801	3.553	0.07854	0.0988:0.392:0.2995:0.2097	.	149	Q7Z4J2	GL6D1_HUMAN	M	149	ENSP00000360829:V149M	ENSP00000360829:V149M	V	-	1	0	GLT6D1	137656150	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.876000	0.01633	-3.190000	0.00220	-1.181000	0.01715	GTG	.	.		0.557	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974	
LCN15	389812	hgsc.bcm.edu	37	9	139651509	139651509	+	IGR	SNP	C	C	T	rs140571672		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:139651509C>T	ENST00000316144.5	-	0	762				LCN8_ENST00000482893.1_5'UTR|LCN15_ENST00000482511.1_5'Flank|LCN8_ENST00000371688.3_Missense_Mutation_p.V46M	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15						lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						GCAACCTTCACGGTCAGGTTA	0.637																																					p.V46M		Atlas-SNP	.											.	LCN8	14	.	0			c.G136A						.	C	MET/VAL	0,4406		0,0,2203	49.0	43.0	45.0		136	2.6	0.0	9	dbSNP_134	45	2,8598	2.2+/-6.3	0,2,4298	no	missense	LCN8	NM_178469.3	21	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	46/153	139651509	2,13004	2203	4300	6503	SO:0001628	intergenic_variant	138307	exon2			CCTTCACGGTCAG		CCDS7006.1	9q34.3	2011-10-24			ENSG00000177984	ENSG00000177984		"""Lipocalins"""	33777	protein-coding gene	gene with protein product							Standard	NM_203347		Approved	UNQ2541, PRO6093	uc004cjd.3	Q6UWW0	OTTHUMG00000020943		chr9.hg19:g.139651509C>T		90.0	0.0		76.0	4.0	NM_178469		Missense_Mutation	SNP	ENST00000316144.5	hg19	CCDS7006.1	.	.	.	.	.	.	.	.	.	.	C	9.175	1.022095	0.19433	0.0	2.33E-4	ENSG00000204001	ENST00000371688	T	0.10763	2.84	3.47	2.57	0.30868	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.	.	.	.	T	0.08891	0.0220	L	0.35723	1.085	0.09310	N	1	D;P	0.58268	0.982;0.847	B;B	0.42593	0.392;0.188	T	0.24440	-1.0160	8	.	.	.	.	7.0423	0.25027	0.0:0.874:0.0:0.126	.	69;46	Q6JVE9;Q6JVE9-2	LCN8_HUMAN;.	M	46	ENSP00000360753:V46M	.	V	-	1	0	LCN8	138771330	0.598000	0.26882	0.032000	0.17829	0.070000	0.16714	1.531000	0.36018	1.053000	0.40415	-0.254000	0.11334	GTG	.	C|1.000;T|0.000		0.637	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347	
FBXW5	54461	hgsc.bcm.edu	37	9	139837940	139837940	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:139837940T>C	ENST00000325285.3	-	3	291	c.212A>G	c.(211-213)gAg>gGg	p.E71G	C8G_ENST00000224181.3_5'Flank|FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	71					centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		CTGGAACTCCTCGTACCAGGA	0.662																																					p.E71G		Atlas-SNP	.											.	FBXW5	36	.	0			c.A212G						.						50.0	38.0	42.0					9																	139837940		2199	4299	6498	SO:0001583	missense	54461	exon3			AACTCCTCGTACC	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13613	protein-coding gene	gene with protein product		609072	"""F-box and WD-40 domain protein 5"""				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.212A>G	chr9.hg19:g.139837940T>C	ENSP00000313034:p.Glu71Gly	71.0	0.0		62.0	4.0	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	hg19	CCDS7014.1	.	.	.	.	.	.	.	.	.	.	t	10.83	1.461751	0.26248	.	.	ENSG00000159069	ENST00000325285;ENST00000428398;ENST00000443788	T;T;T	0.23348	1.91;1.91;1.91	4.58	4.58	0.56647	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);F-box domain, Skp2-like (1);	0.238551	0.42964	D	0.000624	T	0.15522	0.0374	N	0.24115	0.695	0.33244	D	0.55762	B	0.06786	0.001	B	0.06405	0.002	T	0.17137	-1.0379	10	0.20046	T	0.44	-7.7081	9.3994	0.38424	0.0:0.085:0.0:0.915	.	71	Q969U6	FBXW5_HUMAN	G	71	ENSP00000313034:E71G;ENSP00000404829:E71G;ENSP00000394011:E71G	ENSP00000313034:E71G	E	-	2	0	FBXW5	138957761	1.000000	0.71417	0.937000	0.37676	0.417000	0.31264	4.169000	0.58223	1.672000	0.50884	0.454000	0.30748	GAG	.	.		0.662	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998	
PITRM1	10531	hgsc.bcm.edu	37	10	3208567	3208567	+	Missense_Mutation	SNP	T	T	G	rs4266975|rs148472807|rs28416720	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:3208567T>G	ENST00000224949.4	-	4	306	c.272A>C	c.(271-273)cAg>cCg	p.Q91P	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000451104.2_Missense_Mutation_p.Q59P|PITRM1_ENST00000380989.2_Missense_Mutation_p.Q91P|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	91					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						AGTACGGAACTGCACGCTAGG	0.493																																					p.Q91P		Atlas-SNP	.											PITRM1,colon,carcinoma,0,3	PITRM1	109	.	0			c.A272C						.						102.0	102.0	102.0					10																	3208567		2072	4187	6259	SO:0001583	missense	10531	exon4			CGGAACTGCACGC	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.272A>C	chr10.hg19:g.3208567T>G	ENSP00000224949:p.Gln91Pro	38.0	0.0		25.0	6.0	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	hg19	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	t	9.750	1.167171	0.21621	.	.	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000451104	T;T;T	0.25912	1.77;1.77;1.77	5.36	5.36	0.76844	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.051197	0.85682	D	0.000000	T	0.38585	0.1046	M	0.76002	2.32	0.80722	D	1	P;B;P;P;P;P	0.40332	0.609;0.261;0.713;0.457;0.457;0.612	B;B;P;B;B;B	0.45343	0.425;0.222;0.477;0.284;0.284;0.284	T	0.18903	-1.0322	10	0.37606	T	0.19	.	15.3402	0.74290	0.0:0.0:0.0:1.0	rs28416720	84;59;91;91;91;84	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3;B4DH07	.;.;.;.;PREP_HUMAN;.	P	91;84;91;59	ENSP00000224949:Q91P;ENSP00000370377:Q91P;ENSP00000401201:Q59P	ENSP00000224949:Q91P	Q	-	2	0	PITRM1	3198567	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	4.424000	0.59868	2.024000	0.59613	0.379000	0.24179	CAG	.	.		0.493	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
SFMBT2	57713	hgsc.bcm.edu	37	10	7247842	7247842	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:7247842T>C	ENST00000361972.4	-	12	1469	c.1379A>G	c.(1378-1380)gAc>gGc	p.D460G	SFMBT2_ENST00000397167.1_Missense_Mutation_p.D460G	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	460					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						TGGGAAGATGTCCATGGATTC	0.483																																					p.D460G		Atlas-SNP	.											.	SFMBT2	209	.	0			c.A1379G						.						120.0	106.0	111.0					10																	7247842		2203	4300	6503	SO:0001583	missense	57713	exon12			AAGATGTCCATGG	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"""Sterile alpha motif (SAM) domain containing"""	20256	protein-coding gene	gene with protein product		615392	"""Scm-related gene containing four mbt domains 2"""			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.1379A>G	chr10.hg19:g.7247842T>C	ENSP00000355109:p.Asp460Gly	144.0	0.0		95.0	5.0	NM_001029880	A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	hg19	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.814606	0.90790	.	.	ENSG00000198879	ENST00000361972;ENST00000397167	T;T	0.50277	0.75;0.75	5.57	5.57	0.84162	.	0.042810	0.85682	D	0.000000	T	0.69205	0.3085	M	0.74467	2.265	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.73401	-0.3994	10	0.87932	D	0	.	15.742	0.77905	0.0:0.0:0.0:1.0	.	460	Q5VUG0	SMBT2_HUMAN	G	460	ENSP00000355109:D460G;ENSP00000380353:D460G	ENSP00000355109:D460G	D	-	2	0	SFMBT2	7287848	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.911000	0.87458	2.126000	0.65437	0.533000	0.62120	GAC	.	.		0.483	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880	
MLLT10	8028	hgsc.bcm.edu	37	10	22030912	22030912	+	Nonstop_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:22030912A>G	ENST00000307729.7	+	23	3385	c.3207A>G	c.(3205-3207)tgA>tgG	p.*1069W	MLLT10_ENST00000377059.3_3'UTR|MLLT10_ENST00000446906.2_3'UTR|MLLT10_ENST00000377072.3_3'UTR			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	0					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						AGAAAAGTTGACACCTGAGAA	0.403			T	"""MLL, PICALM, CDK6"""	AL																																p.X1069W		Atlas-SNP	.		Dom	yes		10	10p12	8028	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"""		L	.	MLLT10	183	.	0			c.A3207G						.						185.0	176.0	179.0					10																	22030912		876	1991	2867	SO:0001578	stop_lost	8028	exon22			AAGTTGACACCTG	U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"""Zinc fingers, PHD-type"""	16063	protein-coding gene	gene with protein product		602409	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"""			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.3207A>G	chr10.hg19:g.22030912A>G	ENSP00000307411:p.*1069Trpext*6	166.0	0.0		104.0	6.0	NM_001195626	B1ANA8|Q5JT37|Q5VX90|Q66K63	Missense_Mutation	SNP	ENST00000307729.7	hg19	CCDS55708.1	.	.	.	.	.	.	.	.	.	.	A	16.27	3.075709	0.55646	.	.	ENSG00000078403	ENST00000307729	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0859	0.81049	1.0:0.0:0.0:0.0	.	.	.	.	W	1069	.	.	X	+	3	0	MLLT10	22070918	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.113000	0.77095	2.248000	0.74166	0.460000	0.39030	TGA	.	.		0.403	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1		
ZEB1	6935	hgsc.bcm.edu	37	10	31815839	31815839	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:31815839A>G	ENST00000320985.10	+	9	3132	c.3022A>G	c.(3022-3024)Aat>Gat	p.N1008D	ZEB1_ENST00000446923.2_Missense_Mutation_p.N992D|ZEB1_ENST00000542815.3_Missense_Mutation_p.N941D|ZEB1_ENST00000560721.2_Missense_Mutation_p.N988D|ZEB1_ENST00000361642.5_Missense_Mutation_p.N1009D			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	1008	Glu-rich (acidic).				cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				AATCCTCTCGAATGAGCACGT	0.517																																					p.N1009D	Ovarian(40;423 959 14296 36701 49589)	Atlas-SNP	.											.	ZEB1	173	.	0			c.A3025G						.						80.0	70.0	73.0					10																	31815839		2203	4300	6503	SO:0001583	missense	6935	exon9			CTCTCGAATGAGC	AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	11642	protein-coding gene	gene with protein product		189909	"""transcription factor 8 (represses interleukin 2 expression)"", ""posterior polymorphous corneal dystrophy 3"""	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.3022A>G	chr10.hg19:g.31815839A>G	ENSP00000319248:p.Asn1008Asp	77.0	0.0		66.0	4.0	NM_001174096	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	hg19	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	A	5.511	0.279239	0.10458	.	.	ENSG00000148516	ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000543514;ENST00000446923	T;T;T;T;T	0.13089	2.94;2.62;2.68;2.62;2.68	4.8	-2.06	0.07298	.	3.939600	0.00567	N	0.000282	T	0.10337	0.0253	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B	0.20887	0.009;0.049;0.025;0.049;0.029	B;B;B;B;B	0.23018	0.043;0.016;0.028;0.01;0.006	T	0.31024	-0.9958	10	0.26408	T	0.33	2.9472	8.1131	0.30926	0.4587:0.1381:0.4032:0.0	.	941;992;988;1009;1008	F5H4I8;E9PCM7;Q5VZ84;Q2KJ05;P37275	.;.;.;.;ZEB1_HUMAN	D	790;1008;1009;1003;941;1008;988;899;992	ENSP00000444282:N790D;ENSP00000354487:N1009D;ENSP00000444891:N941D;ENSP00000319248:N1008D;ENSP00000391612:N992D	ENSP00000319248:N1008D	N	+	1	0	ZEB1	31855845	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.475000	0.06599	-0.305000	0.08831	0.477000	0.44152	AAT	.	.		0.517	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751	
NRP1	8829	hgsc.bcm.edu	37	10	33552610	33552610	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:33552610A>G	ENST00000265371.4	-	5	1147	c.622T>C	c.(622-624)Tac>Cac	p.Y208H	NRP1_ENST00000374823.5_Missense_Mutation_p.Y208H|NRP1_ENST00000374822.4_Missense_Mutation_p.Y208H|NRP1_ENST00000374821.5_Missense_Mutation_p.Y208H|NRP1_ENST00000432372.2_Missense_Mutation_p.Y208H|NRP1_ENST00000374875.1_Missense_Mutation_p.Y27H|NRP1_ENST00000374867.2_Missense_Mutation_p.Y208H|NRP1_ENST00000395995.1_Missense_Mutation_p.Y208H|NRP1_ENST00000374816.3_Missense_Mutation_p.Y208H			O14786	NRP1_HUMAN	neuropilin 1	208	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	AGCCGGTCGTAGCGACAGAAC	0.468																																					p.Y208H	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											.	NRP1	126	.	0			c.T622C						.						59.0	59.0	59.0					10																	33552610		2203	4300	6503	SO:0001583	missense	8829	exon4			GGTCGTAGCGACA	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"""CD molecules"""	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.622T>C	chr10.hg19:g.33552610A>G	ENSP00000265371:p.Tyr208His	89.0	0.0		84.0	4.0	NM_001244973	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Missense_Mutation	SNP	ENST00000265371.4	hg19	CCDS7177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.5|21.5	4.163909|4.163909	0.78226|0.78226	.|.	.|.	ENSG00000099250|ENSG00000099250	ENST00000455749|ENST00000265371;ENST00000374875;ENST00000374867;ENST00000395995;ENST00000374822;ENST00000374821;ENST00000374823;ENST00000374816;ENST00000374818	.|T;T;T;T;T;T;T;T	.|0.20881	.|2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04	5.76|5.76	5.76|5.76	0.90799|0.90799	.|CUB (5);	.|0.052690	.|0.85682	.|D	.|0.000000	T|T	0.51346|0.51346	0.1669|0.1669	M|M	0.83774|0.83774	2.66|2.66	0.80722|0.80722	D|D	1|1	.|D;D;D;B;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.396;1.0;1.0;1.0;1.0;1.0	.|D;D;D;P;D;D;D;D;D	.|0.91635	.|0.996;0.994;0.994;0.479;0.978;0.999;0.996;0.996;0.976	T|T	0.57694|0.57694	-0.7767|-0.7767	5|10	.|0.87932	.|D	.|0	-20.3856|-20.3856	16.0734|16.0734	0.80951|0.80951	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|208;208;208;208;208;208;208;27;208	.|A8K9V7;E7EX60;Q5T7F0;Q5T7F1;O14786-2;Q68DN3;O14786;Q5JWQ6;E9PEP6	.|.;.;.;.;.;.;NRP1_HUMAN;.;.	P|H	8|208;27;208;208;208;208;208;208;27	.|ENSP00000265371:Y208H;ENSP00000364009:Y27H;ENSP00000364001:Y208H;ENSP00000379317:Y208H;ENSP00000363955:Y208H;ENSP00000363954:Y208H;ENSP00000363956:Y208H;ENSP00000363949:Y208H	.|ENSP00000265371:Y208H	L|Y	-|-	2|1	0|0	NRP1|NRP1	33592616|33592616	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.921000|0.921000	0.55340|0.55340	9.339000|9.339000	0.96797|0.96797	2.195000|2.195000	0.70347|0.70347	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.	.		0.468	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2		
ZNF33B	7582	hgsc.bcm.edu	37	10	43089012	43089012	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:43089012A>G	ENST00000359467.3	-	5	1500	c.1386T>C	c.(1384-1386)acT>acC	p.T462T	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	462					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						CACCTGTGTGAGTTCTCTGGT	0.398																																					p.T462T	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.T1386C						.						96.0	93.0	94.0					10																	43089012		2203	4300	6503	SO:0001819	synonymous_variant	7582	exon5			TGTGTGAGTTCTC	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"""Zinc fingers, C2H2-type"", ""-"""	13097	protein-coding gene	gene with protein product		194522	"""zinc finger protein 33b (KOX 31)"", ""zinc finger protein 11B"""	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1386T>C	chr10.hg19:g.43089012A>G		164.0	0.0		98.0	4.0	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Silent	SNP	ENST00000359467.3	hg19	CCDS7198.1																																																																																			.	.		0.398	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955	
ALOX5	240	hgsc.bcm.edu	37	10	45939627	45939627	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:45939627A>G	ENST00000374391.2	+	13	1791	c.1738A>G	c.(1738-1740)Aag>Gag	p.K580E	ALOX5_ENST00000542434.1_Intron|RP11-67C2.2_ENST00000435635.1_RNA	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	580	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)			breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	ACCGACTGCCAAGGGCGTGGT	0.687																																					p.K580E		Atlas-SNP	.											.	ALOX5	88	.	0			c.A1738G						.						16.0	15.0	16.0					10																	45939627		2154	4245	6399	SO:0001583	missense	240	exon13			ACTGCCAAGGGCG	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"""Arachidonate lipoxygenases"""	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.1738A>G	chr10.hg19:g.45939627A>G	ENSP00000363512:p.Lys580Glu	109.0	0.0		74.0	4.0	NM_000698	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Missense_Mutation	SNP	ENST00000374391.2	hg19	CCDS7212.1	.	.	.	.	.	.	.	.	.	.	A	33	5.211057	0.95069	.	.	ENSG00000012779	ENST00000374391	D	0.90900	-2.75	4.86	4.86	0.63082	Lipoxygenase, C-terminal (3);	0.045241	0.85682	D	0.000000	D	0.94006	0.8080	M	0.66439	2.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94137	0.7393	10	0.59425	D	0.04	-36.3065	12.4482	0.55664	1.0:0.0:0.0:0.0	.	548;580	E5FPY8;P09917	.;LOX5_HUMAN	E	580	ENSP00000363512:K580E	ENSP00000363512:K580E	K	+	1	0	ALOX5	45259633	1.000000	0.71417	0.985000	0.45067	0.969000	0.65631	9.091000	0.94151	2.048000	0.60808	0.528000	0.53228	AAG	.	.		0.687	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1		
FRMPD2	143162	hgsc.bcm.edu	37	10	49457197	49457197	+	Missense_Mutation	SNP	G	G	A	rs142764597		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:49457197G>A	ENST00000374201.3	-	3	478	c.176C>T	c.(175-177)cCc>cTc	p.P59L	FRMPD2_ENST00000305531.3_Missense_Mutation_p.P57L|FRMPD2_ENST00000407470.4_Missense_Mutation_p.P50L	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	59	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		GGCTGACCAGGGGCAAACCAC	0.557																																					p.P59L		Atlas-SNP	.											.	FRMPD2	157	.	0			c.C176T						.						49.0	51.0	50.0					10																	49457197		2203	4300	6503	SO:0001583	missense	143162	exon3			GACCAGGGGCAAA	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.176C>T	chr10.hg19:g.49457197G>A	ENSP00000363317:p.Pro59Leu	89.0	0.0		83.0	4.0	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	hg19	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	G	18.75	3.690406	0.68271	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.36699	1.24;1.24;1.24	5.47	4.57	0.56435	KIND (2);	.	.	.	.	T	0.59542	0.2201	M	0.80982	2.52	0.47621	D	0.999479	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.63804	-0.6554	9	0.87932	D	0	.	10.1642	0.42871	0.0917:0.0:0.9083:0.0	.	57;59;50	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	L	59;57;50	ENSP00000363317:P59L;ENSP00000307079:P57L;ENSP00000384339:P50L	ENSP00000307079:P57L	P	-	2	0	FRMPD2	49127203	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	5.303000	0.65738	1.333000	0.45449	0.655000	0.94253	CCC	.	G|1.000;T|0.000		0.557	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
WDFY4	57705	hgsc.bcm.edu	37	10	49943958	49943958	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:49943958T>C	ENST00000325239.5	+	10	1748	c.1721T>C	c.(1720-1722)aTc>aCc	p.I574T	WDFY4_ENST00000413659.2_Missense_Mutation_p.I574T|WDFY4_ENST00000360890.2_Missense_Mutation_p.I574T	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	574						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						GTGCCCTTCATCAAGATCTTC	0.537																																					p.I574T		Atlas-SNP	.											.	WDFY4	205	.	0			c.T1721C						.						81.0	66.0	71.0					10																	49943958		692	1591	2283	SO:0001583	missense	57705	exon11			CCTTCATCAAGAT	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.1721T>C	chr10.hg19:g.49943958T>C	ENSP00000320563:p.Ile574Thr	67.0	0.0		60.0	4.0	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	hg19	CCDS44385.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.459870	0.84317	.	.	ENSG00000128815	ENST00000360890;ENST00000454161;ENST00000426033;ENST00000325239;ENST00000413659	T;T;T	0.53423	0.62;0.62;0.62	5.03	5.03	0.67393	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.61924	0.2386	L	0.53249	1.67	0.38063	D	0.93613	D;D	0.76494	0.999;0.999	D;D	0.69479	0.922;0.964	T	0.65290	-0.6204	9	0.42905	T	0.14	.	14.2226	0.65839	0.0:0.0:0.0:1.0	.	574;574	Q6ZS81;Q6ZS81-2	WDFY4_HUMAN;.	T	574;583;574;574;574	ENSP00000354141:I574T;ENSP00000320563:I574T;ENSP00000403789:I574T	ENSP00000320563:I574T	I	+	2	0	WDFY4	49613964	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.423000	0.80229	2.016000	0.59253	0.533000	0.62120	ATC	.	.		0.537	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
VSTM4	196740	hgsc.bcm.edu	37	10	50256529	50256529	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:50256529C>T	ENST00000332853.4	-	6	792	c.769G>A	c.(769-771)Gcc>Acc	p.A257T		NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4	257						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						TTACCTTTGGCAGGGACTGCG	0.547																																					p.A257T		Atlas-SNP	.											.	VSTM4	83	.	0			c.G769A						.						101.0	88.0	92.0					10																	50256529		2203	4300	6503	SO:0001583	missense	196740	exon6			CTTTGGCAGGGAC	BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"""Immunoglobulin superfamily / V-set domain containing"""	26470	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 72"""	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.769G>A	chr10.hg19:g.50256529C>T	ENSP00000331062:p.Ala257Thr	87.0	0.0		51.0	4.0	NM_001031746	B4DNI6|Q96MX7	Missense_Mutation	SNP	ENST00000332853.4	hg19	CCDS31198.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.499386	0.85069	.	.	ENSG00000165633	ENST00000332853	T	0.08634	3.07	6.17	6.17	0.99709	.	0.171431	0.50627	D	0.000108	T	0.17066	0.0410	N	0.19112	0.55	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.01702	-1.1292	10	0.45353	T	0.12	-36.3062	16.3795	0.83443	0.0:1.0:0.0:0.0	.	257	Q8IW00	VSTM4_HUMAN	T	257	ENSP00000331062:A257T	ENSP00000331062:A257T	A	-	1	0	VSTM4	49926535	0.996000	0.38824	0.993000	0.49108	0.916000	0.54674	4.440000	0.59975	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.547	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984	
ERCC6	2074	hgsc.bcm.edu	37	10	50701191	50701191	+	Missense_Mutation	SNP	T	T	C	rs376250875		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:50701191T>C	ENST00000355832.5	-	8	1871	c.1793A>G	c.(1792-1794)cAt>cGt	p.H598R	ERCC6_ENST00000542458.1_Intron	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	598	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						ACCGGTTTCATGTAGAATTGC	0.413								Direct reversal of damage;Nucleotide excision repair (NER)																													p.T598R		Atlas-SNP	.											.	ERCC6	162	.	0			c.C1793G						.	T	ARG/HIS	1,4405	2.1+/-5.4	0,1,2202	107.0	90.0	96.0		1793	5.3	0.2	10		96	0,8600		0,0,4300	no	missense	ERCC6	NM_000124.2	29	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	probably-damaging	598/1494	50701191	1,13005	2203	4300	6503	SO:0001583	missense	2074	exon8			GTTTCATGTAGAA	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.1793A>G	chr10.hg19:g.50701191T>C	ENSP00000348089:p.His598Arg	138.0	0.0		98.0	4.0	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	hg19	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.329218	0.81690	2.27E-4	0.0	ENSG00000225830	ENST00000355832	D	0.94092	-3.35	5.31	5.31	0.75309	DEAD-like helicase (2);SNF2-related (1);	.	.	.	.	D	0.97099	0.9052	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97942	1.0326	9	0.87932	D	0	-21.1423	15.5582	0.76216	0.0:0.0:0.0:1.0	.	598	Q03468	ERCC6_HUMAN	R	598	ENSP00000348089:H598R	ENSP00000348089:H598R	H	-	2	0	ERCC6	50371197	1.000000	0.71417	0.225000	0.23894	0.962000	0.63368	7.997000	0.88414	2.135000	0.66039	0.455000	0.32223	CAT	.	.		0.413	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
ERCC6	2074	hgsc.bcm.edu	37	10	50701217	50701217	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:50701217C>T	ENST00000355832.5	-	8	1845	c.1767G>A	c.(1765-1767)tgG>tgA	p.W589*	ERCC6_ENST00000542458.1_Intron	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	589	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TGAACGGAGGCCACCACGTGT	0.448								Direct reversal of damage;Nucleotide excision repair (NER)																													p.F589L		Atlas-SNP	.											.	ERCC6	162	.	0			c.C1767A						.						122.0	103.0	110.0					10																	50701217		2203	4300	6503	SO:0001587	stop_gained	2074	exon8			CGGAGGCCACCAC	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.1767G>A	chr10.hg19:g.50701217C>T	ENSP00000348089:p.Trp589*	150.0	0.0		109.0	5.0	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	hg19	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	C	39	7.768210	0.98480	.	.	ENSG00000225830	ENST00000355832	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.2819	19.3425	0.94349	0.0:1.0:0.0:0.0	.	.	.	.	X	589	.	ENSP00000348089:W589X	W	-	3	0	ERCC6	50371223	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.776000	0.85560	2.643000	0.89663	0.557000	0.71058	TGG	.	.		0.448	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
CHAT	1103	hgsc.bcm.edu	37	10	50830196	50830196	+	Splice_Site	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:50830196G>T	ENST00000337653.2	+	5	905	c.752G>T	c.(751-753)aGc>aTc	p.S251I	CHAT_ENST00000460699.1_3'UTR|CHAT_ENST00000395562.2_Splice_Site_p.S169I|CHAT_ENST00000455728.2_Splice_Site_p.S133I|CHAT_ENST00000351556.3_Splice_Site_p.S133I|CHAT_ENST00000339797.1_Splice_Site_p.S133I|CHAT_ENST00000395559.2_Splice_Site_p.S133I	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	251					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	CTGCTGGACAGGTAGGACTGG	0.587																																					p.S251I		Atlas-SNP	.											.	CHAT	162	.	0			c.G752T						.						226.0	181.0	196.0					10																	50830196		2203	4300	6503	SO:0001630	splice_region_variant	1103	exon5			TGGACAGGTAGGA	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.752+1G>T	chr10.hg19:g.50830196G>T		147.0	0.0		100.0	4.0	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	hg19	CCDS7232.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827050	0.50739	.	.	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	T;T;T;T;T;T	0.81330	-1.48;-1.48;-1.48;-1.48;-1.48;-1.48	4.85	3.88	0.44766	.	0.280060	0.39544	N	0.001326	T	0.78786	0.4338	M	0.81341	2.54	0.49687	D	0.999818	B;P	0.41624	0.232;0.757	B;B	0.33799	0.051;0.17	D	0.83530	0.0090	10	0.56958	D	0.05	-24.6129	14.401	0.67047	0.0:0.3158:0.6842:0.0	.	133;251	F8W8I2;P28329	.;CLAT_HUMAN	I	133;133;133;251;169;133	ENSP00000343486:S133I;ENSP00000345878:S133I;ENSP00000378926:S133I;ENSP00000337103:S251I;ENSP00000378929:S169I;ENSP00000390521:S133I	ENSP00000337103:S251I	S	+	2	0	CHAT	50500202	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	1.702000	0.37836	2.233000	0.73108	0.561000	0.74099	AGC	.	.		0.587	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	Missense_Mutation
CISD1	55847	hgsc.bcm.edu	37	10	60047332	60047332	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:60047332T>C	ENST00000333926.5	+	3	465	c.249T>C	c.(247-249)tgT>tgC	p.C83C	CISD1_ENST00000488388.2_3'UTR	NM_018464.4	NP_060934.1	Q9NZ45	CISD1_HUMAN	CDGSH iron sulfur domain 1	83					regulation of cellular respiration (GO:0043457)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)			breast(1)	1						TCCCATTCTGTGATGGGGCTC	0.388																																					p.C83C		Atlas-SNP	.											.	CISD1	7	.	0			c.T249C						.						85.0	76.0	79.0					10																	60047332		2203	4300	6503	SO:0001819	synonymous_variant	55847	exon3			ATTCTGTGATGGG	AY960578	CCDS7251.1	10q21.3	2011-01-05	2007-08-10	2007-08-10	ENSG00000122873	ENSG00000122873		"""CDGSH iron sulfur domain containing"""	30880	protein-coding gene	gene with protein product		611932	"""chromosome 10 open reading frame 70"", ""zinc finger, CDGSH-type domain 1"""	C10orf70, ZCD1		17376863, 17584744	Standard	NM_018464		Approved	MDS029, mitoNEET	uc001jkc.5	Q9NZ45	OTTHUMG00000018266	ENST00000333926.5:c.249T>C	chr10.hg19:g.60047332T>C		134.0	0.0		99.0	4.0	NM_018464	Q1X902	Silent	SNP	ENST00000333926.5	hg19	CCDS7251.1																																																																																			.	.		0.388	CISD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048137.1	NM_018464	
SUPV3L1	6832	hgsc.bcm.edu	37	10	70968547	70968547	+	Missense_Mutation	SNP	A	A	G	rs370657076		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:70968547A>G	ENST00000359655.4	+	15	2177	c.2117A>G	c.(2116-2118)cAa>cGa	p.Q706R		NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	706	Interaction with LAMTOR5, important for protein stability.				ATP catabolic process (GO:0006200)|chromatin maintenance (GO:0070827)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA surveillance (GO:0035946)|mitochondrial ncRNA surveillance (GO:0035945)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA surveillance (GO:2000827)|mitochondrion morphogenesis (GO:0070584)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|RNA catabolic process (GO:0006401)	mitochondrial degradosome (GO:0045025)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3'-5' RNA helicase activity (GO:0034458)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TTAAAGAGCCAAGCTAGAAGG	0.502																																					p.Q706R		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.A2117G						.	A	ARG/GLN	0,4406		0,0,2203	81.0	79.0	80.0		2117	-1.3	0.3	10		80	1,8599	1.2+/-3.3	0,1,4299	no	missense	SUPV3L1	NM_003171.3	43	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	706/787	70968547	1,13005	2203	4300	6503	SO:0001583	missense	6832	exon15			AGAGCCAAGCTAG	AF042169	CCDS7287.1	10q22.1	2008-08-01	2001-11-28		ENSG00000156502	ENSG00000156502			11471	protein-coding gene	gene with protein product		605122	"""suppressor of var1 (S.cerevisiae) 3-like 1"""			9925937, 16176273	Standard	XM_005270068		Approved	SUV3	uc001jpe.1	Q8IYB8	OTTHUMG00000018375	ENST00000359655.4:c.2117A>G	chr10.hg19:g.70968547A>G	ENSP00000352678:p.Gln706Arg	155.0	0.0		86.0	4.0	NM_003171	A8K301|O43630	Missense_Mutation	SNP	ENST00000359655.4	hg19	CCDS7287.1	.	.	.	.	.	.	.	.	.	.	A	2.513	-0.312547	0.05422	0.0	1.16E-4	ENSG00000156502	ENST00000359655	T	0.30182	1.54	5.9	-1.34	0.09143	.	0.788806	0.12345	N	0.477145	T	0.15305	0.0369	N	0.22421	0.69	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.31503	-0.9941	10	0.15952	T	0.53	-0.4303	5.8797	0.18848	0.3644:0.4659:0.0621:0.1076	.	706	Q8IYB8	SUV3_HUMAN	R	706	ENSP00000352678:Q706R	ENSP00000352678:Q706R	Q	+	2	0	SUPV3L1	70638553	0.000000	0.05858	0.272000	0.24630	0.100000	0.18952	-0.321000	0.08018	-0.125000	0.11703	-0.323000	0.08544	CAA	.	.		0.502	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171	
PRF1	5551	hgsc.bcm.edu	37	10	72357981	72357981	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:72357981T>C	ENST00000441259.1	-	3	1656	c.1496A>G	c.(1495-1497)cAg>cGg	p.Q499R	PRF1_ENST00000373209.2_Missense_Mutation_p.Q499R	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	499					apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CTTGGGAGCCTGATCACAGGT	0.592			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																												p.Q499R		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.A1496G						.						135.0	134.0	134.0					10																	72357981		2203	4300	6503	SO:0001583	missense	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GGAGCCTGATCAC	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.1496A>G	chr10.hg19:g.72357981T>C	ENSP00000398568:p.Gln499Arg	103.0	0.0		88.0	4.0	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	hg19	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	T	1.891	-0.455536	0.04540	.	.	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.90620	-2.7;-2.7	5.97	-6.99	0.01605	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	2.233410	0.01456	N	0.015679	T	0.80265	0.4591	N	0.10972	0.075	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.72623	-0.4237	10	0.02654	T	1	-2.2068	18.8422	0.92189	0.0:0.7791:0.0:0.2209	.	499	P14222	PERF_HUMAN	R	499	ENSP00000362305:Q499R;ENSP00000398568:Q499R	ENSP00000316746:Q499R	Q	-	2	0	PRF1	72027987	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.642000	0.00204	-1.150000	0.02840	-0.256000	0.11100	CAG	.	.		0.592	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
MICU1	10367	hgsc.bcm.edu	37	10	74267928	74267928	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:74267928T>C	ENST00000361114.5	-	6	733	c.637A>G	c.(637-639)Aca>Gca	p.T213A	MICU1_ENST00000398763.4_5'UTR|MICU1_ENST00000401998.3_Missense_Mutation_p.T213A|MICU1_ENST00000398761.4_Missense_Mutation_p.T215A|MICU1_ENST00000418483.2_Intron	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	213					calcium ion import (GO:0070509)|calcium ion transmembrane import into mitochondrion (GO:0036444)|defense response (GO:0006952)|mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein homooligomerization (GO:0051260)	calcium channel complex (GO:0034704)|integral component of mitochondrial membrane (GO:0032592)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										AGAACAGTTGTGAGGAAAATG	0.333																																					p.T213A		Atlas-SNP	.											.	.	.	.	0			c.A637G						.						60.0	56.0	57.0					10																	74267928		1815	4086	5901	SO:0001583	missense	10367	exon6			CAGTTGTGAGGAA	Y17711	CCDS55714.1, CCDS55715.1	10q22.1	2013-01-10	2011-06-23	2011-06-23	ENSG00000107745	ENSG00000107745		"""EF-hand domain containing"""	1530	protein-coding gene	gene with protein product		605084	"""calcium binding atopy-related autoantigen 1"""	CBARA1		9806765, 20693986	Standard	NM_006077		Approved	CALC, EFHA3, FLJ12684	uc001jtb.2	Q9BPX6	OTTHUMG00000018437	ENST00000361114.5:c.637A>G	chr10.hg19:g.74267928T>C	ENSP00000354415:p.Thr213Ala	100.0	0.0		97.0	4.0	NM_001195518	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Missense_Mutation	SNP	ENST00000361114.5	hg19	CCDS55715.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.195170	0.78902	.	.	ENSG00000107745	ENST00000361114;ENST00000398761;ENST00000401998	T;T;T	0.79845	-1.31;-1.31;-1.31	5.23	5.23	0.72850	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.70193	0.3196	N	0.12182	0.205	0.80722	D	1	P	0.45715	0.865	P	0.45913	0.497	T	0.69829	-0.5039	10	0.23302	T	0.38	.	15.0724	0.72049	0.0:0.0:0.0:1.0	.	213	Q9BPX6	MICU1_HUMAN	A	213;215;213	ENSP00000354415:T213A;ENSP00000381745:T215A;ENSP00000384068:T213A	ENSP00000354415:T213A	T	-	1	0	MICU1	73937934	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.704000	0.84595	2.090000	0.63153	0.383000	0.25322	ACA	.	.		0.333	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077	
FUT11	170384	hgsc.bcm.edu	37	10	75532420	75532420	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:75532420G>A	ENST00000372841.3	+	1	372	c.329G>A	c.(328-330)cGa>cAa	p.R110Q	RMRPP1_ENST00000517236.1_RNA|AC022400.2_ENST00000595757.1_5'Flank|FUT11_ENST00000394790.1_Missense_Mutation_p.R110Q|FUT11_ENST00000465695.1_3'UTR	NM_173540.2	NP_775811.2	Q495W5	FUT11_HUMAN	fucosyltransferase 11 (alpha (1,3) fucosyltransferase)	110					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	7	Prostate(51;0.0112)					CGGAACCGCCGAGCGCTGAGG	0.736																																					p.R110Q		Atlas-SNP	.											.	FUT11	30	.	0			c.G329A						.						5.0	5.0	5.0					10																	75532420		1954	3835	5789	SO:0001583	missense	170384	exon1			ACCGCCGAGCGCT	BC036037	CCDS7333.1, CCDS60558.1	10q22.3	2014-01-02			ENSG00000196968	ENSG00000196968		"""Fucosyltransferases"""	19233	protein-coding gene	gene with protein product						11698403, 24318988	Standard	NM_173540		Approved	MGC33202	uc001jva.3	Q495W5	OTTHUMG00000018483	ENST00000372841.3:c.329G>A	chr10.hg19:g.75532420G>A	ENSP00000361932:p.Arg110Gln	15.0	0.0		20.0	4.0	NM_173540	Q495W7|Q8IYE4	Missense_Mutation	SNP	ENST00000372841.3	hg19	CCDS7333.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.176976	0.38413	.	.	ENSG00000196968	ENST00000372841;ENST00000394790	T;T	0.25579	1.79;1.79	5.26	5.26	0.73747	.	0.459795	0.25285	N	0.031767	T	0.21674	0.0522	L	0.31371	0.925	0.09310	N	1	B;B;P	0.47545	0.045;0.062;0.897	B;B;P	0.45856	0.046;0.027;0.495	T	0.11299	-1.0593	10	0.19147	T	0.46	-33.8039	11.9208	0.52791	0.0811:0.0:0.9189:0.0	.	110;110;110	Q495W5;Q495W5-2;B2RC53	FUT11_HUMAN;.;.	Q	110	ENSP00000361932:R110Q;ENSP00000378270:R110Q	ENSP00000361932:R110Q	R	+	2	0	FUT11	75202426	0.990000	0.36364	0.007000	0.13788	0.039000	0.13416	5.570000	0.67398	2.466000	0.83321	0.462000	0.41574	CGA	.	.		0.736	FUT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048689.1	NM_173540	
KAT6B	23522	hgsc.bcm.edu	37	10	76788662	76788662	+	Silent	SNP	A	A	G	rs546432678|rs544824146	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:76788662A>G	ENST00000287239.4	+	18	4569	c.4080A>G	c.(4078-4080)gaA>gaG	p.E1360E	KAT6B_ENST00000372711.1_Silent_p.E1177E|KAT6B_ENST00000372725.1_Silent_p.E1068E|KAT6B_ENST00000372724.1_Silent_p.E1068E|KAT6B_ENST00000372714.1_Silent_p.E1068E	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1360	Poly-Glu.				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)										aggaggaggaagaggaagaag	0.453													A|||	11	0.00219649	0.0	0.0	5008	,	,		20164	0.0		0.0	False		,,,				2504	0.0112				p.E1360E		Atlas-SNP	.											.	.	.	.	0			c.A4080G						.						43.0	42.0	42.0					10																	76788662		2203	4300	6503	SO:0001819	synonymous_variant	23522	exon18			GGAGGAAGAGGAA	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.4080A>G	chr10.hg19:g.76788662A>G		37.0	0.0		39.0	5.0	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.		0.453	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	
RPS24	6229	hgsc.bcm.edu	37	10	79795311	79795311	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:79795311A>G	ENST00000372360.3	+	3	149	c.112A>G	c.(112-114)Aca>Gca	p.T38A	RPS24_ENST00000476545.1_3'UTR|RPS24_ENST00000360830.4_Missense_Mutation_p.T38A|RPS24_ENST00000435275.1_Missense_Mutation_p.T38A|RPS24_ENST00000440692.1_Missense_Mutation_p.T38A	NM_001026.4	NP_001017.1	P62847	RS24_HUMAN	ribosomal protein S24	38					cellular protein metabolic process (GO:0044267)|erythrocyte homeostasis (GO:0034101)|gene expression (GO:0010467)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)|translation initiation factor binding (GO:0031369)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(2)|skin(1)	5	all_cancers(46;0.0343)|all_epithelial(25;0.000959)|Breast(12;0.00113)|Prostate(51;0.0095)		Epithelial(14;0.00128)|OV - Ovarian serous cystadenocarcinoma(4;0.00248)|all cancers(16;0.00428)			AGTGCCTAAGACAGAAATTCG	0.408																																					p.T38A		Atlas-SNP	.											.	RPS24	23	.	0			c.A112G						.						64.0	62.0	63.0					10																	79795311		2203	4300	6503	SO:0001583	missense	6229	exon3			CCTAAGACAGAAA	AB007159	CCDS7355.1, CCDS7356.1, CCDS44443.1	10q22	2011-04-06			ENSG00000138326	ENSG00000138326		"""S ribosomal proteins"""	10411	protein-coding gene	gene with protein product		602412				9027498, 9582194	Standard	NM_001142283		Approved	S24	uc001jzs.3	P62847	OTTHUMG00000018549	ENST00000372360.3:c.112A>G	chr10.hg19:g.79795311A>G	ENSP00000361435:p.Thr38Ala	71.0	0.0		70.0	4.0	NM_001142283	E7EPK6|P16632|Q5T0P7|Q5T0P8|Q7Z3D1	Missense_Mutation	SNP	ENST00000372360.3	hg19	CCDS7355.1	.	.	.	.	.	.	.	.	.	.	A	19.16	3.772812	0.69992	.	.	ENSG00000138326	ENST00000440692;ENST00000435275;ENST00000372360;ENST00000401656;ENST00000360830	.	.	.	5.07	5.07	0.68467	Ribosomal protein L23/L15e (1);Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.68622	0.3021	L	0.55481	1.735	0.80722	D	1	P;P;B;B	0.42248	0.473;0.774;0.329;0.329	B;P;B;B	0.51742	0.329;0.678;0.327;0.327	T	0.67554	-0.5641	8	.	.	.	.	14.8512	0.70297	1.0:0.0:0.0:0.0	.	38;38;38;38	P62847-3;E7EPK6;P62847;E7ETK0	.;.;RS24_HUMAN;.	A	38	.	.	T	+	1	0	RPS24	79465317	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	9.283000	0.95860	1.895000	0.54865	0.496000	0.49642	ACA	.	.		0.408	RPS24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048910.1	NM_001026	
MAT1A	4143	hgsc.bcm.edu	37	10	82049166	82049166	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:82049166A>G	ENST00000372213.3	-	1	274	c.14T>C	c.(13-15)gTg>gCg	p.V5A		NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	5					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	CAAGCCATCCACCGGTCCATT	0.473																																					p.V5A		Atlas-SNP	.											.	MAT1A	52	.	0			c.T14C						.						172.0	154.0	160.0					10																	82049166		2203	4300	6503	SO:0001583	missense	4143	exon1			CCATCCACCGGTC		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"""S-adenosylmethionine synthetase"""	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.14T>C	chr10.hg19:g.82049166A>G	ENSP00000361287:p.Val5Ala	179.0	0.0		85.0	6.0	NM_000429	D3DWD5|Q5QP09	Missense_Mutation	SNP	ENST00000372213.3	hg19	CCDS7365.1	.	.	.	.	.	.	.	.	.	.	A	12.34	1.907577	0.33721	.	.	ENSG00000151224	ENST00000372213;ENST00000372206	D	0.96011	-3.88	5.34	5.34	0.76211	.	0.541473	0.19334	N	0.116836	D	0.86301	0.5900	N	0.02916	-0.46	0.35460	D	0.796464	B	0.02656	0.0	B	0.04013	0.001	D	0.83742	0.0204	10	0.10111	T	0.7	-25.9898	13.554	0.61749	1.0:0.0:0.0:0.0	.	5	Q00266	METK1_HUMAN	A	5	ENSP00000361287:V5A	ENSP00000361280:V5A	V	-	2	0	MAT1A	82039146	1.000000	0.71417	0.990000	0.47175	0.799000	0.45148	3.481000	0.53179	2.156000	0.67533	0.533000	0.62120	GTG	.	.		0.473	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429	
LRIT1	26103	hgsc.bcm.edu	37	10	86001096	86001096	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:86001096T>C	ENST00000372105.3	-	1	121	c.100A>G	c.(100-102)Atg>Gtg	p.M34V		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	34	LRRNT.					integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						CCATCACCCATGATATGGAGG	0.642																																					p.M34V		Atlas-SNP	.											.	LRIT1	73	.	0			c.A100G						.						34.0	34.0	34.0					10																	86001096		2203	4298	6501	SO:0001583	missense	26103	exon1			CACCCATGATATG	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	23404	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 9"""		"""leucine rich repeat containing 21"""	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.100A>G	chr10.hg19:g.86001096T>C	ENSP00000361177:p.Met34Val	89.0	0.0		84.0	4.0	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	hg19	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	T	9.527	1.109711	0.20714	.	.	ENSG00000148602	ENST00000372105	T	0.32753	1.44	4.31	2.4	0.29515	Leucine-rich repeat-containing N-terminal (1);	0.172115	0.39834	N	0.001256	T	0.14399	0.0348	N	0.14661	0.345	0.22253	N	0.999258	B	0.02656	0.0	B	0.01281	0.0	T	0.31943	-0.9925	10	0.02654	T	1	.	11.5821	0.50898	0.0:0.0:0.5319:0.4681	.	34	Q9P2V4	LRIT1_HUMAN	V	34	ENSP00000361177:M34V	ENSP00000361177:M34V	M	-	1	0	LRIT1	85991076	1.000000	0.71417	0.998000	0.56505	0.791000	0.44710	0.975000	0.29449	0.423000	0.26033	-0.677000	0.03784	ATG	.	.		0.642	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
WAPAL	23063	hgsc.bcm.edu	37	10	88259819	88259819	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:88259819T>C	ENST00000298767.5	-	3	1653	c.1181A>G	c.(1180-1182)gAa>gGa	p.E394G		NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	394	Mediates interaction with the cohesin complex.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						ACGACCAGCTTCTCCCAAATC	0.393																																					p.E394G		Atlas-SNP	.											.	WAPAL	81	.	0			c.A1181G						.						59.0	61.0	60.0					10																	88259819		2203	4300	6503	SO:0001583	missense	23063	exon3			CCAGCTTCTCCCA	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"""friend of EBNA2"""	610754	"""KIAA0261"""	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.1181A>G	chr10.hg19:g.88259819T>C	ENSP00000298767:p.Glu394Gly	163.0	0.0		113.0	5.0	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.057235	0.55325	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076	T	0.37584	1.19	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.54838	0.1883	L	0.53249	1.67	0.80722	D	1	D;D;D	0.76494	0.987;0.987;0.999	P;P;D	0.67382	0.755;0.755;0.951	T	0.57860	-0.7738	10	0.87932	D	0	.	15.6594	0.77174	0.0:0.0:0.0:1.0	.	394;394;437	B2RTX8;Q7Z5K2;Q7Z5K2-2	.;WAPL_HUMAN;.	G	479;394;479	ENSP00000298767:E394G	ENSP00000298767:E394G	E	-	2	0	WAPAL	88249799	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.102000	0.63906	0.528000	0.53228	GAA	.	.		0.393	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045	
IFIT2	3433	hgsc.bcm.edu	37	10	91066406	91066406	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:91066406A>G	ENST00000371826.3	+	2	862	c.693A>G	c.(691-693)gaA>gaG	p.E231E	LIPA_ENST00000487618.1_Intron|LIPA_ENST00000371837.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	231					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				AGGAAGGTGAAGGAGAGAAGT	0.473																																					p.E231E		Atlas-SNP	.											.	IFIT2	39	.	0			c.A693G						.						74.0	73.0	73.0					10																	91066406		1980	4178	6158	SO:0001819	synonymous_variant	3433	exon2			AGGTGAAGGAGAG	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"""Tetratricopeptide (TTC) repeat domain containing"""	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.693A>G	chr10.hg19:g.91066406A>G		92.0	0.0		72.0	4.0	NM_001547	Q5T767	Silent	SNP	ENST00000371826.3	hg19	CCDS41548.1																																																																																			.	.		0.473	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547	
IFIT1B	439996	hgsc.bcm.edu	37	10	91144106	91144106	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:91144106C>T	ENST00000371809.3	+	2	1116	c.1036C>T	c.(1036-1038)Ctg>Ttg	p.L346L	LIPA_ENST00000371837.1_Intron	NM_001010987.2	NP_001010987.1	Q5T764	IFT1B_HUMAN	interferon-induced protein with tetratricopeptide repeats 1B	346										endometrium(2)|large_intestine(3)|lung(8)	13						CTATGTTGACCTGGCTGAAAC	0.403																																					p.L346L		Atlas-SNP	.											.	IFIT1B	39	.	0			c.C1036T						.						69.0	66.0	67.0					10																	91144106		2203	4300	6503	SO:0001819	synonymous_variant	439996	exon2			GTTGACCTGGCTG		CCDS31242.1	10q23.31	2014-05-22	2010-03-22	2010-03-22	ENSG00000204010	ENSG00000204010		"""Tetratricopeptide (TTC) repeat domain containing"""	23442	protein-coding gene	gene with protein product			"""interferon-induced protein with tetratricopeptide repeats 1-like"""	IFIT1L			Standard	NM_001010987		Approved	bA149I23.6	uc001kgh.3	Q5T764	OTTHUMG00000018709	ENST00000371809.3:c.1036C>T	chr10.hg19:g.91144106C>T		60.0	0.0		61.0	4.0	NM_001010987	A7E245	Silent	SNP	ENST00000371809.3	hg19	CCDS31242.1																																																																																			.	.		0.403	IFIT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049296.3	NM_001010987	
TCTN3	26123	hgsc.bcm.edu	37	10	97453399	97453399	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:97453399A>G	ENST00000371217.5	-	1	280		c.e1+1		TCTN3_ENST00000430368.2_Splice_Site|TCTN3_ENST00000371209.5_Splice_Site|TCTN3_ENST00000265993.9_Splice_Site			Q6NUS6	TECT3_HUMAN	tectonic family member 3						apoptotic process (GO:0006915)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(3)|endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		GTTTTCCCTCACCTGGGAAGA	0.567											OREG0020392	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	TCTN3	66	.	0			c.256+2T>C						.						34.0	37.0	36.0					10																	97453399		692	1591	2283	SO:0001630	splice_region_variant	26123	exon2			TCCCTCACCTGGG	AK098295	CCDS31258.2, CCDS44461.1	10q24.1	2014-01-28	2007-08-20	2007-08-20	ENSG00000119977	ENSG00000119977		"""Tectonic proteins"""	24519	protein-coding gene	gene with protein product		613847	"""chromosome 10 open reading frame 61"""	C10orf61		12975309	Standard	NM_015631		Approved	DKFZP564D116, TECT3, JBTS18	uc001klb.4	Q6NUS6	OTTHUMG00000018814	ENST00000371217.5:c.256+1T>C	chr10.hg19:g.97453399A>G		72.0	0.0	1328	53.0	4.0	NM_015631	A6NIC8|B0QZ90|B4DR81|Q6P7P3|Q6UW27|Q6ZQQ0|Q8N7K1|Q8NBQ0|Q96GF7|Q9Y3U1	Splice_Site	SNP	ENST00000371217.5	hg19	CCDS31258.2	.	.	.	.	.	.	.	.	.	.	A	9.381	1.073010	0.20147	.	.	ENSG00000119977	ENST00000265993;ENST00000430368;ENST00000371217;ENST00000371209;ENST00000424175	.	.	.	4.54	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5619	0.45150	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TCTN3	97443389	1.000000	0.71417	1.000000	0.80357	0.037000	0.13140	3.854000	0.55949	2.274000	0.75844	0.533000	0.62120	.	.	.		0.567	TCTN3-009	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000471858.1	NM_015631	Intron
C10orf12	26148	hgsc.bcm.edu	37	10	98743214	98743214	+	Silent	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:98743214C>A	ENST00000286067.2	+	1	2174	c.2067C>A	c.(2065-2067)acC>acA	p.T689T		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	689										NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		ACGAAAACACCCAGCAGAAAG	0.522																																					p.T689T		Atlas-SNP	.											.	C10orf12	94	.	0			c.C2067A						.						77.0	68.0	71.0					10																	98743214		2203	4300	6503	SO:0001819	synonymous_variant	26148	exon1			AAACACCCAGCAG	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.2067C>A	chr10.hg19:g.98743214C>A		84.0	0.0		57.0	4.0	NM_015652	Q9H945|Q9Y457	Silent	SNP	ENST00000286067.2	hg19	CCDS7452.1																																																																																			.	.		0.522	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652	
ANKRD2	26287	hgsc.bcm.edu	37	10	99342105	99342105	+	Missense_Mutation	SNP	A	A	G	rs534926101		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:99342105A>G	ENST00000307518.5	+	7	1036	c.769A>G	c.(769-771)Aca>Gca	p.T257A	HOGA1_ENST00000370646.4_5'Flank|HOGA1_ENST00000370647.4_5'Flank|ANKRD2_ENST00000455090.1_Intron|PI4K2A_ENST00000370649.3_5'Flank|ANKRD2_ENST00000370655.1_Missense_Mutation_p.T230A|PI4K2A_ENST00000555577.1_5'Flank|ANKRD2_ENST00000298808.5_Intron			Q9GZV1	ANKR2_HUMAN	ankyrin repeat domain 2 (stretch responsive muscle)	257					muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|euchromatin (GO:0000791)|I band (GO:0031674)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	protein kinase B binding (GO:0043422)|structural constituent of muscle (GO:0008307)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7		all_hematologic(284;1.95e-06)|Colorectal(252;0.0163)		Epithelial(162;1.18e-94)|all cancers(201;9.31e-86)|BRCA - Breast invasive adenocarcinoma(275;0.0233)|STAD - Stomach adenocarcinoma(243;0.181)|KIRC - Kidney renal clear cell carcinoma(50;0.206)|Kidney(138;0.241)		GGCAGTCCGGACAGGGCAGGT	0.622																																					p.T257A		Atlas-SNP	.											.	ANKRD2	27	.	0			c.A769G						.						55.0	42.0	47.0					10																	99342105		2189	4287	6476	SO:0001583	missense	26287	exon7			GTCCGGACAGGGC	AJ304805	CCDS7466.1, CCDS44468.1	10q23	2013-01-10			ENSG00000165887	ENSG00000165887		"""Ankyrin repeat domain containing"""	495	protein-coding gene	gene with protein product		610734				10873377, 15136035, 15677738	Standard	NM_001129981		Approved	ARPP	uc001knw.3	Q9GZV1	OTTHUMG00000018860	ENST00000307518.5:c.769A>G	chr10.hg19:g.99342105A>G	ENSP00000306163:p.Thr257Ala	113.0	0.0		65.0	5.0	NM_020349	Q3B778|Q5T456|Q70EZ9|Q8WUD7|Q96MG0|Q9NQC9	Missense_Mutation	SNP	ENST00000307518.5	hg19	CCDS7466.1	.	.	.	.	.	.	.	.	.	.	A	17.10	3.304274	0.60305	.	.	ENSG00000165887	ENST00000307518;ENST00000370655	T;T	0.61980	0.06;0.06	5.6	5.6	0.85130	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000001	T	0.62768	0.2455	N	0.16016	0.355	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.59600	-0.7424	10	0.15066	T	0.55	-15.7438	14.7787	0.69749	1.0:0.0:0.0:0.0	.	257	Q9GZV1	ANKR2_HUMAN	A	257;230	ENSP00000306163:T257A;ENSP00000359689:T230A	ENSP00000306163:T257A	T	+	1	0	ANKRD2	99332095	1.000000	0.71417	0.983000	0.44433	0.039000	0.13416	8.102000	0.89548	2.131000	0.65755	0.533000	0.62120	ACA	.	.		0.622	ANKRD2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
R3HCC1L	27291	hgsc.bcm.edu	37	10	100003864	100003864	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:100003864A>G	ENST00000298999.3	+	10	2589	c.2286A>G	c.(2284-2286)gaA>gaG	p.E762E	R3HCC1L_ENST00000370584.3_Silent_p.E762E|R3HCC1L_ENST00000370586.2_Silent_p.E168E|R3HCC1L_ENST00000314594.5_Silent_p.E178E	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	776							nucleotide binding (GO:0000166)										AGCGGTTGGAAGCCAAGCAAC	0.393																																					p.E776E		Atlas-SNP	.											.	R3HCC1L	3	.	0			c.A2328G						.						123.0	113.0	116.0					10																	100003864		2203	4300	6503	SO:0001819	synonymous_variant	27291	exon11			GTTGGAAGCCAAG	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 28"""	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.2286A>G	chr10.hg19:g.100003864A>G		112.0	0.0		87.0	4.0	NM_001256619	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Silent	SNP	ENST00000298999.3	hg19	CCDS31267.1																																																																																			.	.		0.393	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472	
CNNM1	26507	hgsc.bcm.edu	37	10	101136951	101136951	+	Silent	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:101136951C>A	ENST00000356713.4	+	7	2605	c.2316C>A	c.(2314-2316)atC>atA	p.I772I	CNNM1_ENST00000370534.4_Silent_p.I428I|CNNM1_ENST00000370528.3_Silent_p.I701I|CNNM1_ENST00000488090.1_3'UTR|CNNM1_ENST00000446890.1_Silent_p.I701I	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	772					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		CAGTCCACATCCTCAGCGATG	0.562																																					p.I772I		Atlas-SNP	.											.	CNNM1	101	.	0			c.C2316A						.						135.0	100.0	112.0					10																	101136951		2203	4300	6503	SO:0001819	synonymous_variant	26507	exon7			CCACATCCTCAGC	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"""cyclin M1"""	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.2316C>A	chr10.hg19:g.101136951C>A		154.0	0.0		100.0	4.0	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Silent	SNP	ENST00000356713.4	hg19	CCDS7478.2																																																																																			.	.		0.562	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348	
HPS6	79803	hgsc.bcm.edu	37	10	103827332	103827332	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:103827332C>T	ENST00000299238.5	+	1	2186	c.2101C>T	c.(2101-2103)Cca>Tca	p.P701S		NM_024747.5	NP_079023.2	Q86YV9	HPS6_HUMAN	Hermansky-Pudlak syndrome 6	701					blood coagulation (GO:0007596)|melanocyte differentiation (GO:0030318)|organelle organization (GO:0006996)|protein localization to membrane (GO:0072657)	BLOC-2 complex (GO:0031084)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|Rab GTPase binding (GO:0017137)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)	11		Colorectal(252;0.122)		Epithelial(162;5.93e-08)|all cancers(201;1.03e-06)		AGAACTGGCTCCAGCTGAGCT	0.617									Hermansky-Pudlak syndrome																												p.P701S		Atlas-SNP	.											.	HPS6	38	.	0			c.C2101T						.						53.0	57.0	55.0					10																	103827332		2203	4300	6503	SO:0001583	missense	79803	exon1	Familial Cancer Database	HPS, HPS1-8	CTGGCTCCAGCTG	BC009258	CCDS7527.1	10q24.32	2014-06-18			ENSG00000166189	ENSG00000166189			18817	protein-coding gene	gene with protein product		607522				12548288	Standard	NM_024747		Approved	FLJ22501	uc001kuj.3	Q86YV9	OTTHUMG00000018945	ENST00000299238.5:c.2101C>T	chr10.hg19:g.103827332C>T	ENSP00000299238:p.Pro701Ser	55.0	0.0		56.0	4.0	NM_024747	Q5VV69|Q9H685	Missense_Mutation	SNP	ENST00000299238.5	hg19	CCDS7527.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.843076	0.51057	.	.	ENSG00000166189	ENST00000299238	T	0.80123	-1.34	4.85	4.85	0.62838	.	0.304358	0.31624	N	0.007329	T	0.78629	0.4313	L	0.54323	1.7	0.32302	N	0.564953	P	0.47910	0.902	P	0.46543	0.52	T	0.83190	-0.0084	10	0.49607	T	0.09	-8.5036	10.2382	0.43297	0.1491:0.7061:0.1447:0.0	.	701	Q86YV9	HPS6_HUMAN	S	701	ENSP00000299238:P701S	ENSP00000299238:P701S	P	+	1	0	HPS6	103817322	0.994000	0.37717	1.000000	0.80357	0.982000	0.71751	1.838000	0.39211	2.520000	0.84964	0.561000	0.74099	CCA	.	.		0.617	HPS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050018.2	NM_024747	
NFKB2	4791	hgsc.bcm.edu	37	10	104160556	104160556	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:104160556G>A	ENST00000369966.3	+	17	2193	c.1943G>A	c.(1942-1944)gGg>gAg	p.G648E	NFKB2_ENST00000428099.1_Missense_Mutation_p.G648E|NFKB2_ENST00000189444.6_Missense_Mutation_p.G648E	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	648			Missing (in truncated form EB308).		extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	GAGGAGCTGGGGTTGGTCACC	0.632			T	IGH@	B-NHL																																p.G648E		Atlas-SNP	.		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	.	NFKB2	48	.	0			c.G1943A						.						25.0	29.0	28.0					10																	104160556		2016	4177	6193	SO:0001583	missense	4791	exon17			AGCTGGGGTTGGT	X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"""Ankyrin repeat domain containing"""	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.1943G>A	chr10.hg19:g.104160556G>A	ENSP00000358983:p.Gly648Glu	115.0	0.0		100.0	4.0	NM_001077494	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	hg19	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	G	14.27	2.486303	0.44147	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	T;T;T	0.58940	0.3;0.3;0.3	4.43	4.43	0.53597	Ankyrin repeat-containing domain (4);	0.177576	0.49916	D	0.000133	T	0.22513	0.0543	N	0.01668	-0.77	0.32311	N	0.563732	P;P	0.43231	0.801;0.801	B;B	0.41374	0.355;0.355	T	0.45702	-0.9243	10	0.05351	T	0.99	.	5.9021	0.18972	0.2381:0.0:0.7619:0.0	.	648;648	Q00653;A8K9D9	NFKB2_HUMAN;.	E	648	ENSP00000410256:G648E;ENSP00000358983:G648E;ENSP00000189444:G648E	ENSP00000189444:G648E	G	+	2	0	NFKB2	104150546	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.852000	0.55934	2.478000	0.83669	0.561000	0.74099	GGG	.	.		0.632	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2		
PSD	5662	hgsc.bcm.edu	37	10	104164802	104164802	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:104164802T>C	ENST00000020673.5	-	14	2934	c.2408A>G	c.(2407-2409)aAg>aGg	p.K803R	PSD_ENST00000406432.1_Missense_Mutation_p.K803R	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	803	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		CTTCCCAGGCTTGTACTCCTC	0.617																																					p.K803R		Atlas-SNP	.											PSD_ENST00000020673,NS,carcinoma,0,2	PSD	164	.	0			c.A2408G						.						77.0	70.0	73.0					10																	104164802		2203	4300	6503	SO:0001583	missense	5662	exon15			CCAGGCTTGTACT	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"""Pleckstrin homology (PH) domain containing"""	9507	protein-coding gene	gene with protein product		602327	"""pleckstrin and Sec7 domain protein"""			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.2408A>G	chr10.hg19:g.104164802T>C	ENSP00000020673:p.Lys803Arg	162.0	1.0		125.0	6.0	NM_001270965	B1AKX7|D3DR87|Q15673|Q8IVG0	Missense_Mutation	SNP	ENST00000020673.5	hg19	CCDS31272.1	.	.	.	.	.	.	.	.	.	.	T	11.20	1.568739	0.28003	.	.	ENSG00000059915	ENST00000020673;ENST00000541902;ENST00000406432	T;T	0.38722	1.12;1.12	4.81	4.81	0.61882	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.336296	0.30859	N	0.008724	T	0.28764	0.0713	N	0.25094	0.71	0.27671	N	0.946755	B;B;B	0.12630	0.0;0.006;0.001	B;B;B	0.17098	0.004;0.017;0.007	T	0.10109	-1.0644	10	0.13108	T	0.6	.	14.5823	0.68300	0.0:0.0:0.0:1.0	.	803;706;424	A5PKW4;Q86YI3;A5PKW4-2	PSD1_HUMAN;.;.	R	803;706;803	ENSP00000020673:K803R;ENSP00000384830:K803R	ENSP00000020673:K803R	K	-	2	0	PSD	104154792	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.382000	0.59594	2.033000	0.60031	0.449000	0.29647	AAG	.	.		0.617	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2		
TRIM8	81603	hgsc.bcm.edu	37	10	104414949	104414949	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:104414949A>G	ENST00000302424.7	+	3	901	c.779A>G	c.(778-780)aAg>aGg	p.K260R	TRIM8_ENST00000487927.1_3'UTR	NM_030912.2	NP_112174.2	Q9BZR9	TRIM8_HUMAN	tripartite motif containing 8	260					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|PML body (GO:0016605)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GCCCAGGCCAAGTTCTGCAGC	0.622																																					p.K260R		Atlas-SNP	.											.	TRIM8	35	.	0			c.A779G						.						58.0	54.0	55.0					10																	104414949		2203	4300	6503	SO:0001583	missense	81603	exon3			AGGCCAAGTTCTG	AF281046	CCDS31274.1	10q24.3	2013-01-09	2011-01-25	2002-06-14	ENSG00000171206	ENSG00000171206		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	15579	protein-coding gene	gene with protein product	"""glioblastoma expressed ring finger protein"""	606125	"""ring finger protein 27"", ""tripartite motif-containing 8"""	RNF27		11118312, 12163497	Standard	NM_030912		Approved	GERP	uc001kvz.2	Q9BZR9	OTTHUMG00000018964	ENST00000302424.7:c.779A>G	chr10.hg19:g.104414949A>G	ENSP00000302120:p.Lys260Arg	124.0	0.0		96.0	4.0	NM_030912	A6NI31|Q9C028	Missense_Mutation	SNP	ENST00000302424.7	hg19	CCDS31274.1	.	.	.	.	.	.	.	.	.	.	A	12.47	1.946762	0.34377	.	.	ENSG00000171206	ENST00000302424;ENST00000369896	T	0.58060	0.36	5.55	5.55	0.83447	.	0.062472	0.64402	D	0.000004	T	0.36331	0.0963	N	0.14661	0.345	0.51482	D	0.99992	B	0.10296	0.003	B	0.04013	0.001	T	0.15435	-1.0437	10	0.20519	T	0.43	.	15.6992	0.77528	1.0:0.0:0.0:0.0	.	260	Q9BZR9	TRIM8_HUMAN	R	260;259	ENSP00000302120:K260R	ENSP00000302120:K260R	K	+	2	0	TRIM8	104404939	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.869000	0.75521	2.122000	0.65172	0.459000	0.35465	AAG	.	.		0.622	TRIM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050084.3	NM_030912	
CALHM3	119395	hgsc.bcm.edu	37	10	105233172	105233172	+	Missense_Mutation	SNP	T	T	G	rs199875922		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:105233172T>G	ENST00000369783.4	-	3	1040	c.833A>C	c.(832-834)gAa>gCa	p.E278A		NM_001129742.1	NP_001123214.1	Q86XJ0	CAHM3_HUMAN	calcium homeostasis modulator 3	284					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)	2						ATCCAGGCCTTCTGGGGGCTC	0.677																																					p.E278A		Atlas-SNP	.											CALHM3_ENST00000369783,caecum,carcinoma,0,2	CALHM3	46	.	0			c.A833C						.						14.0	21.0	19.0					10																	105233172		691	1591	2282	SO:0001583	missense	119395	exon3			AGGCCTTCTGGGG	BC043367	CCDS44476.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000183128	ENSG00000183128			23458	protein-coding gene	gene with protein product			"""family with sequence similarity 26, member A"""	FAM26A		18585350	Standard	NM_001129742		Approved	bA225H22.7	uc001kxg.4	Q86XJ0	OTTHUMG00000018989	ENST00000369783.4:c.833A>C	chr10.hg19:g.105233172T>G	ENSP00000358798:p.Glu278Ala	34.0	0.0		25.0	3.0	NM_001129742	Q5W090|Q8IXR2	Missense_Mutation	SNP	ENST00000369783.4	hg19	CCDS44476.1	.	.	.	.	.	.	.	.	.	.	T	13.96	2.393488	0.42410	.	.	ENSG00000183128	ENST00000369783	T	0.19532	2.14	4.76	3.63	0.41609	.	1.221790	0.05735	N	0.600248	T	0.23210	0.0561	L	0.54323	1.7	0.20307	N	0.999916	B	0.06786	0.001	B	0.09377	0.004	T	0.35375	-0.9791	10	0.21014	T	0.42	0.3558	10.1651	0.42875	0.0:0.0785:0.0:0.9215	.	278	Q86XJ0-2	.	A	278	ENSP00000358798:E278A	ENSP00000358798:E278A	E	-	2	0	CALHM3	105223162	0.000000	0.05858	0.005000	0.12908	0.419000	0.31324	0.156000	0.16382	0.852000	0.35287	0.379000	0.24179	GAA	.	.		0.677	CALHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050157.1	NM_182494	
CALHM3	119395	hgsc.bcm.edu	37	10	105233174	105233174	+	Silent	SNP	T	T	G	rs143800079	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:105233174T>G	ENST00000369783.4	-	3	1038	c.831A>C	c.(829-831)ccA>ccC	p.P277P		NM_001129742.1	NP_001123214.1	Q86XJ0	CAHM3_HUMAN	calcium homeostasis modulator 3	283					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)	2						CCAGGCCTTCTGGGGGCTCAG	0.672																																					p.P277P		Atlas-SNP	.											.,4	CALHM3	46	.	0			c.A831C						.						14.0	21.0	19.0					10																	105233174		691	1591	2282	SO:0001819	synonymous_variant	119395	exon3			GCCTTCTGGGGGC	BC043367	CCDS44476.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000183128	ENSG00000183128			23458	protein-coding gene	gene with protein product			"""family with sequence similarity 26, member A"""	FAM26A		18585350	Standard	NM_001129742		Approved	bA225H22.7	uc001kxg.4	Q86XJ0	OTTHUMG00000018989	ENST00000369783.4:c.831A>C	chr10.hg19:g.105233174T>G		32.0	0.0		24.0	3.0	NM_001129742	Q5W090|Q8IXR2	Silent	SNP	ENST00000369783.4	hg19	CCDS44476.1																																																																																			.	.		0.672	CALHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050157.1	NM_182494	
SLK	9748	hgsc.bcm.edu	37	10	105750545	105750545	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:105750545A>G	ENST00000369755.3	+	2	808	c.263A>G	c.(262-264)cAc>cGc	p.H88R	SLK_ENST00000335753.4_Missense_Mutation_p.H88R	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	88	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		TCTTGTGATCACCCAAATATA	0.353																																					p.H88R	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.A263G						.						128.0	119.0	122.0					10																	105750545		2203	4300	6503	SO:0001583	missense	9748	exon2			GTGATCACCCAAA		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.263A>G	chr10.hg19:g.105750545A>G	ENSP00000358770:p.His88Arg	114.0	0.0		127.0	37.0	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	hg19	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.816069	0.90790	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.78481	-1.18;-1.18	6.17	6.17	0.99709	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	0.93579	0.7950	H	0.99261	4.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96145	0.9103	10	0.87932	D	0	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	88;88	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	R	88	ENSP00000336824:H88R;ENSP00000358770:H88R	ENSP00000336824:H88R	H	+	2	0	SLK	105740535	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.213000	0.95133	2.371000	0.80710	0.533000	0.62120	CAC	.	.		0.353	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720	
SMNDC1	10285	hgsc.bcm.edu	37	10	112054041	112054041	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:112054041T>C	ENST00000369603.5	-	6	787	c.584A>G	c.(583-585)aAg>aGg	p.K195R	SMNDC1_ENST00000369592.1_Missense_Mutation_p.K195R	NM_005871.3	NP_005862.1	O75940	SPF30_HUMAN	survival motor neuron domain containing 1	195					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)	4		Breast(234;0.174)		Epithelial(162;6.86e-05)|all cancers(201;0.00149)|BRCA - Breast invasive adenocarcinoma(275;0.119)		AATACTCCTCTTTACCTAAGG	0.323																																					p.K195R		Atlas-SNP	.											.	SMNDC1	9	.	0			c.A584G						.						110.0	105.0	107.0					10																	112054041		2203	4300	6503	SO:0001583	missense	10285	exon6			CTCCTCTTTACCT	AF083385	CCDS7565.1	10q23	2013-01-23			ENSG00000119953	ENSG00000119953		"""Tudor domain containing"""	16900	protein-coding gene	gene with protein product	"""splicing factor 30, survival of motor neuron-related"", ""tudor domain containing 16C"""	603519				9731529, 9817934	Standard	NM_005871		Approved	SPF30, SMNR, TDRD16C	uc001kzc.4	O75940	OTTHUMG00000019036	ENST00000369603.5:c.584A>G	chr10.hg19:g.112054041T>C	ENSP00000358616:p.Lys195Arg	115.0	0.0		95.0	4.0	NM_005871	B2RA27|D3DRB1|Q5T3K6	Missense_Mutation	SNP	ENST00000369603.5	hg19	CCDS7565.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.306303	0.81247	.	.	ENSG00000119953	ENST00000369603;ENST00000369592	D;D	0.89485	-2.52;-2.52	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.92011	0.7469	L	0.46885	1.475	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	D	0.91304	0.5069	10	0.38643	T	0.18	-17.0481	16.1699	0.81801	0.0:0.0:0.0:1.0	.	195	O75940	SPF30_HUMAN	R	195	ENSP00000358616:K195R;ENSP00000358605:K195R	ENSP00000358605:K195R	K	-	2	0	SMNDC1	112044031	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.008000	0.88588	2.229000	0.72834	0.533000	0.62120	AAG	.	.		0.323	SMNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050325.2	NM_005871	
ATRNL1	26033	hgsc.bcm.edu	37	10	116931101	116931101	+	Intron	SNP	C	C	T	rs397754330|rs3086141|rs113157696	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:116931101C>T	ENST00000355044.3	+	8	1474				ATRNL1_ENST00000529665.1_3'UTR	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1						G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		ATGTTTTTCTCTAATAAAATC	0.234																																					p.L467L		Atlas-SNP	.											.	ATRNL1	219	.	0			c.C1399T						.						33.0	35.0	35.0					10																	116931101		2174	4276	6450	SO:0001627	intron_variant	26033	exon8			TTTTCTCTAATAA	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.1348+51C>T	chr10.hg19:g.116931101C>T		171.0	0.0		128.0	9.0	NM_001276282	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	hg19	CCDS7592.1																																																																																			.	C|0.500;T|0.500		0.234	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349	
TACC2	10579	hgsc.bcm.edu	37	10	123842981	123842981	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr10:123842981A>G	ENST00000369005.1	+	4	1306	c.966A>G	c.(964-966)gaA>gaG	p.E322E	TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515273.1_Silent_p.E322E|TACC2_ENST00000453444.2_Silent_p.E322E|TACC2_ENST00000334433.3_Silent_p.E322E|TACC2_ENST00000515603.1_Silent_p.E322E|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	322					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CTGCCCCAGAAGCAGAAGTGA	0.607																																					p.E322E		Atlas-SNP	.											.	TACC2	271	.	0			c.A966G						.						33.0	41.0	38.0					10																	123842981		2203	4299	6502	SO:0001819	synonymous_variant	10579	exon4			CCCAGAAGCAGAA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.966A>G	chr10.hg19:g.123842981A>G		64.0	0.0		61.0	5.0	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.		0.607	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
LRRC56	115399	hgsc.bcm.edu	37	11	552650	552650	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:552650A>G	ENST00000270115.7	+	13	1763	c.1263A>G	c.(1261-1263)caA>caG	p.Q421Q		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	421										kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGAAGAGCAAGTGCACCAGG	0.687																																					p.Q421Q		Atlas-SNP	.											.	LRRC56	23	.	0			c.A1263G						.						24.0	27.0	26.0					11																	552650		2188	4295	6483	SO:0001819	synonymous_variant	115399	exon13			AGAGCAAGTGCAC		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.1263A>G	chr11.hg19:g.552650A>G		116.0	0.0		124.0	5.0	NM_198075	Q8N3Q4	Silent	SNP	ENST00000270115.7	hg19	CCDS7700.1																																																																																			.	.		0.687	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075	
PNPLA2	57104	hgsc.bcm.edu	37	11	821745	821745	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:821745T>C	ENST00000336615.4	+	3	507	c.305T>C	c.(304-306)cTg>cCg	p.L102P	AP006621.8_ENST00000528982.1_RNA|AP006621.8_ENST00000532946.1_RNA	NM_020376.3	NP_065109.1	Q96AD5	PLPL2_HUMAN	patatin-like phospholipase domain containing 2	102	Patatin.				acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|negative regulation of sequestering of triglyceride (GO:0010891)|phospholipid metabolic process (GO:0006644)|positive regulation of triglyceride catabolic process (GO:0010898)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|lung(4)|prostate(1)|urinary_tract(1)	9		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.63e-25)|Epithelial(43;1.28e-24)|OV - Ovarian serous cystadenocarcinoma(40;7.09e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGAAGGTCCTGCCTGCTGAT	0.567																																					p.L102P		Atlas-SNP	.											.	PNPLA2	26	.	0			c.T305C						.						72.0	65.0	67.0					11																	821745		2203	4299	6502	SO:0001583	missense	57104	exon3			AGGTCCTGCCTGC	AJ278475	CCDS7718.1	11p15.5	2014-03-14			ENSG00000177666	ENSG00000177666	3.1.1.3	"""Patatin-like phospholipase domain containing"""	30802	protein-coding gene	gene with protein product		609059				8619474, 16799181, 19029121	Standard	NM_020376		Approved	desnutrin, TTS-2.2, ATGL, FP17548, iPLA2zeta	uc001lrt.3	Q96AD5	OTTHUMG00000133309	ENST00000336615.4:c.305T>C	chr11.hg19:g.821745T>C	ENSP00000337701:p.Leu102Pro	102.0	0.0		99.0	4.0	NM_020376	O60643|Q5EFF5|Q6XYE5|Q96ET6|Q9NQ61|Q9NQ62	Missense_Mutation	SNP	ENST00000336615.4	hg19	CCDS7718.1	.	.	.	.	.	.	.	.	.	.	T	16.38	3.105865	0.56291	.	.	ENSG00000177666	ENST00000336615	D	0.85013	-1.93	4.24	4.24	0.50183	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.077664	0.53938	D	0.000054	D	0.94182	0.8133	H	0.95679	3.705	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.95603	0.8665	10	0.87932	D	0	-15.3366	13.4886	0.61382	0.0:0.0:0.0:1.0	.	102	Q96AD5	PLPL2_HUMAN	P	102	ENSP00000337701:L102P	ENSP00000337701:L102P	L	+	2	0	PNPLA2	811745	1.000000	0.71417	0.700000	0.30305	0.055000	0.15305	7.753000	0.85153	1.781000	0.52344	0.459000	0.35465	CTG	.	.		0.567	PNPLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257106.1	NM_020376	
MUC6	4588	hgsc.bcm.edu	37	11	1025876	1025876	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:1025876T>C	ENST00000421673.2	-	22	2778	c.2728A>G	c.(2728-2730)Atc>Gtc	p.I910V		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	910	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCTGTCAGGATCTTGAAGGTG	0.647																																					p.I910V		Atlas-SNP	.											.	MUC6	408	.	0			c.A2728G						.						50.0	56.0	54.0					11																	1025876		2091	4210	6301	SO:0001583	missense	4588	exon22			TCAGGATCTTGAA	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.2728A>G	chr11.hg19:g.1025876T>C	ENSP00000406861:p.Ile910Val	113.0	0.0		81.0	4.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	T	0.026	-1.368889	0.01225	.	.	ENSG00000184956	ENST00000421673	T	0.57107	0.42	4.15	-2.45	0.06481	von Willebrand factor, type D domain (3);	.	.	.	.	T	0.26011	0.0634	N	0.11673	0.155	0.09310	N	1	B	0.25272	0.122	B	0.25884	0.064	T	0.29882	-0.9997	9	0.06625	T	0.88	.	9.5356	0.39220	0.0:0.4365:0.0:0.5635	.	910	Q6W4X9	MUC6_HUMAN	V	910	ENSP00000406861:I910V	ENSP00000406861:I910V	I	-	1	0	MUC6	1015876	0.006000	0.16342	0.025000	0.17156	0.373000	0.29922	0.056000	0.14256	-0.434000	0.07275	0.260000	0.18958	ATC	.	.		0.647	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
C11orf40	143501	hgsc.bcm.edu	37	11	4592711	4592712	+	Missense_Mutation	DNP	TT	TT	AG	rs78543312|rs78387367		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:4592711_4592712TT>AG	ENST00000307616.1	-	4	594_595	c.595_596AA>CT	c.(595-597)AAc>CTc	p.N199L		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	199										large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		atccatacagtttttccCTGCA	0.441																																					p.N199I|p.N199H		Atlas-SNP	.											.	C11orf40	37	.	0			c.A596T|c.A595C						.																																			SO:0001583	missense	143501	exon4			ATACAGTTTTTCC|TACAGTTTTTCCC		CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.595_596delinsAG	chr11.hg19:g.4592711_4592712delinsAG	ENSP00000302918:p.Asn199Leu	236.0|234.0	0.0		203.0|198.0	17.0|12.0	NM_144663		Missense_Mutation	SNP	ENST00000307616.1	hg19	CCDS31354.1																																																																																			.	.		0.441	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663	
OR51B4	79339	hgsc.bcm.edu	37	11	5322255	5322255	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:5322255T>C	ENST00000380224.1	-	1	971	c.922A>G	c.(922-924)Agt>Ggt	p.S308G	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_033179.2	NP_149419.2	Q9Y5P0	O51B4_HUMAN	olfactory receptor, family 51, subfamily B, member 4	308					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)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAAGCCCTACTCTGCCCAGAA	0.403																																					p.S308G		Atlas-SNP	.											.	OR51B4	64	.	0			c.A922G						.						49.0	49.0	49.0					11																	5322255		2201	4297	6498	SO:0001583	missense	79339	exon1			CCCTACTCTGCCC	BC069094	CCDS7757.1	11p15.4	2012-08-09			ENSG00000183251	ENSG00000183251		"""GPCR / Class A : Olfactory receptors"""	14708	protein-coding gene	gene with protein product							Standard	NM_033179		Approved		uc010qza.2	Q9Y5P0	OTTHUMG00000066665	ENST00000380224.1:c.922A>G	chr11.hg19:g.5322255T>C	ENSP00000369573:p.Ser308Gly	84.0	0.0		72.0	4.0	NM_033179	A7MAV5|Q6NTD7	Missense_Mutation	SNP	ENST00000380224.1	hg19	CCDS7757.1	.	.	.	.	.	.	.	.	.	.	T	4.688	0.127852	0.08981	.	.	ENSG00000183251	ENST00000380224	T	0.00005	9.78	4.01	1.67	0.24075	.	1.351800	0.05103	N	0.487474	T	0.00039	0.0001	N	0.08118	0	0.09310	N	1	B	0.19331	0.035	B	0.14578	0.011	T	0.01228	-1.1412	10	0.32370	T	0.25	.	5.6113	0.17406	0.0:0.2286:0.0:0.7714	.	308	Q9Y5P0	O51B4_HUMAN	G	308	ENSP00000369573:S308G	ENSP00000369573:S308G	S	-	1	0	OR51B4	5278831	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.894000	0.28350	0.238000	0.21222	-0.256000	0.11100	AGT	.	.		0.403	OR51B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142956.2	NM_033179	
TRIM3	10612	hgsc.bcm.edu	37	11	6471835	6471835	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:6471835A>G	ENST00000525074.1	-	10	2281	c.1887T>C	c.(1885-1887)gcT>gcC	p.A629A	TRIM3_ENST00000536344.1_Silent_p.A510A|TRIM3_ENST00000359518.3_Silent_p.A629A|TRIM3_ENST00000537602.1_Silent_p.A551A|TRIM3_ENST00000345851.3_Silent_p.A629A	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	629					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)		TGTTGTTCACAGCCACAAAAT	0.478																																					p.A629A	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.T1887C						.						94.0	81.0	86.0					11																	6471835		2201	4296	6497	SO:0001819	synonymous_variant	10612	exon10			GTTCACAGCCACA	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.1887T>C	chr11.hg19:g.6471835A>G		84.0	0.0		101.0	5.0	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	hg19	CCDS7764.1																																																																																			.	.		0.478	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
DNHD1	144132	hgsc.bcm.edu	37	11	6567219	6567219	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:6567219A>G	ENST00000527990.2	+	19	5050	c.5050A>G	c.(5050-5052)Acc>Gcc	p.T1684A	DNHD1_ENST00000254579.6_Missense_Mutation_p.T1684A			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1684					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)		GGCCTGTGGGACCGTACTGGG	0.587																																					p.T1684A		Atlas-SNP	.											.	DNHD1	198	.	0			c.A5050G						.						90.0	79.0	82.0					11																	6567219		692	1591	2283	SO:0001583	missense	144132	exon21			TGTGGGACCGTAC	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.5050A>G	chr11.hg19:g.6567219A>G	ENSP00000436180:p.Thr1684Ala	145.0	0.0		118.0	5.0	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.694861	0.00731	.	.	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.05319	3.46;3.46	5.56	-0.506	0.11989	.	0.419590	0.26590	N	0.023525	T	0.01523	0.0049	N	0.00771	-1.2	0.20975	N	0.999812	B	0.14805	0.011	B	0.15052	0.012	T	0.48127	-0.9062	10	0.02654	T	1	.	9.9803	0.41809	0.4312:0.0:0.5688:0.0	.	1684	Q96M86	DNHD1_HUMAN	A	1684	ENSP00000254579:T1684A;ENSP00000436180:T1684A	ENSP00000254579:T1684A	T	+	1	0	DNHD1	6523795	0.724000	0.28038	0.921000	0.36526	0.296000	0.27459	0.190000	0.17057	0.089000	0.17243	0.533000	0.62120	ACC	.	.		0.587	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
ZNF215	7762	hgsc.bcm.edu	37	11	6977409	6977409	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:6977409C>T	ENST00000278319.5	+	7	1789	c.1201C>T	c.(1201-1203)Cac>Tac	p.H401Y	ZNF215_ENST00000529903.1_Intron|ZNF215_ENST00000414517.2_Missense_Mutation_p.H401Y	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	401					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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(4)	32				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		TCAGATCATTCACACAGGAGA	0.403																																					p.H401Y		Atlas-SNP	.											.	ZNF215	72	.	0			c.C1201T						.						74.0	72.0	73.0					11																	6977409		2201	4296	6497	SO:0001583	missense	7762	exon7			ATCATTCACACAG	AF056618	CCDS7775.1	11p15.4	2013-01-09			ENSG00000149054	ENSG00000149054		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13007	protein-coding gene	gene with protein product		605016					Standard	XM_005253130		Approved	ZKSCAN11, ZSCAN43	uc001mey.3	Q9UL58	OTTHUMG00000165507	ENST00000278319.5:c.1201C>T	chr11.hg19:g.6977409C>T	ENSP00000278319:p.His401Tyr	68.0	0.0		76.0	4.0	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	hg19	CCDS7775.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.777075	0.90195	.	.	ENSG00000149054	ENST00000278319;ENST00000414517	T;T	0.67523	-0.27;-0.27	4.85	4.85	0.62838	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47852	D	0.000220	D	0.86037	0.5837	M	0.93978	3.48	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89404	0.3698	10	0.87932	D	0	-8.6708	15.8711	0.79119	0.0:1.0:0.0:0.0	.	401	Q9UL58	ZN215_HUMAN	Y	401	ENSP00000278319:H401Y;ENSP00000393202:H401Y	ENSP00000278319:H401Y	H	+	1	0	ZNF215	6933985	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.504000	0.66968	2.689000	0.91719	0.655000	0.94253	CAC	.	.		0.403	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1		
RPL27A	6157	hgsc.bcm.edu	37	11	8704765	8704765	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:8704765A>G	ENST00000314138.6	+	2	423	c.20A>G	c.(19-21)aAg>aGg	p.K7R	RPL27A_ENST00000526562.1_5'UTR|RPL27A_ENST00000531978.1_Missense_Mutation_p.K7R|RP11-152H18.4_ENST00000534169.1_RNA|SNORA45_ENST00000391305.1_RNA|RPL27A_ENST00000530913.1_5'Flank|SNORA3_ENST00000364113.1_RNA|RPL27A_ENST00000532359.1_Missense_Mutation_p.K7R|RPL27A_ENST00000530022.1_5'UTR|RPL27A_ENST00000524496.1_5'UTR	NM_000990.4	NP_000981.1	P46776	RL27A_HUMAN	ribosomal protein L27a	7					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|lung(1)	2				Epithelial(150;3.24e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGACTGAGGAAGACCCGGAAA	0.622																																					p.K7R		Atlas-SNP	.											.	RPL27A	5	.	0			c.A20G						.						69.0	71.0	70.0					11																	8704765		2201	4296	6497	SO:0001583	missense	6157	exon2			TGAGGAAGACCCG	U14968	CCDS7790.1	11p15	2011-04-06				ENSG00000166441		"""L ribosomal proteins"""	10329	protein-coding gene	gene with protein product		603637				7772601, 9582194	Standard	NM_000990		Approved	L27A	uc001mgs.4	P46776		ENST00000314138.6:c.20A>G	chr11.hg19:g.8704765A>G	ENSP00000346015:p.Lys7Arg	101.0	0.0		78.0	4.0	NM_000990	B2R4B3	Missense_Mutation	SNP	ENST00000314138.6	hg19	CCDS7790.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.3|23.3	4.403285|4.403285	0.83230|0.83230	.|.	.|.	ENSG00000166441|ENSG00000166441	ENST00000314138;ENST00000531978;ENST00000532359|ENST00000525981	.|.	.|.	.|.	4.96|4.96	4.96|4.96	0.65561|0.65561	Ribosomal protein L18e/L15P (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.78285|0.78285	0.4259|0.4259	M|M	0.84683|0.84683	2.71|2.71	0.80722|0.80722	D|D	1|1	P|.	0.42620|.	0.785|.	P|.	0.50049|.	0.629|.	T|T	0.81093|0.81093	-0.1089|-0.1089	9|5	0.72032|.	D|.	0.01|.	-18.0389|-18.0389	14.773|14.773	0.69693|0.69693	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	7|.	P46776|.	RL27A_HUMAN|.	R|G	7|2	.|.	ENSP00000346015:K7R|.	K|R	+|+	2|1	0|2	RPL27A|RPL27A	8661341|8661341	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.146000|8.146000	0.89626|0.89626	2.207000|2.207000	0.71202|0.71202	0.533000|0.533000	0.62120|0.62120	AAG|AGA	.	.		0.622	RPL27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386506.1	NM_000990	
NUCB2	4925	hgsc.bcm.edu	37	11	17352477	17352477	+	Nonsense_Mutation	SNP	T	T	A	rs535406012|rs3842269	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:17352477T>A	ENST00000529010.1	+	13	1421	c.1202T>A	c.(1201-1203)tTa>tAa	p.L401*	NUCB2_ENST00000458064.2_Nonsense_Mutation_p.L371*|NUCB2_ENST00000323688.6_Nonsense_Mutation_p.L401*	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	401	Binds to necdin. {ECO:0000250}.					cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						CAAAAAAAATTACAACAAGGA	0.323																																					p.L401X		Atlas-SNP	.											.	NUCB2	31	.	0			c.T1202A						.						47.0	42.0	44.0					11																	17352477		1800	4062	5862	SO:0001587	stop_gained	4925	exon13			AAAAATTACAACA	AF052642	CCDS41623.1	11p15.1	2013-01-10						"""EF-hand domain containing"""	8044	protein-coding gene	gene with protein product		608020				7811391	Standard	NM_005013		Approved	NEFA	uc001mmw.3	P80303		ENST00000529010.1:c.1202T>A	chr11.hg19:g.17352477T>A	ENSP00000436455:p.Leu401*	300.0	0.0		304.0	17.0	NM_005013	A8K642|D3DQX5|Q8NFT5	Nonsense_Mutation	SNP	ENST00000529010.1	hg19	CCDS41623.1	.	.	.	.	.	.	.	.	.	.	T	37	6.521637	0.97633	.	.	ENSG00000070081	ENST00000323688;ENST00000529010;ENST00000458064	.	.	.	5.46	5.46	0.80206	.	0.481828	0.22040	N	0.065466	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	-0.1802	9.9647	0.41717	0.0:0.076:0.0:0.924	.	.	.	.	X	401;401;371	.	ENSP00000320168:L401X	L	+	2	0	NUCB2	17309053	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.443000	0.44881	2.063000	0.61619	0.460000	0.39030	TTA	.	.		0.323	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387614.2	NM_005013	
NUCB2	4925	hgsc.bcm.edu	37	11	17352479	17352480	+	Missense_Mutation	DNP	CA	CA	TT	rs189362726|rs535406012|rs3842269	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:17352479_17352480CA>TT	ENST00000529010.1	+	13	1423_1424	c.1204_1205CA>TT	c.(1204-1206)CAa>TTa	p.Q402L	NUCB2_ENST00000458064.2_Missense_Mutation_p.Q372L|NUCB2_ENST00000323688.6_Missense_Mutation_p.Q402L	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	402	Binds to necdin. {ECO:0000250}.		Missing. {ECO:0000269|PubMed:12087473, ECO:0000269|PubMed:14702039}.			cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						AAAAAAATTACAACAAGGAATT	0.322																																					p.Q402X|p.Q402L		Atlas-SNP	.											.	NUCB2	31	.	0			c.C1204T|c.A1205T						.																																			SO:0001583	missense	4925	exon13			AAATTACAACAAG|AATTACAACAAGG	AF052642	CCDS41623.1	11p15.1	2013-01-10						"""EF-hand domain containing"""	8044	protein-coding gene	gene with protein product		608020				7811391	Standard	NM_005013		Approved	NEFA	uc001mmw.3	P80303		Exception_encountered	chr11.hg19:g.17352479_17352480delinsTT	ENSP00000436455:p.Gln402Leu	9.0|6.0	0.0		43.0	18.0|20.0	NM_005013	A8K642|D3DQX5|Q8NFT5	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000529010.1	hg19	CCDS41623.1																																																																																			.	.		0.322	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387614.2	NM_005013	
FIBIN	387758	hgsc.bcm.edu	37	11	27016470	27016470	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:27016470T>C	ENST00000318627.2	+	1	843	c.397T>C	c.(397-399)Tcg>Ccg	p.S133P		NM_203371.1	NP_976249.1	Q8TAL6	FIBIN_HUMAN	fin bud initiation factor homolog (zebrafish)	133						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)				breast(1)|endometrium(2)|lung(7)|upper_aerodigestive_tract(1)	11						CTACTCCAACTCGGACAAATC	0.582																																					p.S133P		Atlas-SNP	.											.	FIBIN	19	.	0			c.T397C						.						72.0	64.0	67.0					11																	27016470		2203	4299	6502	SO:0001583	missense	387758	exon1			TCCAACTCGGACA	BC026873	CCDS7861.1	11p14.2	2008-12-03				ENSG00000176971			33747	protein-coding gene	gene with protein product						17196583	Standard	NM_203371		Approved	MGC24932	uc001mrd.3	Q8TAL6		ENST00000318627.2:c.397T>C	chr11.hg19:g.27016470T>C	ENSP00000321962:p.Ser133Pro	43.0	0.0		51.0	5.0	NM_203371		Missense_Mutation	SNP	ENST00000318627.2	hg19	CCDS7861.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.228808	0.79576	.	.	ENSG00000176971	ENST00000318627	.	.	.	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.65491	0.2696	L	0.29908	0.895	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.65635	-0.6120	9	0.42905	T	0.14	-8.3857	15.0311	0.71708	0.0:0.0:0.0:1.0	.	133	Q8TAL6	FIBIN_HUMAN	P	133	.	ENSP00000321962:S133P	S	+	1	0	FIBIN	26973046	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.612000	0.82975	2.240000	0.73641	0.477000	0.44152	TCG	.	.		0.582	FIBIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387945.1	NM_203371	
DCDC1	341019	hgsc.bcm.edu	37	11	30900222	30900222	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:30900222G>C	ENST00000597505.1	-	36	5260	c.5261C>G	c.(5260-5262)gCc>gGc	p.A1754G				P59894	DCDC1_HUMAN	doublecortin domain containing 1	0					intracellular signal transduction (GO:0035556)					central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|pancreas(2)|prostate(1)|skin(1)|stomach(1)	31	Lung SC(675;0.225)					TCGGATTCTGGCATAATTTGC	0.393																																					p.A861G		Atlas-SNP	.											.	DCDC5	137	.	0			c.C2582G						.						96.0	92.0	93.0					11																	30900222		1937	4136	6073	SO:0001583	missense	100506627	exon19			ATTCTGGCATAAT	AY247970	CCDS7872.1	11p14.1	2013-05-22			ENSG00000170959	ENSG00000170959			20625	protein-coding gene	gene with protein product		608062				12820024	Standard	NM_181807		Approved		uc001msv.3	P59894	OTTHUMG00000150144	ENST00000597505.1:c.5261C>G	chr11.hg19:g.30900222G>C	ENSP00000472625:p.Ala1754Gly	90.0	0.0		95.0	39.0	NM_020869	A6PVL6|B7WNX6|Q6ZU04	Missense_Mutation	SNP	ENST00000597505.1	hg19																																																																																				.	.		0.393	DCDC1-010	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000463167.1	NM_181807	
QSER1	79832	hgsc.bcm.edu	37	11	32955843	32955843	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:32955843T>C	ENST00000399302.2	+	4	2987	c.2652T>C	c.(2650-2652)ggT>ggC	p.G884G	QSER1_ENST00000527788.1_Silent_p.G645G	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	884										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					TTGAAGATGGTGATTCTAAAT	0.388																																					p.G884G		Atlas-SNP	.											.	QSER1	153	.	0			c.T2652C						.						81.0	76.0	78.0					11																	32955843		1887	4118	6005	SO:0001819	synonymous_variant	79832	exon4			AGATGGTGATTCT	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.2652T>C	chr11.hg19:g.32955843T>C		189.0	0.0		112.0	5.0	NM_001076786	Q6ZU30|Q6ZUR5	Silent	SNP	ENST00000399302.2	hg19	CCDS41631.1																																																																																			.	.		0.388	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774	
CD44	960	hgsc.bcm.edu	37	11	35222635	35222635	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:35222635C>T	ENST00000428726.2	+	8	1052	c.929C>T	c.(928-930)aCc>aTc	p.T310I	CD44_ENST00000449691.2_Missense_Mutation_p.T310I|CD44_ENST00000526669.2_Intron|CD44_ENST00000433354.2_Missense_Mutation_p.T310I|CD44_ENST00000352818.4_Intron|CD44_ENST00000415148.2_Missense_Mutation_p.T267I|CD44_ENST00000278386.6_Intron|CD44_ENST00000434472.2_Intron|CD44_ENST00000437706.2_Missense_Mutation_p.T310I|CD44_ENST00000433892.2_Intron|CD44_ENST00000263398.6_Intron|CD44_ENST00000360158.4_Intron	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	310	Stem.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	ACAGTTTCAACCACACCACGG	0.463																																					p.T310I		Atlas-SNP	.											.	CD44	48	.	0			c.C929T						.						158.0	163.0	162.0					11																	35222635		2202	4298	6500	SO:0001583	missense	960	exon8			TTTCAACCACACC	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.929C>T	chr11.hg19:g.35222635C>T	ENSP00000398632:p.Thr310Ile	62.0	0.0		67.0	4.0	NM_000610	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Missense_Mutation	SNP	ENST00000428726.2	hg19	CCDS7897.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.606861	0.46527	.	.	ENSG00000026508	ENST00000415148;ENST00000433354;ENST00000449691;ENST00000437706;ENST00000428726	T;T;T;T;T	0.21031	2.75;2.03;2.03;2.03;2.03	5.64	3.73	0.42828	.	0.340058	0.25464	N	0.030500	T	0.19805	0.0476	L	0.53249	1.67	0.47698	D	0.999494	B;B	0.17465	0.004;0.022	B;B	0.17433	0.007;0.018	T	0.03202	-1.1061	10	0.41790	T	0.15	-3.7328	8.3869	0.32505	0.0:0.7611:0.1543:0.0846	.	267;310	P16070-4;P16070	.;CD44_HUMAN	I	267;310;310;310;310	ENSP00000389830:T267I;ENSP00000414567:T310I;ENSP00000391008:T310I;ENSP00000403990:T310I;ENSP00000398632:T310I	ENSP00000389830:T267I	T	+	2	0	CD44	35179211	0.991000	0.36638	0.847000	0.33407	0.816000	0.46133	1.332000	0.33805	0.690000	0.31570	0.655000	0.94253	ACC	.	.		0.463	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
AMBRA1	55626	hgsc.bcm.edu	37	11	46456589	46456589	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:46456589T>C	ENST00000458649.2	-	13	3051		c.e13-2		AMBRA1_ENST00000314845.3_Splice_Site|AMBRA1_ENST00000534300.1_Splice_Site|AMBRA1_ENST00000528950.1_Splice_Site|AMBRA1_ENST00000298834.3_Splice_Site|AMBRA1_ENST00000426438.1_Splice_Site|AMBRA1_ENST00000533727.1_Splice_Site			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1						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)		TCACGGAAGCTGCATCAGACA	0.468																																					.		Atlas-SNP	.											.	AMBRA1	201	.	0			c.2363-2A>G						.						26.0	24.0	25.0					11																	46456589		2201	4299	6500	SO:0001630	splice_region_variant	55626	exon15			GGAAGCTGCATCA	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.2633-2A>G	chr11.hg19:g.46456589T>C		78.0	0.0		96.0	4.0	NM_017749	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Splice_Site	SNP	ENST00000458649.2	hg19		.	.	.	.	.	.	.	.	.	.	T	26.7	4.763378	0.89932	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000458649;ENST00000528950	.	.	.	5.95	5.95	0.96441	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4237	0.83790	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	AMBRA1	46413165	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.853000	0.86934	2.279000	0.76181	0.533000	0.62120	.	.	.		0.468	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749	Intron
OR4B1	119765	hgsc.bcm.edu	37	11	48239231	48239231	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:48239231A>G	ENST00000309562.2	+	1	888	c.870A>G	c.(868-870)gcA>gcG	p.A290A		NM_001005470.1	NP_001005470.1	Q8NGF8	OR4B1_HUMAN	olfactory receptor, family 4, subfamily B, member 1	290						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						TCAGGAATGCAGAGGTGAAAA	0.433																																					p.A290A		Atlas-SNP	.											.	OR4B1	52	.	0			c.A870G						.						73.0	68.0	70.0					11																	48239231		2201	4298	6499	SO:0001819	synonymous_variant	119765	exon1			GAATGCAGAGGTG	AB065848	CCDS31485.1	11p11.2	2012-08-09			ENSG00000175619	ENSG00000175619		"""GPCR / Class A : Olfactory receptors"""	8290	protein-coding gene	gene with protein product							Standard	NM_001005470		Approved	OST208	uc010rhs.2	Q8NGF8	OTTHUMG00000166576	ENST00000309562.2:c.870A>G	chr11.hg19:g.48239231A>G		61.0	0.0		74.0	4.0	NM_001005470	Q6IF75|Q96R64	Silent	SNP	ENST00000309562.2	hg19	CCDS31485.1																																																																																			.	.		0.433	OR4B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390554.1	NM_001005470	
OR5M1	390168	hgsc.bcm.edu	37	11	56380553	56380553	+	Silent	SNP	G	G	C	rs200393978		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:56380553G>C	ENST00000526538.1	-	1	425	c.426C>G	c.(424-426)gtC>gtG	p.V142V		NM_001004740.1	NP_001004740.1	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M, member 1	142						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(1)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|upper_aerodigestive_tract(1)	12						TGACCAGACAGACACAGATGT	0.443																																					p.V142V		Atlas-SNP	.											.	OR5M1	92	.	0			c.C426G						.						133.0	115.0	120.0					11																	56380553		1971	4166	6137	SO:0001819	synonymous_variant	390168	exon1			CAGACAGACACAG	AB065742	CCDS53631.1	11q11	2012-08-09				ENSG00000255012		"""GPCR / Class A : Olfactory receptors"""	8352	protein-coding gene	gene with protein product							Standard	NM_001004740		Approved	OST050	uc001nja.1	Q8NGP8		ENST00000526538.1:c.426C>G	chr11.hg19:g.56380553G>C		197.0	0.0		168.0	9.0	NM_001004740	Q6IF60|Q96RB6	Silent	SNP	ENST00000526538.1	hg19	CCDS53631.1																																																																																			.	.		0.443	OR5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391610.1	NM_001004740	
SERPING1	710	hgsc.bcm.edu	37	11	57374013	57374013	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:57374013A>G	ENST00000278407.4	+	6	1249	c.1022A>G	c.(1021-1023)aAa>aGa	p.K341R	SERPING1_ENST00000340687.6_Missense_Mutation_p.K341R|SERPING1_ENST00000378323.4_Missense_Mutation_p.K346R|SERPING1_ENST00000403558.1_Missense_Mutation_p.K384R|SERPING1_ENST00000378324.2_Missense_Mutation_p.K289R	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	341					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						CAAACTTTGAAAGCCAAGGTA	0.408																																					p.K341R		Atlas-SNP	.											.	SERPING1	57	.	0			c.A1022G						.						173.0	164.0	167.0					11																	57374013		2201	4296	6497	SO:0001583	missense	710	exon5			CTTTGAAAGCCAA	X54486	CCDS7962.1	11q12.1	2014-09-17	2008-07-31		ENSG00000149131	ENSG00000149131		"""Serine (or cysteine) peptidase inhibitors"""	1228	protein-coding gene	gene with protein product	"""plasma protease C1 inhibitor"", ""angioedema, hereditary"""	606860	"""serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)"""	C1NH		2026152, 24172014	Standard	NM_000062		Approved	C1IN, C1-INH, HAE1, HAE2	uc001nkp.1	P05155	OTTHUMG00000150304	ENST00000278407.4:c.1022A>G	chr11.hg19:g.57374013A>G	ENSP00000278407:p.Lys341Arg	82.0	0.0		65.0	4.0	NM_001032295	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Missense_Mutation	SNP	ENST00000278407.4	hg19	CCDS7962.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.639032	0.47153	.	.	ENSG00000149131	ENST00000278407;ENST00000340687;ENST00000378323;ENST00000378324;ENST00000403558	D;D;D;D;D	0.88509	-2.39;-2.39;-2.39;-2.39;-2.39	5.49	4.37	0.52481	Serpin domain (3);	0.056073	0.64402	D	0.000001	D	0.85754	0.5770	M	0.64404	1.975	0.39768	D	0.972124	B;B;B;B	0.27140	0.153;0.169;0.153;0.153	B;B;B;B	0.26770	0.073;0.067;0.073;0.073	T	0.82184	-0.0583	10	0.45353	T	0.12	.	8.9441	0.35747	0.9144:0.0:0.0856:0.0	.	346;384;341;341	B4E1F0;E9PGN7;E9KL26;P05155	.;.;.;IC1_HUMAN	R	341;341;346;289;384	ENSP00000278407:K341R;ENSP00000341861:K341R;ENSP00000367574:K346R;ENSP00000367575:K289R;ENSP00000384420:K384R	ENSP00000278407:K341R	K	+	2	0	SERPING1	57130589	1.000000	0.71417	0.888000	0.34837	0.983000	0.72400	3.594000	0.54008	0.935000	0.37341	0.533000	0.62120	AAA	.	.		0.408	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062	
OR5B21	219968	hgsc.bcm.edu	37	11	58275280	58275280	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:58275280A>G	ENST00000360374.2	-	1	298	c.299T>C	c.(298-300)tTc>tCc	p.F100S		NM_001005218.1	NP_001005218.1	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B, member 21	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CACAAAGAAGAAGAACTGAGC	0.547																																					p.F100S		Atlas-SNP	.											.	OR5B21	59	.	0			c.T299C						.						127.0	98.0	108.0					11																	58275280		2201	4295	6496	SO:0001583	missense	219968	exon1			AAGAAGAAGAACT		CCDS31552.1	11q12.1	2012-08-09			ENSG00000198283	ENSG00000198283		"""GPCR / Class A : Olfactory receptors"""	19616	protein-coding gene	gene with protein product							Standard	NM_001005218		Approved		uc010rki.2	A6NL26	OTTHUMG00000167519	ENST00000360374.2:c.299T>C	chr11.hg19:g.58275280A>G	ENSP00000353537:p.Phe100Ser	123.0	0.0		94.0	4.0	NM_001005218		Missense_Mutation	SNP	ENST00000360374.2	hg19	CCDS31552.1	.	.	.	.	.	.	.	.	.	.	A	16.67	3.188781	0.57909	.	.	ENSG00000198283	ENST00000360374	T	0.00397	7.57	5.2	4.07	0.47477	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38837	U	0.001544	T	0.00384	0.0012	M	0.74389	2.26	0.29433	N	0.859748	P	0.43973	0.823	B	0.42827	0.399	T	0.31420	-0.9944	10	0.72032	D	0.01	-9.5501	5.4771	0.16702	0.765:0.0:0.0822:0.1528	.	100	A6NL26	OR5BL_HUMAN	S	100	ENSP00000353537:F100S	ENSP00000353537:F100S	F	-	2	0	OR5B21	58031856	0.006000	0.16342	0.980000	0.43619	0.998000	0.95712	0.425000	0.21346	0.994000	0.38892	0.533000	0.62120	TTC	.	.		0.547	OR5B21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394891.1	NM_001005218	
MS4A6A	64231	hgsc.bcm.edu	37	11	59947428	59947428	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:59947428A>G	ENST00000530839.1	-	4	650	c.158T>C	c.(157-159)aTc>aCc	p.I53T	MS4A6A_ENST00000529906.1_5'UTR|MS4A6A_ENST00000528851.1_Missense_Mutation_p.I53T|MS4A6A_ENST00000532169.1_Missense_Mutation_p.I53T|MS4A6A_ENST00000426738.2_Intron|MS4A6A_ENST00000533023.1_Intron|MS4A6A_ENST00000420732.2_Missense_Mutation_p.I53T|MS4A6A_ENST00000412309.2_Missense_Mutation_p.I81T|MS4A6A_ENST00000323961.3_Missense_Mutation_p.I53T|MS4A6A_ENST00000529054.1_Missense_Mutation_p.I81T	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	53						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GCCACACAAGATCTGGATAGT	0.443																																					p.I81T		Atlas-SNP	.											.	MS4A6A	85	.	0			c.T242C						.						92.0	85.0	88.0					11																	59947428		2201	4295	6496	SO:0001583	missense	64231	exon4			CACAAGATCTGGA	AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.158T>C	chr11.hg19:g.59947428A>G	ENSP00000436979:p.Ile53Thr	153.0	0.0		145.0	6.0	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Missense_Mutation	SNP	ENST00000530839.1	hg19	CCDS7981.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.181779	0.38511	.	.	ENSG00000110077	ENST00000323961;ENST00000528851;ENST00000420732;ENST00000530839;ENST00000529054;ENST00000412309;ENST00000532169;ENST00000534596	T;T;T;T;T;T;T;T	0.27557	3.35;3.35;3.35;3.35;3.35;3.35;3.35;1.66	4.32	3.2	0.36748	.	0.207171	0.36972	N	0.002306	T	0.51991	0.1707	M	0.86097	2.795	0.80722	D	1	D;D;D;P	0.56287	0.969;0.975;0.975;0.94	P;D;D;P	0.68621	0.871;0.959;0.921;0.798	T	0.54754	-0.8246	9	.	.	.	.	5.951	0.19246	0.8842:0.0:0.1158:0.0	.	81;81;53;53	F8W9K1;E9PSA9;Q9H2W1;Q9H2W1-3	.;.;M4A6A_HUMAN;.	T	53;53;53;53;81;81;53;81	ENSP00000315878:I53T;ENSP00000431901:I53T;ENSP00000392921:I53T;ENSP00000436979:I53T;ENSP00000435844:I81T;ENSP00000403212:I81T;ENSP00000431266:I53T;ENSP00000433436:I81T	.	I	-	2	0	MS4A6A	59704004	0.978000	0.34361	0.979000	0.43373	0.380000	0.30137	2.367000	0.44213	1.929000	0.55896	0.533000	0.62120	ATC	.	.		0.443	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1		
MS4A14	84689	hgsc.bcm.edu	37	11	60165354	60165354	+	Silent	SNP	T	T	A	rs3217518	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:60165354T>A	ENST00000300187.6	+	2	445	c.168T>A	c.(166-168)atT>atA	p.I56I	MS4A14_ENST00000395005.2_Silent_p.I56I|MS4A14_ENST00000531787.1_Intron|MS4A14_ENST00000395001.1_De_novo_Start_InFrame|MS4A14_ENST00000531783.1_Silent_p.I56I	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	56						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						CTCTAATCATTGTGGGCTTTG	0.478																																					p.I56I		Atlas-SNP	.											.	MS4A14	120	.	0			c.T168A						.						112.0	78.0	91.0					11																	60165354		1817	2868	4685	SO:0001819	synonymous_variant	84689	exon2			AATCATTGTGGGC	AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"""membrane-spanning 4-domains, subfamily A, member 16"""	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.168T>A	chr11.hg19:g.60165354T>A		1.0	0.0		22.0	14.0	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Silent	SNP	ENST00000300187.6	hg19	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	T	8.441	0.850792	0.17034	.	.	ENSG00000166928	ENST00000534688	.	.	.	4.94	-1.76	0.08006	.	.	.	.	.	.	.	.	.	.	.	0.30288	N	0.790644	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.4396	4.4751	0.11731	0.0:0.3068:0.3384:0.3548	.	.	.	.	X	15	.	.	L	+	2	0	MS4A14	59921930	0.001000	0.12720	0.066000	0.19879	0.254000	0.26022	-0.793000	0.04589	-0.152000	0.11156	0.482000	0.46254	TTG	.	.		0.478	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
VPS37C	55048	hgsc.bcm.edu	37	11	60900811	60900811	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:60900811T>C	ENST00000301765.5	-	4	498		c.e4-2			NM_017966.4	NP_060436.4	A5D8V6	VP37C_HUMAN	vacuolar protein sorting 37 homolog C (S. cerevisiae)						endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7						AAAATTTCTCTGGAAGGGAGG	0.527																																					.		Atlas-SNP	.											.	VPS37C	30	.	0			c.266-2A>G						.						65.0	50.0	55.0					11																	60900811		2203	4299	6502	SO:0001630	splice_region_variant	55048	exon5			TTTCTCTGGAAGG	AK097326	CCDS31573.1	11q12.2	2008-02-05	2006-04-04			ENSG00000167987			26097	protein-coding gene	gene with protein product		610038	"""vacuolar protein sorting 37C (yeast)"""			15509564	Standard	XM_005274077		Approved	FLJ20847	uc001nqv.1	A5D8V6		ENST00000301765.5:c.266-2A>G	chr11.hg19:g.60900811T>C		69.0	0.0		61.0	4.0	NM_017966	Q8N3K4	Splice_Site	SNP	ENST00000301765.5	hg19	CCDS31573.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.956540	0.73902	.	.	ENSG00000167987	ENST00000301765;ENST00000540084;ENST00000538036	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3137	0.60394	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	VPS37C	60657387	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.060000	0.64312	1.880000	0.54463	0.459000	0.35465	.	.	.		0.527	VPS37C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396467.1	NM_017966	Intron
DDB1	1642	hgsc.bcm.edu	37	11	61097525	61097525	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:61097525A>G	ENST00000301764.7	-	3	629	c.232T>C	c.(232-234)Ttt>Ctt	p.F78L	DDB1_ENST00000545930.1_5'Flank|DDB1_ENST00000450997.2_Intron	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	78	Interaction with CDT1.|WD repeat beta-propeller A.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						GTCAAGATAAACAGCAGGTCC	0.453								Nucleotide excision repair (NER)																													p.F78L		Atlas-SNP	.											.	DDB1	100	.	0			c.T232C						.						108.0	95.0	99.0					11																	61097525		2203	4299	6502	SO:0001583	missense	1642	exon3			AGATAAACAGCAG	AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"""damage-specific DNA binding protein 1 (127kD)"""			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.232T>C	chr11.hg19:g.61097525A>G	ENSP00000301764:p.Phe78Leu	141.0	0.0		142.0	6.0	NM_001923	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Missense_Mutation	SNP	ENST00000301764.7	hg19	CCDS31576.1	.	.	.	.	.	.	.	.	.	.	A	33	5.197625	0.94997	.	.	ENSG00000167986	ENST00000301764;ENST00000539426;ENST00000535283;ENST00000542337;ENST00000543627	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.60869	0.2302	M	0.72894	2.215	0.80722	D	1	D;D	0.71674	0.968;0.998	P;D	0.68192	0.691;0.956	T	0.59963	-0.7355	10	0.30854	T	0.27	-16.3001	14.6448	0.68754	1.0:0.0:0.0:0.0	.	78;78	B7Z2A1;Q16531	.;DDB1_HUMAN	L	78;22;22;78;78	ENSP00000301764:F78L;ENSP00000445554:F22L;ENSP00000441825:F22L;ENSP00000444105:F78L	ENSP00000301764:F78L	F	-	1	0	DDB1	60854101	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.095000	0.94175	1.914000	0.55421	0.460000	0.39030	TTT	.	.		0.453	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923	
SCGB1A1	7356	hgsc.bcm.edu	37	11	62189867	62189867	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:62189867T>C	ENST00000278282.2	+	2	291	c.230T>C	c.(229-231)aTc>aCc	p.I77T	SCGB1A1_ENST00000534397.1_Missense_Mutation_p.I42T|CTD-2531D15.4_ENST00000528983.1_RNA	NM_003357.4	NP_003348.1	P11684	UTER_HUMAN	secretoglobin, family 1A, member 1 (uteroglobin)	77					embryo implantation (GO:0007566)|female pregnancy (GO:0007565)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of inflammatory response (GO:0050727)|regulation of mRNA stability (GO:0043488)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fibroblast growth factor (GO:0071774)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to silicon dioxide (GO:0034021)|response to xenobiotic stimulus (GO:0009410)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nuclear envelope (GO:0005635)|rough endoplasmic reticulum (GO:0005791)|secretory granule (GO:0030141)	phospholipase A2 inhibitor activity (GO:0019834)			lung(1)	1						AGAGAAAGCATCATTAAGCTC	0.537																																					p.I77T		Atlas-SNP	.											.	SCGB1A1	5	.	0			c.T230C						.						118.0	105.0	110.0					11																	62189867		2202	4299	6501	SO:0001583	missense	7356	exon2			AAAGCATCATTAA		CCDS8020.1	11q12.3	2011-12-14	2002-03-22	2002-03-22	ENSG00000149021	ENSG00000149021		"""Secretoglobins"""	12523	protein-coding gene	gene with protein product	"""Uteroglobin (Clara-cell specific 10-kD protein)"""	192020	"""uteroglobin"""	UGB		1284526, 22155607	Standard	NM_003357		Approved	CC10, CCSP, CC16	uc001ntj.3	P11684	OTTHUMG00000167526	ENST00000278282.2:c.230T>C	chr11.hg19:g.62189867T>C	ENSP00000278282:p.Ile77Thr	97.0	0.0		71.0	4.0	NM_003357	B2R5F2|Q6FHH3|Q9UCM2|Q9UCM4	Missense_Mutation	SNP	ENST00000278282.2	hg19	CCDS8020.1	.	.	.	.	.	.	.	.	.	.	T	13.41	2.229648	0.39399	.	.	ENSG00000149021	ENST00000534397;ENST00000278282	T;T	0.18810	2.19;2.19	4.74	3.61	0.41365	.	1.410380	0.04639	N	0.404942	T	0.34919	0.0914	.	.	.	0.09310	N	1	P	0.48089	0.905	P	0.52823	0.71	T	0.11251	-1.0595	9	0.87932	D	0	-1.5553	7.1299	0.25496	0.0:0.1038:0.0:0.8962	.	77	P11684	UTER_HUMAN	T	42;77	ENSP00000432866:I42T;ENSP00000278282:I77T	ENSP00000278282:I77T	I	+	2	0	SCGB1A1	61946443	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	1.224000	0.32539	0.786000	0.33708	0.533000	0.62120	ATC	.	.		0.537	SCGB1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394925.1	NM_003357	
INTS5	80789	hgsc.bcm.edu	37	11	62416122	62416122	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:62416122A>G	ENST00000330574.2	-	2	1482	c.1430T>C	c.(1429-1431)cTc>cCc	p.L477P	GANAB_ENST00000356638.3_5'Flank|GANAB_ENST00000534779.1_5'Flank|GANAB_ENST00000540933.1_5'Flank|GANAB_ENST00000346178.4_5'Flank	NM_030628.1	NP_085131.1	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	477					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(6)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	36						ATGGTTTTTGAGCGCATCTAA	0.587																																					p.L477P		Atlas-SNP	.											.	INTS5	81	.	0			c.T1430C						.						77.0	79.0	78.0					11																	62416122		2202	4299	6501	SO:0001583	missense	80789	exon2			TTTTTGAGCGCAT	AK123587	CCDS8027.1	11q12.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000185085	ENSG00000185085			29352	protein-coding gene	gene with protein product		611349	"""KIAA1698"""	KIAA1698		16239144	Standard	NM_030628		Approved	INT5	uc001nud.3	Q6P9B9	OTTHUMG00000167605	ENST00000330574.2:c.1430T>C	chr11.hg19:g.62416122A>G	ENSP00000327889:p.Leu477Pro	66.0	0.0		69.0	4.0	NM_030628	Q8N6W5|Q9C0G5	Missense_Mutation	SNP	ENST00000330574.2	hg19	CCDS8027.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.155447	0.38021	.	.	ENSG00000185085	ENST00000330574	.	.	.	4.87	4.87	0.63330	.	0.084051	0.49916	D	0.000121	T	0.61502	0.2352	N	0.24115	0.695	0.52501	D	0.999959	D	0.76494	0.999	D	0.69479	0.964	T	0.66316	-0.5954	9	0.87932	D	0	.	12.476	0.55814	1.0:0.0:0.0:0.0	.	477	Q6P9B9	INT5_HUMAN	P	477	.	ENSP00000327889:L477P	L	-	2	0	INTS5	62172698	1.000000	0.71417	0.108000	0.21378	0.554000	0.35429	8.598000	0.90852	2.052000	0.61016	0.533000	0.62120	CTC	.	.		0.587	INTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395327.1	NM_030628	
ATL3	25923	hgsc.bcm.edu	37	11	63396832	63396832	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:63396832C>A	ENST00000398868.3	-	13	1861	c.1585G>T	c.(1585-1587)Gca>Tca	p.A529S	ATL3_ENST00000538786.1_Missense_Mutation_p.A511S|ATL3_ENST00000332645.4_Missense_Mutation_p.A556S	NM_015459.3	NP_056274.3	Q6DD88	ATLA3_HUMAN	atlastin GTPase 3	529					endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	11						CCAACAACTGCATCCCTCACA	0.388																																					p.A529S		Atlas-SNP	.											.	ATL3	31	.	0			c.G1585T						.						124.0	117.0	119.0					11																	63396832		1905	4120	6025	SO:0001583	missense	25923	exon13			CAACTGCATCCCT		CCDS41663.1, CCDS73309.1	11q13.1	2008-09-17			ENSG00000184743	ENSG00000184743			24526	protein-coding gene	gene with protein product		609369				18270207	Standard	XM_005273891		Approved	DKFZP564J0863	uc001nxk.1	Q6DD88	OTTHUMG00000167854	ENST00000398868.3:c.1585G>T	chr11.hg19:g.63396832C>A	ENSP00000381844:p.Ala529Ser	277.0	0.0		249.0	102.0	NM_015459	Q8N7W5|Q9H8Q5|Q9UFL1	Missense_Mutation	SNP	ENST00000398868.3	hg19	CCDS41663.1	.	.	.	.	.	.	.	.	.	.	C	8.508	0.865783	0.17250	.	.	ENSG00000184743	ENST00000398868;ENST00000332645;ENST00000538786	T;T;T	0.80480	-1.25;-1.38;-1.24	5.63	1.39	0.22231	.	0.572977	0.18801	N	0.130797	T	0.52948	0.1766	N	0.04959	-0.14	0.09310	N	1	B	0.28820	0.224	B	0.24701	0.055	T	0.38564	-0.9655	10	0.29301	T	0.29	-7.3235	1.6857	0.02841	0.1828:0.4839:0.155:0.1782	.	529	Q6DD88	ATLA3_HUMAN	S	529;556;511	ENSP00000381844:A529S;ENSP00000329034:A556S;ENSP00000437593:A511S	ENSP00000329034:A556S	A	-	1	0	ATL3	63153408	0.002000	0.14202	0.425000	0.26659	0.009000	0.06853	0.010000	0.13242	0.298000	0.22638	-0.274000	0.10170	GCA	.	.		0.388	ATL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396637.1	NM_015459	
KCNK4	50801	hgsc.bcm.edu	37	11	64060629	64060629	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:64060629C>A	ENST00000539216.1	+	1	499	c.139C>A	c.(139-141)Ctg>Atg	p.L47M	RP11-783K16.10_ENST00000539086.1_RNA|Y_RNA_ENST00000384297.1_RNA|KCNK4_ENST00000422670.2_Missense_Mutation_p.L47M|KCNK4_ENST00000538767.1_Intron|KCNK4_ENST00000394525.2_Missense_Mutation_p.L47M|KCNK4_ENST00000539651.1_Intron			Q9NYG8	KCNK4_HUMAN	potassium channel, subfamily K, member 4	47					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(2)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	10						AGAGAAGTTCCTGAGGGCCCA	0.667																																					p.L47M		Atlas-SNP	.											.	KCNK4	22	.	0			c.C139A						.						39.0	37.0	37.0					11																	64060629		1872	3553	5425	SO:0001583	missense	50801	exon2			AAGTTCCTGAGGG	AF247042	CCDS8067.1	11q13	2012-03-07			ENSG00000182450	ENSG00000182450		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6279	protein-coding gene	gene with protein product		605720				10767409, 16382106	Standard	NM_033310		Approved	K2p4.1, TRAAK	uc001nzk.1	Q9NYG8	OTTHUMG00000168006	ENST00000539216.1:c.139C>A	chr11.hg19:g.64060629C>A	ENSP00000444948:p.Leu47Met	74.0	0.0		68.0	4.0	NM_033310	B5TJL1|Q96T94	Missense_Mutation	SNP	ENST00000539216.1	hg19	CCDS8067.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.922849	0.73213	.	.	ENSG00000182450	ENST00000422670;ENST00000539852;ENST00000394525;ENST00000544845;ENST00000539216	T;T;T	0.20069	2.1;2.1;2.1	4.28	3.35	0.38373	.	0.186190	0.36200	N	0.002725	T	0.38639	0.1048	M	0.71036	2.16	0.47584	D	0.999462	D	0.54964	0.969	P	0.60012	0.867	T	0.15178	-1.0446	10	0.46703	T	0.11	.	11.1218	0.48296	0.1862:0.8138:0.0:0.0	.	47	Q9NYG8	KCNK4_HUMAN	M	47;72;47;109;47	ENSP00000402797:L47M;ENSP00000378033:L47M;ENSP00000444948:L47M	ENSP00000378033:L47M	L	+	1	2	KCNK4	63817205	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.478000	0.60230	0.989000	0.38761	0.455000	0.32223	CTG	.	.		0.667	KCNK4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396430.1	NM_033311	
MEN1	4221	hgsc.bcm.edu	37	11	64577196	64577196	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:64577196A>G	ENST00000337652.1	-	2	889	c.386T>C	c.(385-387)cTc>cCc	p.L129P	MEN1_ENST00000377321.1_Missense_Mutation_p.L129P|MEN1_ENST00000315422.4_Missense_Mutation_p.L129P|MEN1_ENST00000394374.2_Missense_Mutation_p.L129P|MEN1_ENST00000377326.3_Missense_Mutation_p.L129P|MEN1_ENST00000377316.2_Missense_Mutation_p.L129P|MEN1_ENST00000394376.1_Missense_Mutation_p.L129P|MEN1_ENST00000312049.6_Missense_Mutation_p.L129P|MEN1_ENST00000443283.1_Missense_Mutation_p.L129P|MEN1_ENST00000377313.1_Missense_Mutation_p.L129P	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	129					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.I125fs*53(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						GGAGCGGCTGAGGCTGTTCCA	0.572			"""D, Mis, N, F, S"""		"""parathyroid tumors, Pancreatic neuroendocrine tumors"""	"""parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"""			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												p.L129P	Esophageal Squamous(1;83 158 15500 18603 18803 29295)	Atlas-SNP	.	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	.	MEN1	442	.	1	Deletion - Frameshift(1)	parathyroid(1)	c.T386C						.						114.0	115.0	115.0					11																	64577196		2201	4297	6498	SO:0001583	missense	4221	exon2	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	CGGCTGAGGCTGT	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"""menin"""	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.386T>C	chr11.hg19:g.64577196A>G	ENSP00000337088:p.Leu129Pro	106.0	0.0		118.0	8.0	NM_130800	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	hg19	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.271310	0.80469	.	.	ENSG00000133895	ENST00000377316;ENST00000377321;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313;ENST00000440873;ENST00000450708;ENST00000413626;ENST00000429702;ENST00000424912	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.99719	-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52;-6.52	4.93	4.93	0.64822	.	0.000000	0.64402	D	0.000002	D	0.99542	0.9836	M	0.67397	2.05	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.997;0.999	D	0.98014	1.0367	10	0.87932	D	0	-28.6783	12.8611	0.57913	1.0:0.0:0.0:0.0	.	129;129;129	O00255-2;O00255-3;O00255	.;.;MEN1_HUMAN	P	129	ENSP00000366533:L129P;ENSP00000366538:L129P;ENSP00000366543:L129P;ENSP00000308975:L129P;ENSP00000323747:L129P;ENSP00000337088:L129P;ENSP00000377901:L129P;ENSP00000377899:L129P;ENSP00000396940:L129P;ENSP00000366530:L129P;ENSP00000413944:L129P;ENSP00000394933:L129P;ENSP00000411218:L129P;ENSP00000402752:L129P;ENSP00000388016:L129P	ENSP00000308975:L129P	L	-	2	0	MEN1	64333772	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	8.364000	0.90105	1.988000	0.58038	0.402000	0.26972	CTC	.	.		0.572	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1		
EHBP1L1	254102	hgsc.bcm.edu	37	11	65351097	65351097	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:65351097A>G	ENST00000309295.4	+	9	3219	c.2954A>G	c.(2953-2955)gAg>gGg	p.E985G		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	985						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						TTGGGAAATGAGAAGGGGAAA	0.602																																					p.E985G		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.A2954G						.						14.0	15.0	14.0					11																	65351097		1846	4093	5939	SO:0001583	missense	254102	exon9			GAAATGAGAAGGG	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.2954A>G	chr11.hg19:g.65351097A>G	ENSP00000312671:p.Glu985Gly	80.0	0.0		83.0	4.0	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	hg19	CCDS44649.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.883|6.883	0.532444|0.532444	0.13127|0.13127	.|.	.|.	ENSG00000173442|ENSG00000173442	ENST00000309295|ENST00000533465	T|.	0.66638|.	-0.22|.	4.87|4.87	2.49|2.49	0.30216|0.30216	.|.	0.894455|.	0.09376|.	N|.	0.810556|.	T|.	0.28599|.	0.0708|.	L|L	0.27053|0.27053	0.805|0.805	0.30589|0.30589	N|N	0.761684|0.761684	B|.	0.06786|.	0.001|.	B|.	0.04013|.	0.001|.	T|.	0.26503|.	-1.0101|.	10|.	0.32370|.	T|.	0.25|.	.|.	4.5776|4.5776	0.12241|0.12241	0.7238:0.0:0.0973:0.179|0.7238:0.0:0.0973:0.179	.|.	985|.	Q8N3D4|.	EH1L1_HUMAN|.	G|W	985|34	ENSP00000312671:E985G|.	ENSP00000312671:E985G|.	E|X	+|+	2|3	0|0	EHBP1L1|EHBP1L1	65107673|65107673	0.318000|0.318000	0.24598|0.24598	0.089000|0.089000	0.20774|0.20774	0.255000|0.255000	0.26057|0.26057	0.987000|0.987000	0.29603|0.29603	0.666000|0.666000	0.31087|0.31087	0.358000|0.358000	0.22013|0.22013	GAG|TGA	.	.		0.602	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
OVOL1	5017	hgsc.bcm.edu	37	11	65562182	65562182	+	Silent	SNP	C	C	T	rs377708693		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:65562182C>T	ENST00000335987.3	+	3	844	c.492C>T	c.(490-492)caC>caT	p.H164H	RP11-770G2.5_ENST00000531155.1_RNA|OVOL1_ENST00000532448.1_Silent_p.H102H	NM_004561.3	NP_004552.2	O14753	OVOL1_HUMAN	ovo-like zinc finger 1	164					cytoskeleton organization (GO:0007010)|epidermal cell differentiation (GO:0009913)|germline cell cycle switching, mitotic to meiotic cell cycle (GO:0051729)|kidney development (GO:0001822)|mesoderm development (GO:0007498)|negative regulation of meiotic cell cycle phase transition (GO:1901994)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.H164H(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	6				READ - Rectum adenocarcinoma(159;0.17)		TCAAGAGACACGTCCGAACTC	0.617													C|||	1	0.000199681	0.0	0.0	5008	,	,		21988	0.0		0.0	False		,,,				2504	0.001				p.H164H		Atlas-SNP	.											OVOL1,NS,carcinoma,0,1	OVOL1	15	.	1	Substitution - coding silent(1)	endometrium(1)	c.C492T						.	C		0,4402		0,0,2201	123.0	96.0	105.0		492	-5.8	0.8	11		105	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	OVOL1	NM_004561.3		0,1,6497	TT,TC,CC		0.0116,0.0,0.0077		164/268	65562182	1,12995	2201	4297	6498	SO:0001819	synonymous_variant	5017	exon3			GAGACACGTCCGA	BC059408	CCDS8112.1	11q13	2013-10-17	2013-10-17		ENSG00000172818	ENSG00000172818		"""Zinc fingers, C2H2-type"""	8525	protein-coding gene	gene with protein product		602313	"""ovo (Drosophila) homolog-like 1"", ""ovo-like 1(Drosophila)"""			9383297	Standard	NM_004561		Approved	HOVO1	uc001ofp.3	O14753	OTTHUMG00000166600	ENST00000335987.3:c.492C>T	chr11.hg19:g.65562182C>T		70.0	0.0		58.0	3.0	NM_004561	Q6PCB1	Silent	SNP	ENST00000335987.3	hg19	CCDS8112.1																																																																																			.	.		0.617	OVOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390690.1	NM_004561	
DPP3	10072	hgsc.bcm.edu	37	11	66249887	66249887	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:66249887C>T	ENST00000360510.2	+	2	281	c.216C>T	c.(214-216)ccC>ccT	p.P72P	DPP3_ENST00000531863.1_Silent_p.P92P|CTD-3074O7.5_ENST00000527274.2_RNA|CTD-3074O7.5_ENST00000533502.1_RNA|CTD-3074O7.5_ENST00000527092.1_RNA|DPP3_ENST00000532677.1_Silent_p.P91P|DPP3_ENST00000541961.1_Silent_p.P72P|DPP3_ENST00000530165.1_Silent_p.P72P|CTD-3074O7.5_ENST00000525142.1_RNA|DPP3_ENST00000453114.1_Silent_p.P72P			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	72					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						CCCAGGACCCCGACCAGCTGC	0.632																																					p.P72P		Atlas-SNP	.											.	DPP3	61	.	0			c.C216T						.						41.0	43.0	42.0					11																	66249887		2200	4295	6495	SO:0001819	synonymous_variant	10072	exon2			GGACCCCGACCAG	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"""dipeptidylpeptidase III"", ""dipeptidylpeptidase 3"""			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.216C>T	chr11.hg19:g.66249887C>T		30.0	0.0		34.0	4.0	NM_001256670	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Silent	SNP	ENST00000360510.2	hg19	CCDS8141.1																																																																																			.	.		0.632	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2		
PC	5091	hgsc.bcm.edu	37	11	66636393	66636393	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:66636393T>C	ENST00000393958.2	-	9	1039	c.946A>G	c.(946-948)Agg>Ggg	p.R316G	PC_ENST00000355677.3_Missense_Mutation_p.R316G|PC_ENST00000393955.2_Missense_Mutation_p.R316G|PC_ENST00000393960.1_Missense_Mutation_p.R316G|PC_ENST00000524491.1_Missense_Mutation_p.R276G	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	316	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|oxaloacetate metabolic process (GO:0006107)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|pyruvate carboxylase activity (GO:0004736)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	TTGCCGTGCCTGTCCACCAGG	0.662																																					p.R316G		Atlas-SNP	.											.	PC	116	.	0			c.A946G						.						94.0	82.0	86.0					11																	66636393		2200	4295	6495	SO:0001583	missense	5091	exon9			CGTGCCTGTCCAC	U04641	CCDS8152.1	11q13.4-q13.5	2012-07-11			ENSG00000173599	ENSG00000173599	6.4.1.1		8636	protein-coding gene	gene with protein product		608786				6548474	Standard	NM_022172		Approved	PCB	uc001ojn.1	P11498	OTTHUMG00000167099	ENST00000393958.2:c.946A>G	chr11.hg19:g.66636393T>C	ENSP00000377530:p.Arg316Gly	181.0	0.0		148.0	7.0	NM_000920	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	hg19	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.357478	0.41801	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960;ENST00000524491;ENST00000355677	D;D;D;D;D	0.97688	-4.49;-4.49;-4.49;-4.49;-4.49	4.36	3.2	0.36748	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.487758	0.17767	N	0.162713	D	0.90810	0.7114	N	0.05050	-0.12	0.28376	N	0.919783	B	0.02656	0.0	B	0.06405	0.002	T	0.81099	-0.1086	10	0.10377	T	0.69	-9.4352	9.118	0.36769	0.0:0.0:0.1854:0.8146	.	316	P11498	PYC_HUMAN	G	316;316;316;276;316	ENSP00000377527:R316G;ENSP00000377530:R316G;ENSP00000377532:R316G;ENSP00000434192:R276G;ENSP00000347900:R316G	ENSP00000347900:R316G	R	-	1	2	PC	66392969	0.996000	0.38824	0.633000	0.29310	0.861000	0.49209	1.935000	0.40173	0.511000	0.28236	0.459000	0.35465	AGG	.	.		0.662	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716	
KDM2A	22992	hgsc.bcm.edu	37	11	67020287	67020287	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:67020287T>C	ENST00000529006.2	+	18	3337	c.2891T>C	c.(2890-2892)aTc>aCc	p.I964T	KDM2A_ENST00000308783.5_Missense_Mutation_p.I422T|KDM2A_ENST00000526258.1_3'UTR|KDM2A_ENST00000530342.1_Missense_Mutation_p.I525T|KDM2A_ENST00000398645.2_3'UTR	NM_012308.2	NP_036440.1	Q9Y2K7	KDM2A_HUMAN	lysine (K)-specific demethylase 2A	964					histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2)	36						TGGACCAACATCTCTAAAAAG	0.532											OREG0021121	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I964T		Atlas-SNP	.											.	KDM2A	80	.	0			c.T2891C						.						70.0	69.0	70.0					11																	67020287		1975	4160	6135	SO:0001583	missense	22992	exon18			CCAACATCTCTAA	BC047486	CCDS44657.1, CCDS58148.1	11q13.1	2014-02-18	2009-04-06	2009-04-06	ENSG00000173120	ENSG00000173120		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13606	protein-coding gene	gene with protein product	"""F-box protein FBL11"", ""jumonji C domain-containing histone demethylase 1A"""	605657	"""F-box and leucine-rich repeat protein 11"""	FBXL11		10231032, 10531037	Standard	NM_012308		Approved	KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A	uc001ojw.3	Q9Y2K7	OTTHUMG00000167103	ENST00000529006.2:c.2891T>C	chr11.hg19:g.67020287T>C	ENSP00000432786:p.Ile964Thr	86.0	0.0	1096	73.0	4.0	NM_012308	D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66	Missense_Mutation	SNP	ENST00000529006.2	hg19	CCDS44657.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.720220	0.89205	.	.	ENSG00000173120	ENST00000529006;ENST00000530342;ENST00000308783	T;T;T	0.37058	1.22;1.22;1.22	5.44	5.44	0.79542	.	0.108661	0.64402	D	0.000004	T	0.42585	0.1209	M	0.77486	2.375	0.80722	D	1	P;P;B	0.40144	0.458;0.704;0.319	B;B;B	0.36922	0.218;0.236;0.1	T	0.50759	-0.8790	10	0.62326	D	0.03	-10.9482	15.6519	0.77104	0.0:0.0:0.0:1.0	.	525;422;964	E9PIL6;D4QA03;Q9Y2K7	.;.;KDM2A_HUMAN	T	964;525;422	ENSP00000432786:I964T;ENSP00000435776:I525T;ENSP00000309302:I422T	ENSP00000309302:I422T	I	+	2	0	KDM2A	66776863	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.841000	0.86834	2.285000	0.76669	0.528000	0.53228	ATC	.	.		0.532	KDM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393140.2	NM_012308	
P2RY2	5029	hgsc.bcm.edu	37	11	72945625	72945625	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:72945625T>C	ENST00000311131.2	+	3	888	c.421T>C	c.(421-423)Tcc>Ccc	p.S141P	P2RY2_ENST00000393596.2_Missense_Mutation_p.S141P|P2RY2_ENST00000393597.2_Missense_Mutation_p.S141P	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	141					cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	ACCTCTGCGCTCCCTGCGCTG	0.667																																					p.S141P		Atlas-SNP	.											.	P2RY2	54	.	0			c.T421C						.						62.0	59.0	60.0					11																	72945625		2200	4293	6493	SO:0001583	missense	5029	exon3			CTGCGCTCCCTGC	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.421T>C	chr11.hg19:g.72945625T>C	ENSP00000310305:p.Ser141Pro	41.0	0.0		74.0	4.0	NM_176071	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	hg19	CCDS8219.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.197562	0.58126	.	.	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.38722	1.12;1.12;1.12	5.37	5.37	0.77165	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67683	0.2919	M	0.85041	2.73	0.50813	D	0.999899	D	0.71674	0.998	D	0.75484	0.986	T	0.73069	-0.4099	10	0.59425	D	0.04	.	14.5447	0.68020	0.0:0.0:0.0:1.0	.	141	P41231	P2RY2_HUMAN	P	141	ENSP00000377222:S141P;ENSP00000310305:S141P;ENSP00000377221:S141P	ENSP00000310305:S141P	S	+	1	0	P2RY2	72623273	0.845000	0.29573	0.882000	0.34594	0.912000	0.54170	2.238000	0.43070	2.039000	0.60335	0.533000	0.62120	TCC	.	.		0.667	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072	
C2CD3	26005	hgsc.bcm.edu	37	11	73824846	73824846	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:73824846A>G	ENST00000334126.7	-	11	2048	c.1822T>C	c.(1822-1824)Tcc>Ccc	p.S608P	C2CD3_ENST00000313663.7_Missense_Mutation_p.S608P			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	608					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					ATTTTACTGGAGGCGAGTCGA	0.393																																					p.S608P		Atlas-SNP	.											.	C2CD3	288	.	0			c.T1822C						.						129.0	126.0	127.0					11																	73824846		2200	4293	6493	SO:0001583	missense	26005	exon11			TACTGGAGGCGAG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1822T>C	chr11.hg19:g.73824846A>G	ENSP00000334379:p.Ser608Pro	90.0	0.0		76.0	5.0	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	A	23.6	4.431412	0.83776	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	T;T	0.19105	2.17;2.23	5.27	5.27	0.74061	C2 calcium-dependent membrane targeting (1);	0.062950	0.64402	D	0.000003	T	0.45558	0.1348	M	0.71581	2.175	0.39755	D	0.971948	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.50583	-0.8811	10	0.87932	D	0	-10.2501	13.4225	0.61007	1.0:0.0:0.0:0.0	.	608;608	Q4AC94;Q4AC94-1	C2CD3_HUMAN;.	P	608	ENSP00000334379:S608P;ENSP00000323339:S608P	ENSP00000323339:S608P	S	-	1	0	C2CD3	73502494	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.086000	0.76885	1.996000	0.58369	0.374000	0.22700	TCC	.	.		0.393	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
DLG2	1740	hgsc.bcm.edu	37	11	83173062	83173062	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:83173062A>G	ENST00000532653.1	-	22	2737	c.2435T>C	c.(2434-2436)tTt>tCt	p.F812S	DLG2_ENST00000404783.3_Missense_Mutation_p.F308S|DLG2_ENST00000531015.1_Missense_Mutation_p.F797S|DLG2_ENST00000376104.2_Missense_Mutation_p.F935S|DLG2_ENST00000398309.2_Missense_Mutation_p.F830S|DLG2_ENST00000426717.2_Missense_Mutation_p.F294S|DLG2_ENST00000524982.1_Missense_Mutation_p.F826S|DLG2_ENST00000330014.6_Missense_Mutation_p.F751S|DLG2_ENST00000376106.3_Missense_Mutation_p.F294S|DLG2_ENST00000280241.8_Missense_Mutation_p.F869S|DLG2_ENST00000543673.1_Missense_Mutation_p.F935S|DLG2_ENST00000418306.2_Missense_Mutation_p.F709S|DLG2_ENST00000537455.1_Missense_Mutation_p.F580S			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	536					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				ATATTCTCCAAATTCTTGTTC	0.413																																					p.F935S		Atlas-SNP	.											.	DLG2	448	.	0			c.T2804C						.						153.0	146.0	148.0					11																	83173062		1867	4121	5988	SO:0001583	missense	1740	exon27			TCTCCAAATTCTT	U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	2901	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 58"""	603583	"""discs, large homolog 2, chapsyn-110 (Drosophila)"""			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.2435T>C	chr11.hg19:g.83173062A>G	ENSP00000435849:p.Phe812Ser	552.0	0.0		496.0	53.0	NM_001142699	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000532653.1	hg19		.	.	.	.	.	.	.	.	.	.	A	22.3	4.272603	0.80580	.	.	ENSG00000150672	ENST00000398309;ENST00000426717;ENST00000376104;ENST00000418306;ENST00000543673;ENST00000280241;ENST00000404783;ENST00000330014;ENST00000537455;ENST00000376106;ENST00000524982;ENST00000532653;ENST00000546021;ENST00000531015	T;T;T;T;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;0.86;0.86;0.86;0.86	5.01	5.01	0.66863	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.000000	0.64402	D	0.000001	T	0.67078	0.2855	M	0.72576	2.205	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.996;0.999;0.995;1.0;1.0;0.992	D;D;D;D;D;D;D;D	0.97110	1.0;0.997;0.978;0.995;0.967;0.999;0.999;0.977	T	0.68557	-0.5377	9	.	.	.	.	14.8932	0.70625	1.0:0.0:0.0:0.0	.	797;812;826;751;308;935;830;709	E9PIW2;B7Z2T4;E9PN83;B7Z264;B5MCC5;Q15700-2;Q15700;Q15700-3	.;.;.;.;.;.;DLG2_HUMAN;.	S	830;294;935;709;935;869;308;751;580;294;826;812;935;797	ENSP00000381355:F830S;ENSP00000393049:F294S;ENSP00000365272:F935S;ENSP00000402275:F709S;ENSP00000441994:F935S;ENSP00000280241:F869S;ENSP00000385113:F308S;ENSP00000381353:F751S;ENSP00000443248:F580S;ENSP00000365274:F294S;ENSP00000432894:F826S;ENSP00000435849:F812S;ENSP00000433848:F797S	.	F	-	2	0	DLG2	82850710	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.761000	0.91691	2.106000	0.64143	0.533000	0.62120	TTT	.	.		0.413	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364	
KIAA1731	85459	hgsc.bcm.edu	37	11	93432054	93432054	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:93432054A>G	ENST00000325212.6	+	15	4138	c.3976A>G	c.(3976-3978)Agc>Ggc	p.S1326G	KIAA1731_ENST00000411936.1_Missense_Mutation_p.S1326G|KIAA1731_ENST00000344196.4_5'UTR|KIAA1731_ENST00000531700.1_Intron			Q9C0D2	K1731_HUMAN	KIAA1731	1326						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)				AATTTTTTCAAGCCACCTTCA	0.418																																					p.S1326G		Atlas-SNP	.											.	KIAA1731	173	.	0			c.A3976G						.						49.0	39.0	42.0					11																	93432054		692	1591	2283	SO:0001583	missense	85459	exon15			TTTTCAAGCCACC	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.3976A>G	chr11.hg19:g.93432054A>G	ENSP00000316681:p.Ser1326Gly	148.0	0.0		100.0	4.0	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Missense_Mutation	SNP	ENST00000325212.6	hg19	CCDS44708.1	.	.	.	.	.	.	.	.	.	.	A	7.362	0.625085	0.14257	.	.	ENSG00000166004	ENST00000325212;ENST00000411936	T;T	0.25250	1.81;1.81	5.16	-0.0411	0.13869	.	0.529823	0.18944	N	0.126864	T	0.19886	0.0478	L	0.52905	1.665	0.09310	N	0.999995	B	0.09022	0.002	B	0.09377	0.004	T	0.16867	-1.0388	10	0.49607	T	0.09	0.743	5.2069	0.15295	0.6349:0.0:0.2379:0.1272	.	1326	Q9C0D2	K1731_HUMAN	G	1326	ENSP00000316681:S1326G;ENSP00000406505:S1326G	ENSP00000316681:S1326G	S	+	1	0	KIAA1731	93071702	0.760000	0.28428	0.013000	0.15412	0.002000	0.02628	0.961000	0.29267	-0.155000	0.11098	-2.200000	0.00306	AGC	.	.		0.418	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
MED17	9440	hgsc.bcm.edu	37	11	93528080	93528080	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:93528080C>T	ENST00000251871.3	+	6	1153	c.866C>T	c.(865-867)cCa>cTa	p.P289L	MED17_ENST00000533367.1_Intron|snoU13_ENST00000459243.1_RNA	NM_004268.4	NP_004259.3	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	289					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)|transcription factor complex (GO:0005667)	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)			large_intestine(2)|lung(11)|ovary(1)	14		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TCAGGTTCCCCACATTGGCAG	0.338																																					p.P289L		Atlas-SNP	.											.	MED17	37	.	0			c.C866T						.						74.0	77.0	76.0					11																	93528080		2201	4297	6498	SO:0001583	missense	9440	exon6			GTTCCCCACATTG	AF104254	CCDS8295.1	11q21	2007-07-30	2007-07-30	2007-07-30	ENSG00000042429	ENSG00000042429			2375	protein-coding gene	gene with protein product		603810	"""cofactor required for Sp1 transcriptional activation, subunit 6 (77kD)"", ""cofactor required for Sp1 transcriptional activation, subunit 6, 77kDa"""	CRSP6		9989412, 10198638	Standard	NM_004268		Approved	CRSP77, TRAP80, DRIP80	uc001pem.4	Q9NVC6	OTTHUMG00000167497	ENST00000251871.3:c.866C>T	chr11.hg19:g.93528080C>T	ENSP00000251871:p.Pro289Leu	99.0	0.0		84.0	4.0	NM_004268	B3KN07|Q9HA81|Q9UNP7|Q9Y2W0|Q9Y660	Missense_Mutation	SNP	ENST00000251871.3	hg19	CCDS8295.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.360129	0.41801	.	.	ENSG00000042429	ENST00000251871;ENST00000427225	T	0.52754	0.65	5.57	5.57	0.84162	.	0.048996	0.85682	D	0.000000	T	0.38214	0.1032	L	0.38175	1.15	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.12016	-1.0564	10	0.27082	T	0.32	-16.3463	13.7988	0.63188	0.0:0.9268:0.0:0.0732	.	289	Q9NVC6	MED17_HUMAN	L	289;259	ENSP00000251871:P289L	ENSP00000251871:P289L	P	+	2	0	MED17	93167728	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.665000	0.54532	2.639000	0.89480	0.655000	0.94253	CCA	.	.		0.338	MED17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394800.2	NM_004268	
HEPHL1	341208	hgsc.bcm.edu	37	11	93844145	93844145	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:93844145A>G	ENST00000315765.9	+	18	3130	c.3122A>G	c.(3121-3123)cAc>cGc	p.H1041R		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	1041	Plastocyanin-like 6.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TTTGCAGATCACCCAGGGACA	0.438																																					p.H1041R		Atlas-SNP	.											.	HEPHL1	144	.	0			c.A3122G						.						82.0	83.0	83.0					11																	93844145		2108	4251	6359	SO:0001583	missense	341208	exon18			CAGATCACCCAGG	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.3122A>G	chr11.hg19:g.93844145A>G	ENSP00000313699:p.His1041Arg	134.0	0.0		125.0	5.0	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	hg19	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	A	15.60	2.880444	0.51801	.	.	ENSG00000181333	ENST00000315765	D	0.99619	-6.28	5.97	5.97	0.96955	Cupredoxin (2);Multicopper oxidase, type 2 (1);	0.045878	0.85682	D	0.000000	D	0.98068	0.9363	N	0.21194	0.64	0.35325	D	0.785137	B	0.30542	0.284	B	0.27887	0.084	D	0.99975	1.2176	10	0.59425	D	0.04	0.0867	16.4566	0.84019	1.0:0.0:0.0:0.0	.	1041	Q6MZM0	HPHL1_HUMAN	R	1041	ENSP00000313699:H1041R	ENSP00000313699:H1041R	H	+	2	0	HEPHL1	93483793	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.865000	0.75500	2.291000	0.77112	0.533000	0.62120	CAC	.	.		0.438	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947	
HEPHL1	341208	hgsc.bcm.edu	37	11	93845031	93845031	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:93845031T>C	ENST00000315765.9	+	20	3459	c.3451T>C	c.(3451-3453)Tcc>Ccc	p.S1151P		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	1151					copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				GCAAGTCCAGTCCTGTGCTCT	0.527																																					p.S1151P		Atlas-SNP	.											.	HEPHL1	144	.	0			c.T3451C						.						184.0	179.0	181.0					11																	93845031		2026	4192	6218	SO:0001583	missense	341208	exon20			GTCCAGTCCTGTG	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.3451T>C	chr11.hg19:g.93845031T>C	ENSP00000313699:p.Ser1151Pro	138.0	0.0		94.0	4.0	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	hg19	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	T	14.25	2.480697	0.44044	.	.	ENSG00000181333	ENST00000315765	D	0.99304	-5.72	5.45	1.38	0.22167	.	.	.	.	.	D	0.96405	0.8827	N	0.19112	0.55	0.28284	N	0.92386	P	0.37466	0.596	B	0.34991	0.193	D	0.93821	0.7119	9	0.54805	T	0.06	-4.5314	9.2422	0.37504	0.4762:0.0:0.0:0.5238	.	1151	Q6MZM0	HPHL1_HUMAN	P	1151	ENSP00000313699:S1151P	ENSP00000313699:S1151P	S	+	1	0	HEPHL1	93484679	0.993000	0.37304	1.000000	0.80357	0.873000	0.50193	0.141000	0.16076	0.311000	0.23014	0.459000	0.35465	TCC	.	.		0.527	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947	
EXPH5	23086	hgsc.bcm.edu	37	11	108398908	108398908	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:108398908A>G	ENST00000265843.4	-	4	557	c.447T>C	c.(445-447)tgT>tgC	p.C149C	EXPH5_ENST00000443411.1_Intron|EXPH5_ENST00000525344.1_Silent_p.C142C|EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Silent_p.C73C	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	149					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CATGGCCATCACATCTGTGGA	0.398																																					p.C149C		Atlas-SNP	.											.	EXPH5	193	.	0			c.T447C						.						88.0	86.0	86.0					11																	108398908		2201	4298	6499	SO:0001819	synonymous_variant	23086	exon4			GCCATCACATCTG		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.447T>C	chr11.hg19:g.108398908A>G		84.0	0.0		66.0	4.0	NM_015065	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	hg19	CCDS8341.1																																																																																			.	.		0.398	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
EXPH5	23086	hgsc.bcm.edu	37	11	108464205	108464205	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:108464205T>C	ENST00000265843.4	-	1	169	c.59A>G	c.(58-60)aAg>aGg	p.K20R	EXPH5_ENST00000525344.1_Missense_Mutation_p.K13R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	20	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CTGAAGGATCTTCCTGGCCTC	0.478																																					p.K20R		Atlas-SNP	.											.	EXPH5	193	.	0			c.A59G						.						120.0	116.0	117.0					11																	108464205		2201	4298	6499	SO:0001583	missense	23086	exon1			AGGATCTTCCTGG		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.59A>G	chr11.hg19:g.108464205T>C	ENSP00000265843:p.Lys20Arg	202.0	0.0		199.0	8.0	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	hg19	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.062149	0.76187	.	.	ENSG00000110723	ENST00000265843;ENST00000525344	T;T	0.02631	4.22;4.24	5.22	2.73	0.32206	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);	0.440551	0.19410	N	0.114963	T	0.05823	0.0152	L	0.47716	1.5	0.80722	D	1	P	0.50156	0.932	P	0.51135	0.66	T	0.38286	-0.9668	10	0.48119	T	0.1	-6.9512	9.9736	0.41770	0.0:0.0:0.3285:0.6715	.	20	Q8NEV8	EXPH5_HUMAN	R	20;13	ENSP00000265843:K20R;ENSP00000432546:K13R	ENSP00000265843:K20R	K	-	2	0	EXPH5	107969415	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.278000	0.33179	0.257000	0.21650	0.379000	0.24179	AAG	.	.		0.478	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
PAFAH1B2	5049	hgsc.bcm.edu	37	11	117031926	117031926	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:117031926A>G	ENST00000527958.1	+	4	396	c.237A>G	c.(235-237)agA>agG	p.R79R	PAFAH1B2_ENST00000419197.2_Silent_p.R79R|PAFAH1B2_ENST00000530272.1_Silent_p.R79R|PAFAH1B2_ENST00000526888.1_Intron|PAFAH1B2_ENST00000529887.2_Silent_p.R79R	NM_002572.3	NP_002563.1	P68402	PA1B2_HUMAN	platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa)	79					brain development (GO:0007420)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|positive regulation of macroautophagy (GO:0016239)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)			kidney(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;1.68e-05)|Epithelial(105;0.000162)|all cancers(92;0.00111)		ATACAACAAGACATGTTTTGT	0.348			T	IGH@	MLCLS																																p.R79R		Atlas-SNP	.		Dom	yes		11	11q23	5049	"""platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa"""		L	.	PAFAH1B2	19	.	0			c.A237G						.						112.0	117.0	115.0					11																	117031926		2201	4296	6497	SO:0001819	synonymous_variant	5049	exon4			AACAAGACATGTT	D63390	CCDS8380.1, CCDS53713.1, CCDS53714.1, CCDS53715.1	11q23	2011-10-24	2010-02-10			ENSG00000168092			8575	protein-coding gene	gene with protein product	"""PAF-AH1b alpha 2 subunit"""	602508	"""platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa"", ""platelet-activating factor acetylhydrolase, isoform Ib, subunit 2 (30kDa)"""			9144386, 9693049	Standard	NM_002572		Approved		uc001pqe.2	P68402		ENST00000527958.1:c.237A>G	chr11.hg19:g.117031926A>G		116.0	0.0		107.0	5.0	NM_001184747	A8DPS5|A8DPS6|A8DPS7|E9PEJ5|E9PLP3|O00687|Q29459|Q6IBR6	Silent	SNP	ENST00000527958.1	hg19	CCDS8380.1																																																																																			.	.		0.348	PAFAH1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392826.1	NM_002572	
CEP164	22897	hgsc.bcm.edu	37	11	117222658	117222658	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:117222658A>G	ENST00000278935.3	+	5	494	c.347A>G	c.(346-348)aAg>aGg	p.K116R		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	116	Interaction with ATRIP.|Lys-rich.				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)		aaaaaaaaaaaggaaaagaaa	0.502																																					p.K116R		Atlas-SNP	.											CEP164,caecum,carcinoma,0,1	CEP164	121	.	0			c.A347G						.						33.0	34.0	34.0					11																	117222658		2201	4296	6497	SO:0001583	missense	22897	exon4			AAAAAAAGGAAAA	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.347A>G	chr11.hg19:g.117222658A>G	ENSP00000278935:p.Lys116Arg	76.0	1.0		73.0	3.0	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	hg19	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744661	0.49151	.	.	ENSG00000110274	ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000533570;ENST00000529538	T;T;T;T	0.76060	-0.34;-0.03;-0.29;-0.99	5.95	4.82	0.62117	.	0.243999	0.29172	N	0.012934	T	0.80221	0.4583	M	0.62723	1.935	0.34770	D	0.733632	D;P;B;D	0.56521	0.959;0.482;0.023;0.976	P;B;B;P	0.56960	0.65;0.11;0.01;0.81	D	0.85776	0.1358	10	0.62326	D	0.03	-27.2573	11.2799	0.49188	0.9276:0.0:0.0724:0.0	.	116;70;116;116	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	R	70;116;70;70;116;116	ENSP00000436034:K70R;ENSP00000278935:K116R;ENSP00000435759:K70R;ENSP00000431302:K116R	ENSP00000278935:K116R	K	+	2	0	CEP164	116727868	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	8.713000	0.91408	1.068000	0.40764	0.533000	0.62120	AAG	.	.		0.502	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
HINFP	25988	hgsc.bcm.edu	37	11	119004976	119004976	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:119004976A>G	ENST00000350777.2	+	10	1385	c.1322A>G	c.(1321-1323)gAg>gGg	p.E441G	HINFP_ENST00000527410.1_3'UTR	NM_001243259.1|NM_015517.4|NM_198971.2	NP_001230188.1|NP_056332.2|NP_945322.1	Q9BQA5	HINFP_HUMAN	histone H4 transcription factor	441	Interaction with NPAT.|Poly-Glu.				DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|establishment of protein localization (GO:0045184)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|myoblast differentiation (GO:0045445)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CGTAAGGAAGAGGAAGAGGAG	0.582											OREG0021397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E441G		Atlas-SNP	.											.	HINFP	50	.	0			c.A1322G						.						100.0	98.0	99.0					11																	119004976		2200	4295	6495	SO:0001583	missense	25988	exon11			AGGAAGAGGAAGA	AL080201	CCDS8414.1, CCDS58188.1	11q23.3	2013-01-08	2009-01-22	2009-01-22	ENSG00000172273	ENSG00000172273		"""Zinc fingers, C2H2-type"""	17850	protein-coding gene	gene with protein product	"""histone nuclear factor P"""	607099	"""MBD2-interacting zinc finger 1"", ""MBD2-interacting zinc finger"""	MIZF		11553631	Standard	NM_015517		Approved	DKFZP434F162, HiNF-P, ZNF743	uc001pvq.3	Q9BQA5	OTTHUMG00000166168	ENST00000350777.2:c.1322A>G	chr11.hg19:g.119004976A>G	ENSP00000318085:p.Glu441Gly	118.0	0.0	1492	90.0	4.0	NM_015517	B3KPH6|B4DWB4|E9PQF4|Q96E65|Q9Y4M7	Missense_Mutation	SNP	ENST00000350777.2	hg19	CCDS8414.1	.	.	.	.	.	.	.	.	.	.	A	15.00	2.704586	0.48412	.	.	ENSG00000172273	ENST00000350777	T	0.10192	2.9	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000001	T	0.10723	0.0262	L	0.43152	1.355	0.80722	D	1	P	0.40970	0.734	B	0.37731	0.257	T	0.15093	-1.0449	10	0.29301	T	0.29	1.7937	13.32	0.60428	1.0:0.0:0.0:0.0	.	441	Q9BQA5	HINFP_HUMAN	G	441	ENSP00000318085:E441G	ENSP00000318085:E441G	E	+	2	0	HINFP	118510186	0.877000	0.30153	0.405000	0.26409	0.790000	0.44656	2.810000	0.47979	2.163000	0.67991	0.533000	0.62120	GAG	.	.		0.582	HINFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388201.2	NM_015517	
TRIM29	23650	hgsc.bcm.edu	37	11	120007994	120007994	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:120007994A>G	ENST00000341846.5	-	1	1167	c.746T>C	c.(745-747)tTc>tCc	p.F249S		NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	249					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		GTGCTCCTGGAACATGCAAAG	0.607																																					p.F249S		Atlas-SNP	.											.	TRIM29	78	.	0			c.T746C						.						96.0	89.0	91.0					11																	120007994		2203	4300	6503	SO:0001583	missense	23650	exon1			TCCTGGAACATGC	AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"""Tripartite motif containing / Tripartite motif containing"""	17274	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM29"", ""ataxia-telangiectasia group D-associated protein"""	610658	"""tripartite motif-containing 29"""			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.746T>C	chr11.hg19:g.120007994A>G	ENSP00000343129:p.Phe249Ser	96.0	0.0		94.0	5.0	NM_012101	Q96AA9|Q9BZY7	Missense_Mutation	SNP	ENST00000341846.5	hg19	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.013488	0.75161	.	.	ENSG00000137699	ENST00000341846	T	0.39997	1.05	5.91	4.77	0.60923	Zinc finger, B-box (3);	0.000000	0.85682	D	0.000000	T	0.39064	0.1064	N	0.03224	-0.385	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.41106	-0.9527	9	.	.	.	.	13.3279	0.60469	0.868:0.1319:0.0:0.0	.	249	Q14134	TRI29_HUMAN	S	249	ENSP00000343129:F249S	.	F	-	2	0	TRIM29	119513204	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.193000	0.72075	1.041000	0.40125	0.533000	0.62120	TTC	.	.		0.607	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101	
OAF	220323	hgsc.bcm.edu	37	11	120096467	120096467	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:120096467A>G	ENST00000328965.4	+	2	842	c.329A>G	c.(328-330)gAg>gGg	p.E110G	OAF_ENST00000531220.1_5'UTR	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	110						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(5)	6		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)		CAGCACAATGAGATCATCCCC	0.647																																					p.E110G		Atlas-SNP	.											.	OAF	12	.	0			c.A329G						.						127.0	122.0	124.0					11																	120096467		2203	4300	6503	SO:0001583	missense	220323	exon2			ACAATGAGATCAT	BC047726	CCDS8430.1	11q23.3	2010-11-23			ENSG00000184232	ENSG00000184232			28752	protein-coding gene	gene with protein product						12477932	Standard	NM_178507		Approved	MGC52117	uc001pxb.3	Q86UD1	OTTHUMG00000166139	ENST00000328965.4:c.329A>G	chr11.hg19:g.120096467A>G	ENSP00000332613:p.Glu110Gly	62.0	0.0		70.0	4.0	NM_178507		Missense_Mutation	SNP	ENST00000328965.4	hg19	CCDS8430.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.904200	0.92035	.	.	ENSG00000184232	ENST00000328965	T	0.37584	1.19	4.96	4.96	0.65561	.	0.116380	0.56097	D	0.000025	T	0.53626	0.1808	M	0.72118	2.19	0.80722	D	1	D	0.63046	0.992	P	0.57101	0.813	T	0.59778	-0.7390	10	0.72032	D	0.01	-21.2797	14.6307	0.68653	1.0:0.0:0.0:0.0	.	110	Q86UD1	OAF_HUMAN	G	110	ENSP00000332613:E110G	ENSP00000332613:E110G	E	+	2	0	OAF	119601677	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.629000	0.90983	1.852000	0.53769	0.459000	0.35465	GAG	.	.		0.647	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507	
OR8B4	283162	hgsc.bcm.edu	37	11	124294157	124294157	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:124294157A>T	ENST00000356130.3	-	1	632	c.611T>A	c.(610-612)gTa>gAa	p.V204E		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CATGGTGATTACTCCAACAAC	0.468																																					p.V204E		Atlas-SNP	.											.	OR8B4	60	.	0			c.T611A						.						84.0	67.0	73.0					11																	124294157		2201	4299	6500	SO:0001583	missense	283162	exon1			GTGATTACTCCAA	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.611T>A	chr11.hg19:g.124294157A>T	ENSP00000348449:p.Val204Glu	126.0	0.0		112.0	6.0	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	hg19	CCDS31710.1	.	.	.	.	.	.	.	.	.	.	a	5.455	0.269109	0.10349	.	.	ENSG00000198657	ENST00000356130	T	0.40225	1.04	4.02	0.421	0.16451	GPCR, rhodopsin-like superfamily (1);	1.353600	0.05172	N	0.499731	T	0.44973	0.1319	M	0.78801	2.425	0.09310	N	1	B	0.29671	0.254	B	0.31337	0.128	T	0.44360	-0.9333	10	0.87932	D	0	.	4.6979	0.12813	0.6613:0.1626:0.1761:0.0	.	204	Q96RC9	OR8B4_HUMAN	E	204	ENSP00000348449:V204E	ENSP00000348449:V204E	V	-	2	0	OR8B4	123799367	0.000000	0.05858	0.002000	0.10522	0.023000	0.10783	0.406000	0.21032	0.065000	0.16485	0.529000	0.55759	GTA	.	.		0.468	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
ROBO4	54538	hgsc.bcm.edu	37	11	124764172	124764172	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:124764172A>G	ENST00000306534.3	-	8	1728	c.1243T>C	c.(1243-1245)Tcc>Ccc	p.S415P	ROBO4_ENST00000526899.1_5'Flank|ROBO4_ENST00000533054.1_Missense_Mutation_p.S270P	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	415	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.S415A(1)		NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		ACGCAGTAGGAGCCTGGCATA	0.607																																					p.S415P		Atlas-SNP	.											ROBO4,colon,carcinoma,0,1	ROBO4	130	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1243C						.						105.0	83.0	91.0					11																	124764172		2201	4299	6500	SO:0001583	missense	54538	exon8			AGTAGGAGCCTGG	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.1243T>C	chr11.hg19:g.124764172A>G	ENSP00000304945:p.Ser415Pro	132.0	0.0		109.0	5.0	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	hg19	CCDS8455.1	.	.	.	.	.	.	.	.	.	.	A	17.69	3.451082	0.63290	.	.	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.58652	0.32;0.32	4.93	4.93	0.64822	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.227101	0.22905	N	0.054205	T	0.69486	0.3116	M	0.65975	2.015	0.33960	D	0.645526	D;D	0.71674	0.993;0.998	P;D	0.64321	0.801;0.924	T	0.77275	-0.2648	10	0.39692	T	0.17	.	10.9978	0.47587	1.0:0.0:0.0:0.0	.	305;415	Q8WZ75-3;Q8WZ75	.;ROBO4_HUMAN	P	415;305;270	ENSP00000304945:S415P;ENSP00000437129:S270P	ENSP00000304945:S415P	S	-	1	0	ROBO4	124269382	0.999000	0.42202	0.999000	0.59377	0.848000	0.48234	1.518000	0.35877	1.851000	0.53745	0.533000	0.62120	TCC	.	.		0.607	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
NFRKB	4798	hgsc.bcm.edu	37	11	129752348	129752348	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:129752348T>C	ENST00000446488.3	-	9	1183	c.1080A>G	c.(1078-1080)gaA>gaG	p.E360E	NFRKB_ENST00000524746.1_Silent_p.E360E|NFRKB_ENST00000304521.5_Silent_p.E360E|NFRKB_ENST00000524794.1_Silent_p.E385E	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	360					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		TCACTTACTCTTCCTTGATAG	0.547																																					p.E385E		Atlas-SNP	.											.	NFRKB	101	.	0			c.A1155G						.						122.0	125.0	124.0					11																	129752348		2201	4297	6498	SO:0001819	synonymous_variant	4798	exon8			TTACTCTTCCTTG		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"""INO80 complex subunits"""	7802	protein-coding gene	gene with protein product	"""nuclear factor related to kappa B binding protein"", ""DNA-binding protein R kappa B"", ""INO80 complex subunit G"""	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.1080A>G	chr11.hg19:g.129752348T>C		96.0	0.0		120.0	6.0	NM_006165	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	hg19	CCDS44770.1																																																																																			.	.		0.547	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165	
SLC6A13	6540	hgsc.bcm.edu	37	12	352865	352865	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:352865T>C	ENST00000343164.4	-	3	369	c.317A>G	c.(316-318)aAg>aGg	p.K106R	SLC6A13_ENST00000445055.2_Intron	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	106					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			GGGGCAGATCTTCCTCCAGGC	0.502																																					p.K106R		Atlas-SNP	.											.	SLC6A13	62	.	0			c.A317G						.						118.0	97.0	104.0					12																	352865		2203	4300	6503	SO:0001583	missense	6540	exon3			CAGATCTTCCTCC	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"""Solute carriers"""	11046	protein-coding gene	gene with protein product	"""GABA transporter 2"""	615097	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 13"""				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.317A>G	chr12.hg19:g.352865T>C	ENSP00000339260:p.Lys106Arg	134.0	0.0		114.0	5.0	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	hg19	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	T	14.86	2.662792	0.47572	.	.	ENSG00000010379	ENST00000313154;ENST00000343164	T	0.74632	-0.86	6.17	3.78	0.43462	.	0.239426	0.49305	N	0.000154	T	0.61160	0.2325	N	0.20986	0.625	0.80722	D	1	B;B	0.19583	0.037;0.015	B;B	0.32289	0.143;0.143	T	0.50617	-0.8807	10	0.30078	T	0.28	.	8.5203	0.33270	0.0:0.2629:0.0:0.7371	.	85;106	B4DJS3;Q9NSD5	.;S6A13_HUMAN	R	85;106	ENSP00000339260:K106R	ENSP00000318097:K85R	K	-	2	0	SLC6A13	223126	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.245000	0.32790	0.539000	0.28788	0.533000	0.62120	AAG	.	.		0.502	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615	
CRACR2A	84766	hgsc.bcm.edu	37	12	3788250	3788250	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:3788250T>C	ENST00000252322.1	-	6	823	c.355A>G	c.(355-357)Agc>Ggc	p.S119G	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.S119G|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.S119G	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		119	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			TTATTCTGGCTGAAGAAGAAG	0.532																																					p.S119G		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.A355G						.						115.0	99.0	104.0					12																	3788250		2203	4300	6503	SO:0001583	missense	84766	exon6			TCTGGCTGAAGAA																												ENST00000252322.1:c.355A>G	chr12.hg19:g.3788250T>C	ENSP00000252322:p.Ser119Gly	130.0	0.0		69.0	4.0	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	hg19	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490302	0.26686	.	.	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.24350	1.86;1.86;1.86	4.76	3.6	0.41247	EF-hand-like domain (1);	0.102697	0.64402	D	0.000001	T	0.13884	0.0336	N	0.24115	0.695	0.26995	N	0.96505	B;B;B	0.13145	0.003;0.0;0.007	B;B;B	0.10450	0.003;0.001;0.005	T	0.30179	-0.9987	10	0.12430	T	0.62	-14.8863	7.2263	0.26018	0.0:0.1036:0.0:0.8964	.	119;119;119	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	G	119	ENSP00000409382:S119G;ENSP00000412496:S119G;ENSP00000252322:S119G	ENSP00000252322:S119G	S	-	1	0	EFCAB4B	3658511	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.128000	0.31369	0.660000	0.30964	0.459000	0.35465	AGC	.	.		0.532	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
PARP11	57097	hgsc.bcm.edu	37	12	3931065	3931065	+	Silent	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:3931065G>A	ENST00000228820.4	-	6	666	c.522C>T	c.(520-522)aaC>aaT	p.N174N	PARP11_ENST00000397096.2_Silent_p.N167N|PARP11_ENST00000447133.3_Silent_p.N93N|PARP11_ENST00000476985.1_5'UTR|PARP11_ENST00000427057.2_Silent_p.N93N	NM_020367.4	NP_065100.2	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11	167	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)			ACAAATCTAGGTTTTGAATTC	0.338																																					p.N174N		Atlas-SNP	.											.	PARP11	39	.	0			c.C522T						.						73.0	79.0	77.0					12																	3931065		2202	4300	6502	SO:0001819	synonymous_variant	57097	exon6			ATCTAGGTTTTGA	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.522C>T	chr12.hg19:g.3931065G>A		119.0	0.0		90.0	4.0	NM_020367	B4DRQ0|Q68DS1|Q8N5Y9	Silent	SNP	ENST00000228820.4	hg19	CCDS8523.2																																																																																			.	.		0.338	PARP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344213.1		
FGF6	2251	hgsc.bcm.edu	37	12	4553334	4553334	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:4553334C>T	ENST00000228837.2	-	2	458	c.415G>A	c.(415-417)Gtt>Att	p.V139I		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	139					angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|sarcolemma (GO:0042383)	growth factor activity (GO:0008083)	p.V139I(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)			TTCATGGCAACGAAGAGGGCA	0.512																																					p.V139I		Atlas-SNP	.											FGF6,NS,carcinoma,0,1	FGF6	40	.	1	Substitution - Missense(1)	prostate(1)	c.G415A						.						106.0	81.0	89.0					12																	4553334		2203	4300	6503	SO:0001583	missense	2251	exon2			TGGCAACGAAGAG	X63454	CCDS8527.1	12p13	2014-01-30				ENSG00000111241		"""Endogenous ligands"""	3684	protein-coding gene	gene with protein product		134921				16597617	Standard	NM_020996		Approved		uc001qmr.1	P10767		ENST00000228837.2:c.415G>A	chr12.hg19:g.4553334C>T	ENSP00000228837:p.Val139Ile	103.0	0.0		95.0	24.0	NM_020996	Q0VAE1	Missense_Mutation	SNP	ENST00000228837.2	hg19	CCDS8527.1	.	.	.	.	.	.	.	.	.	.	c	8.440	0.850726	0.17034	.	.	ENSG00000111241	ENST00000543077;ENST00000228837	D;T	0.85861	-2.04;1.5	5.63	-3.46	0.04767	.	0.271169	0.41605	N	0.000859	T	0.77198	0.4095	L	0.43923	1.385	0.40032	D	0.975543	B	0.13594	0.008	B	0.17433	0.018	T	0.55786	-0.8086	10	0.42905	T	0.14	.	13.631	0.62196	0.0:0.4678:0.0:0.5322	.	139	P10767	FGF6_HUMAN	I	18;139	ENSP00000445479:V18I;ENSP00000228837:V139I	ENSP00000228837:V139I	V	-	1	0	FGF6	4423595	0.002000	0.14202	0.017000	0.16124	0.633000	0.38033	-1.160000	0.03147	-1.177000	0.02744	-2.144000	0.00337	GTT	.	.		0.512	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996	
APOBEC1	339	hgsc.bcm.edu	37	12	7805229	7805229	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:7805229A>G	ENST00000229304.4	-	3	267	c.247T>C	c.(247-249)Tcc>Ccc	p.S83P		NM_001644.3	NP_001635.2	P41238	ABEC1_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	83				S -> T (in Ref. 5; AAD10701). {ECO:0000305}.	cellular response to insulin stimulus (GO:0032869)|cytidine deamination (GO:0009972)|cytidine to uridine editing (GO:0016554)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|gene expression (GO:0010467)|lipid metabolic process (GO:0006629)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein transport (GO:0042953)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to osmotic stress (GO:0006970)|response to zinc ion (GO:0010043)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	AU-rich element binding (GO:0017091)|cytidine deaminase activity (GO:0004126)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|stomach(1)	17						CAGGTGATGGAGCAGCTCATG	0.468																																					p.S83P	Pancreas(135;929 1826 4531 10527 41012)	Atlas-SNP	.											.	APOBEC1	43	.	0			c.T247C						.						48.0	47.0	47.0					12																	7805229		2203	4300	6503	SO:0001583	missense	339	exon3			TGATGGAGCAGCT	U72891	CCDS8579.1	12p13.1	2007-02-01			ENSG00000111701	ENSG00000111701		"""Apolipoprotein B mRNA editing enzymes"""	604	protein-coding gene	gene with protein product		600130					Standard	XM_005253355		Approved	BEDP, CDAR1, APOBEC-1, HEPR	uc001qtb.3	P41238	OTTHUMG00000141288	ENST00000229304.4:c.247T>C	chr12.hg19:g.7805229A>G	ENSP00000229304:p.Ser83Pro	94.0	0.0		64.0	4.0	NM_001644	Q9UE64|Q9UM71	Missense_Mutation	SNP	ENST00000229304.4	hg19	CCDS8579.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.237759	0.58886	.	.	ENSG00000111701	ENST00000229304	T	0.66460	-0.21	4.48	3.23	0.37069	APOBEC-like, N-terminal (1);APOBEC/CMP deaminase, zinc-binding (1);	0.236214	0.30528	N	0.009438	T	0.76478	0.3993	M	0.79805	2.47	0.27360	N	0.955992	D	0.65815	0.995	D	0.63283	0.913	T	0.66952	-0.5793	10	0.51188	T	0.08	-13.8594	6.849	0.24005	0.7934:0.0:0.0:0.2066	.	83	P41238	ABEC1_HUMAN	P	83	ENSP00000229304:S83P	ENSP00000229304:S83P	S	-	1	0	APOBEC1	7696496	1.000000	0.71417	0.999000	0.59377	0.886000	0.51366	0.820000	0.27323	1.805000	0.52779	0.379000	0.24179	TCC	.	.		0.468	APOBEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280523.1	NM_001644	
FOXJ2	55810	hgsc.bcm.edu	37	12	8202064	8202064	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:8202064T>C	ENST00000162391.3	+	9	2579	c.1434T>C	c.(1432-1434)ggT>ggC	p.G478G	FOXJ2_ENST00000428177.2_Silent_p.G478G	NM_018416.2	NP_060886.1	Q9P0K8	FOXJ2_HUMAN	forkhead box J2	478					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			autonomic_ganglia(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	16				Kidney(36;0.0944)		CTCAGACTGGTCACGTGCCCC	0.592																																					p.G478G		Atlas-SNP	.											.	FOXJ2	43	.	0			c.T1434C						.						141.0	105.0	117.0					12																	8202064		2203	4300	6503	SO:0001819	synonymous_variant	55810	exon9			GACTGGTCACGTG	AF155132	CCDS8587.1	12p13.31	2006-12-15				ENSG00000065970		"""Forkhead boxes"""	24818	protein-coding gene	gene with protein product						10777590, 10966786	Standard	NM_018416		Approved	FHX	uc001qtu.3	Q9P0K8		ENST00000162391.3:c.1434T>C	chr12.hg19:g.8202064T>C		81.0	0.0		70.0	4.0	NM_018416	A0AVK4|B2RMP3|Q96PS9|Q9NSN5	Silent	SNP	ENST00000162391.3	hg19	CCDS8587.1																																																																																			.	.		0.592	FOXJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400088.1	NM_018416	
C3AR1	719	hgsc.bcm.edu	37	12	8212440	8212440	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:8212440A>G	ENST00000307637.4	-	2	545	c.342T>C	c.(340-342)acT>acC	p.T114T		NM_004054.2	NP_004045.1	Q16581	C3AR_HUMAN	complement component 3a receptor 1	114					blood circulation (GO:0008015)|chemotaxis (GO:0006935)|complement receptor mediated signaling pathway (GO:0002430)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation vascular endothelial growth factor production (GO:0010575)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C3a anaphylatoxin receptor activity (GO:0004943)|complement component C3a receptor activity (GO:0004876)|G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)	20				Kidney(36;0.0893)		GGCTAATGGCAGTAAGCAGGA	0.517																																					p.T114T		Atlas-SNP	.											.	C3AR1	61	.	0			c.T342C						.						182.0	148.0	160.0					12																	8212440		2203	4300	6503	SO:0001819	synonymous_variant	719	exon2			AATGGCAGTAAGC	U28488	CCDS8588.1	12p13.31	2012-08-10				ENSG00000171860		"""Complement system"", ""GPCR / Class A : Complement component receptors"""	1319	protein-coding gene	gene with protein product		605246				8605247	Standard	NM_004054		Approved	C3AR, AZ3B	uc001qtv.1	Q16581		ENST00000307637.4:c.342T>C	chr12.hg19:g.8212440A>G		162.0	0.0		81.0	4.0	NM_004054	O43771|Q92868	Silent	SNP	ENST00000307637.4	hg19	CCDS8588.1																																																																																			.	.		0.517	C3AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400254.1		
PZP	5858	hgsc.bcm.edu	37	12	9318676	9318676	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:9318676T>C	ENST00000261336.2	-	18	2258	c.2230A>G	c.(2230-2232)Act>Gct	p.T744A	PZP_ENST00000381997.2_Missense_Mutation_p.T613A|PZP_ENST00000539983.1_5'UTR	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	744					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						CAGATCCAAGTCTCAGGAAAA	0.428																																					p.T744A	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A2230G						.						152.0	142.0	146.0					12																	9318676		2203	4300	6503	SO:0001583	missense	5858	exon18			TCCAAGTCTCAGG	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.2230A>G	chr12.hg19:g.9318676T>C	ENSP00000261336:p.Thr744Ala	135.0	0.0		89.0	5.0	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	hg19	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	19.39	3.818181	0.71028	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.29655	1.56;1.56	3.85	3.85	0.44370	Alpha-2-macroglobulin (1);	0.094329	0.44285	U	0.000465	T	0.56217	0.1970	M	0.87381	2.88	0.26229	N	0.979042	D;D;D	0.67145	0.976;0.996;0.995	D;D;D	0.68621	0.912;0.959;0.946	T	0.52653	-0.8547	10	0.62326	D	0.03	.	10.6921	0.45877	0.0:0.0:0.0:1.0	.	744;613;744	B2R950;P20742-2;P20742	.;.;PZP_HUMAN	A	744;613	ENSP00000261336:T744A;ENSP00000371427:T613A	ENSP00000261336:T744A	T	-	1	0	PZP	9209943	1.000000	0.71417	1.000000	0.80357	0.664000	0.39144	4.955000	0.63638	1.707000	0.51288	0.383000	0.25322	ACT	.	.		0.428	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
KLRF1	51348	hgsc.bcm.edu	37	12	9994450	9994450	+	Missense_Mutation	SNP	G	G	A	rs3052097|rs111928232		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:9994450G>A	ENST00000279544.3	+	4	441	c.377G>A	c.(376-378)tGt>tAt	p.C126Y	KLRF1_ENST00000354855.3_Intron|KLRF1_ENST00000324214.4_Missense_Mutation_p.C76Y|KLRF1_ENST00000537723.1_Intron	NM_016523.1	NP_057607	Q9NZS2	KLRF1_HUMAN	killer cell lectin-like receptor subfamily F, member 1	126	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|MHC class I receptor activity (GO:0032393)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)	13						GGGAAGTGTTGTTATTGGTTC	0.323																																					p.C126Y		Atlas-SNP	.											.	KLRF1	27	.	0			c.G377A						.						142.0	134.0	136.0					12																	9994450		1842	4083	5925	SO:0001583	missense	51348	exon4			AGTGTTGTTATTG	AF175206	CCDS41750.1	12p13.31	2011-08-30			ENSG00000150045	ENSG00000150045		"""Killer cell lectin-like receptors"", ""C-type lectin domain containing"""	13342	protein-coding gene	gene with protein product		605029				10671213	Standard	NM_001291823		Approved	CLEC5C, NKp80	uc021qux.1	Q9NZS2		ENST00000279544.3:c.377G>A	chr12.hg19:g.9994450G>A	ENSP00000279544:p.Cys126Tyr	230.0	0.0		221.0	13.0	NM_016523	Q4KMT5|Q96PR2|Q96PR3|Q9NZS1	Missense_Mutation	SNP	ENST00000279544.3	hg19	CCDS41750.1	.	.	.	.	.	.	.	.	.	.	-	4.237	0.042890	0.08196	.	.	ENSG00000150045	ENST00000324214;ENST00000279544	T;T	0.38401	1.14;1.14	.	.	.	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	.	.	.	.	T	0.62708	0.2450	M	0.91090	3.175	0.80722	D	1	D;D	0.89917	1.0;0.988	D;D	0.87578	0.998;0.983	T	0.65162	-0.6235	6	.	.	.	.	.	.	.	.	126;76	Q9NZS2;Q9NZS2-2	KLRF1_HUMAN;.	Y	76;126	ENSP00000322487:C76Y;ENSP00000279544:C126Y	.	C	+	2	0	KLRF1	9885717	1.000000	0.71417	0.998000	0.56505	0.846000	0.48090	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	TGT	.	G|0.500;A|0.500		0.323	KLRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399535.1	NM_016523	
LRP6	4040	hgsc.bcm.edu	37	12	12279675	12279675	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:12279675A>G	ENST00000261349.4	-	20	4338	c.4262T>C	c.(4261-4263)gTg>gCg	p.V1421A	LRP6_ENST00000540415.1_Intron|LRP6_ENST00000543091.1_Missense_Mutation_p.V1376A|BCL2L14_ENST00000396369.1_Intron	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1421					anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				ACCAAGAGGCACAGAAGCTGG	0.458																																					p.V1421A		Atlas-SNP	.											.	LRP6	170	.	0			c.T4262C						.						197.0	160.0	173.0					12																	12279675		2203	4300	6503	SO:0001583	missense	4040	exon20			AGAGGCACAGAAG	AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.4262T>C	chr12.hg19:g.12279675A>G	ENSP00000261349:p.Val1421Ala	132.0	0.0		106.0	5.0	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	hg19	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813240	0.50527	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	T;T	0.36520	1.25;1.25	5.7	5.7	0.88788	.	0.000000	0.53938	D	0.000042	T	0.50463	0.1617	L	0.50333	1.59	0.80722	D	1	D;D	0.65815	0.99;0.995	D;D	0.73380	0.98;0.917	T	0.40887	-0.9539	10	0.08179	T	0.78	.	15.96	0.79923	1.0:0.0:0.0:0.0	.	1376;1421	F5H7J9;O75581	.;LRP6_HUMAN	A	1421;1376	ENSP00000261349:V1421A;ENSP00000442472:V1376A	ENSP00000261349:V1421A	V	-	2	0	LRP6	12170942	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.923000	0.92808	2.165000	0.68154	0.460000	0.39030	GTG	.	.		0.458	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
PTPRO	5800	hgsc.bcm.edu	37	12	15704607	15704607	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:15704607T>C	ENST00000281171.4	+	15	2888		c.e15+2		PTPRO_ENST00000445537.2_Splice_Site|PTPRO_ENST00000544244.1_Splice_Site|PTPRO_ENST00000348962.2_Splice_Site|PTPRO_ENST00000442921.2_Splice_Site|PTPRO_ENST00000542557.1_Splice_Site	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O						axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				GATGGCTAGGTAAGTTAAGTT	0.353																																					.		Atlas-SNP	.											.	PTPRO	148	.	0			c.2558+2T>C						.						133.0	119.0	124.0					12																	15704607		2203	4300	6503	SO:0001630	splice_region_variant	5800	exon15			GCTAGGTAAGTTA	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9678	protein-coding gene	gene with protein product	"""osteoclastic transmembrane protein-tyrosine phosphatase"""	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.2558+2T>C	chr12.hg19:g.15704607T>C		128.0	0.0		84.0	4.0	NM_030667	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Splice_Site	SNP	ENST00000281171.4	hg19	CCDS8675.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.946854	0.53186	.	.	ENSG00000151490	ENST00000281171;ENST00000348962;ENST00000442921;ENST00000542557;ENST00000445537;ENST00000544244	.	.	.	5.03	3.85	0.44370	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9622	0.53015	0.0:0.0:0.1452:0.8548	.	.	.	.	.	-1	.	.	.	+	.	.	PTPRO	15595874	1.000000	0.71417	0.919000	0.36401	0.776000	0.43924	6.961000	0.76042	0.892000	0.36259	0.421000	0.28195	.	.	.		0.353	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1		Intron
PLEKHA5	54477	hgsc.bcm.edu	37	12	19410367	19410367	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:19410367A>G	ENST00000299275.6	+	6	439	c.433A>G	c.(433-435)Act>Gct	p.T145A	PLEKHA5_ENST00000424268.1_Splice_Site_p.T37A|PLEKHA5_ENST00000355397.3_Splice_Site_p.T145A|PLEKHA5_ENST00000309364.4_Splice_Site_p.T145A|PLEKHA5_ENST00000429027.2_Splice_Site_p.T145A|PLEKHA5_ENST00000539256.1_5'UTR|PLEKHA5_ENST00000317589.4_Splice_Site_p.T145A|PLEKHA5_ENST00000359180.3_Splice_Site_p.T145A|PLEKHA5_ENST00000543806.1_Splice_Site_p.T37A|PLEKHA5_ENST00000538714.1_Splice_Site_p.T145A	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	145					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					TTCTATTTAGACTTCACGAGC	0.333																																					p.T145A	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A433G						.						69.0	77.0	74.0					12																	19410367		2203	4298	6501	SO:0001630	splice_region_variant	54477	exon6			ATTTAGACTTCAC	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.433-1A>G	chr12.hg19:g.19410367A>G		84.0	0.0		79.0	4.0	NM_001143821	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	3.063	-0.192906	0.06259	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000309364;ENST00000412219;ENST00000429027;ENST00000299275;ENST00000538714;ENST00000538305;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T;T;T;T;T;T;T	0.12039	2.72;2.72;2.72;2.72;2.72;2.72;2.72;2.72;2.72;2.72;2.72	4.93	2.43	0.29744	.	0.322311	0.33670	N	0.004672	T	0.03651	0.0104	N	0.00926	-1.1	0.80722	D	1	B;B;B;B;B;P	0.35575	0.114;0.162;0.101;0.036;0.044;0.51	B;B;B;B;B;B	0.36567	0.078;0.075;0.034;0.006;0.012;0.228	T	0.45891	-0.9230	9	.	.	.	-11.6171	6.2473	0.20825	0.7043:0.0:0.0793:0.2164	.	145;37;37;145;145;145	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;Q9HAU0;Q9HAU0-2	.;.;.;.;PKHA5_HUMAN;.	A	145;145;145;145;145;145;145;145;145;37;37;37;37	ENSP00000325155:T145A;ENSP00000347560:T145A;ENSP00000352104:T145A;ENSP00000311239:T145A;ENSP00000404296:T145A;ENSP00000299275:T145A;ENSP00000439673:T145A;ENSP00000446308:T37A;ENSP00000400411:T37A;ENSP00000439837:T37A;ENSP00000440371:T37A	.	T	+	1	0	PLEKHA5	19301634	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	3.219000	0.51200	0.910000	0.36722	-0.256000	0.11100	ACT	.	.		0.333	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	Missense_Mutation
PLEKHA5	54477	hgsc.bcm.edu	37	12	19499936	19499936	+	Intron	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:19499936A>G	ENST00000299275.6	+	18	2406				PLEKHA5_ENST00000424268.1_Silent_p.E729E|PLEKHA5_ENST00000355397.3_Intron|PLEKHA5_ENST00000429027.2_Silent_p.E906E|PLEKHA5_ENST00000539256.1_Intron|PLEKHA5_ENST00000317589.4_Silent_p.E803E|PLEKHA5_ENST00000359180.3_Intron|PLEKHA5_ENST00000543806.1_Silent_p.E722E|PLEKHA5_ENST00000538714.1_Intron	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5						reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					AGGAAGAGGAAGTAGTCCCAC	0.418																																					p.E906E	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A2718G						.						60.0	54.0	56.0					12																	19499936		692	1591	2283	SO:0001627	intron_variant	54477	exon24			AGAGGAAGTAGTC	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.2400+1114A>G	chr12.hg19:g.19499936A>G		128.0	0.0		78.0	4.0	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Silent	SNP	ENST00000299275.6	hg19	CCDS8682.1																																																																																			.	.		0.418	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	
MED21	9412	hgsc.bcm.edu	37	12	27181241	27181241	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:27181241A>G	ENST00000282892.3	+	4	312	c.282A>G	c.(280-282)gaA>gaG	p.E94E	MED21_ENST00000536503.1_3'UTR|MED21_ENST00000546323.1_Silent_p.E94E	NM_001271811.1|NM_004264.3	NP_001258740.1|NP_004255.2	Q13503	MED21_HUMAN	mediator complex subunit 21	94					blastocyst development (GO:0001824)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	mediator complex (GO:0016592)	DNA-directed RNA polymerase activity (GO:0003899)|transcription coactivator activity (GO:0003713)					Colorectal(261;0.0847)					ATAAGCTAGAAGAAGAAAACC	0.368																																					p.E94E		Atlas-SNP	.											.	MED21	7	.	0			c.A282G						.						134.0	135.0	135.0					12																	27181241		2203	4300	6503	SO:0001819	synonymous_variant	9412	exon4			GCTAGAAGAAGAA	U46837	CCDS8711.1	12p12	2007-07-30	2007-07-30	2007-07-30		ENSG00000152944			11473	protein-coding gene	gene with protein product		603800	"""SRB7 (suppressor of RNA polymerase B, yeast) homolog"", ""SRB7 suppressor of RNA polymerase B homolog (yeast)"""	SURB7		8598913	Standard	NM_004264		Approved	SRB7	uc001rhp.2	Q13503		ENST00000282892.3:c.282A>G	chr12.hg19:g.27181241A>G		90.0	0.0		74.0	4.0	NM_004264	B2R4I3|Q6IB05|Q92811	Silent	SNP	ENST00000282892.3	hg19	CCDS8711.1																																																																																			.	.		0.368	MED21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403262.1	NM_004264	
DENND5B	160518	hgsc.bcm.edu	37	12	31605207	31605207	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:31605207T>C	ENST00000389082.5	-	5	1560	c.1296A>G	c.(1294-1296)aaA>aaG	p.K432K	DENND5B_ENST00000536562.1_Silent_p.K467K|DENND5B_ENST00000306833.6_Silent_p.K467K|snoU13_ENST00000458765.1_RNA|DENND5B_ENST00000354285.4_Silent_p.K454K	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	432					positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						TGCCGTTCTTTTTGTCATTGA	0.458																																					p.K432K		Atlas-SNP	.											DENND5B,caecum,carcinoma,0,1	DENND5B	114	.	0			c.A1296G						.						142.0	138.0	139.0					12																	31605207		1925	4134	6059	SO:0001819	synonymous_variant	160518	exon5			GTTCTTTTTGTCA	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"""DENN/MADD domain containing"""	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.1296A>G	chr12.hg19:g.31605207T>C		144.0	0.0		88.0	4.0	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Silent	SNP	ENST00000389082.5	hg19	CCDS44857.1																																																																																			.	.		0.458	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973	
FGD4	121512	hgsc.bcm.edu	37	12	32735126	32735126	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:32735126A>G	ENST00000427716.2	+	4	749	c.325A>G	c.(325-327)Act>Gct	p.T109A	FGD4_ENST00000531134.1_Missense_Mutation_p.T194A|FGD4_ENST00000472289.1_Missense_Mutation_p.T109A|FGD4_ENST00000534526.2_Missense_Mutation_p.T246A|FGD4_ENST00000546442.1_Missense_Mutation_p.T16A|FGD4_ENST00000266482.3_5'UTR|FGD4_ENST00000525053.1_Missense_Mutation_p.T221A	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	109	Actin filament-binding. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					GAAAGCTGCCACTCTTAGCTC	0.473																																					p.T109A		Atlas-SNP	.											.	FGD4	86	.	0			c.A325G						.						161.0	127.0	139.0					12																	32735126		2203	4300	6503	SO:0001583	missense	121512	exon4			GCTGCCACTCTTA	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19125	protein-coding gene	gene with protein product		611104	"""FGD1 family, member 4"""			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.325A>G	chr12.hg19:g.32735126A>G	ENSP00000394487:p.Thr109Ala	162.0	0.0		100.0	5.0	NM_139241	Q6ULS2|Q8TCP6	Missense_Mutation	SNP	ENST00000427716.2	hg19	CCDS8727.1	.	.	.	.	.	.	.	.	.	.	A	3.830	-0.036041	0.07497	.	.	ENSG00000139132	ENST00000534526;ENST00000531134;ENST00000472289;ENST00000427716;ENST00000546442;ENST00000525053;ENST00000395742	T;T;T;T;T	0.68765	-0.35;-0.35;-0.34;-0.32;-0.35	4.91	-2.4	0.06583	.	1.440510	0.04464	N	0.374939	T	0.40094	0.1103	N	0.08118	0	0.09310	N	1	B;B;B;B	0.11235	0.0;0.0;0.0;0.004	B;B;B;B	0.09377	0.0;0.0;0.0;0.004	T	0.24119	-1.0169	10	0.08837	T	0.75	0.263	6.275	0.20975	0.3963:0.2885:0.3152:0.0	.	221;194;109;109	E9PJX4;B7Z493;Q96M96;E9PQT1	.;.;FGD4_HUMAN;.	A	246;194;109;109;16;221;90	ENSP00000449273:T246A;ENSP00000431323:T194A;ENSP00000394487:T109A;ENSP00000446695:T16A;ENSP00000433666:T221A	ENSP00000379089:T109A	T	+	1	0	FGD4	32626393	0.000000	0.05858	0.000000	0.03702	0.354000	0.29330	-1.203000	0.03019	-0.385000	0.07833	0.383000	0.25322	ACT	.	.		0.473	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241	
DNM1L	10059	hgsc.bcm.edu	37	12	32854462	32854462	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:32854462A>G	ENST00000549701.1	+	2	290	c.216A>G	c.(214-216)caA>caG	p.Q72Q	DNM1L_ENST00000547312.1_Silent_p.Q72Q|DNM1L_ENST00000553257.1_Silent_p.Q72Q|DNM1L_ENST00000452533.2_Silent_p.Q72Q|DNM1L_ENST00000548671.1_3'UTR|DNM1L_ENST00000414834.2_Missense_Mutation_p.K4R|DNM1L_ENST00000358214.5_Silent_p.Q72Q|DNM1L_ENST00000266481.6_Silent_p.Q72Q|DNM1L_ENST00000381000.4_Silent_p.Q72Q			O00429	DNM1L_HUMAN	dynamin 1-like	72	Dynamin-type G.|GTPase domain.				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)					ATGTTTCACAAGAAGATAAAC	0.403																																					p.Q72Q		Atlas-SNP	.											.	DNM1L	52	.	0			c.A216G						.						85.0	88.0	87.0					12																	32854462		2203	4300	6503	SO:0001819	synonymous_variant	10059	exon2			TTCACAAGAAGAT	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.216A>G	chr12.hg19:g.32854462A>G		93.0	0.0		88.0	4.0	NM_012062	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Silent	SNP	ENST00000549701.1	hg19	CCDS8729.1	.	.	.	.	.	.	.	.	.	.	a	13.25	2.179630	0.38511	.	.	ENSG00000087470	ENST00000414834	T	0.79653	-1.29	5.58	-1.55	0.08558	.	.	.	.	.	T	0.66973	0.2844	.	.	.	0.22317	N	0.999208	B	0.02656	0.0	B	0.01281	0.0	T	0.56456	-0.7976	8	0.87932	D	0	.	3.4462	0.07481	0.4556:0.3351:0.0693:0.1401	.	4	B4DGC9	.	R	4	ENSP00000404160:K4R	ENSP00000404160:K4R	K	+	2	0	DNM1L	32745729	0.442000	0.25633	0.996000	0.52242	0.991000	0.79684	-0.048000	0.11944	-0.174000	0.10743	0.520000	0.50463	AAG	.	.		0.403	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062	
CNTN1	1272	hgsc.bcm.edu	37	12	41337846	41337846	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:41337846A>G	ENST00000551295.2	+	14	1674	c.1557A>G	c.(1555-1557)ggA>ggG	p.G519G	CNTN1_ENST00000547702.1_Silent_p.G519G|CNTN1_ENST00000347616.1_Silent_p.G519G|CNTN1_ENST00000547849.1_Silent_p.G519G|CNTN1_ENST00000360099.3_Silent_p.G519G|CNTN1_ENST00000348761.2_Silent_p.G508G	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	519	Ig-like C2-type 6.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TCACAGTTGGAGAAAACGCCA	0.383																																					p.G519G		Atlas-SNP	.											.	CNTN1	207	.	0			c.A1557G						.						151.0	121.0	131.0					12																	41337846		2203	4299	6502	SO:0001819	synonymous_variant	1272	exon14			AGTTGGAGAAAAC	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"", ""Endogenous ligands"""	2171	protein-coding gene	gene with protein product	"""glycoprotein gP135"""	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.1557A>G	chr12.hg19:g.41337846A>G		132.0	0.0		74.0	4.0	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Silent	SNP	ENST00000551295.2	hg19	CCDS8737.1																																																																																			.	.		0.383	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843	
H1FNT	341567	hgsc.bcm.edu	37	12	48723755	48723755	+	Silent	SNP	G	G	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:48723755G>C	ENST00000335017.1	+	1	993	c.681G>C	c.(679-681)ccG>ccC	p.P227P		NM_181788.1	NP_861453.1	Q75WM6	H1FNT_HUMAN	H1 histone family, member N, testis-specific	227					chromosome condensation (GO:0030261)|multicellular organismal development (GO:0007275)|sperm chromatin condensation (GO:0035092)|spermatid nucleus elongation (GO:0007290)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	13						ACACCACGCCGAGGTCAGGGA	0.657																																					p.P227P		Atlas-SNP	.											H1FNT,NS,carcinoma,0,1	H1FNT	30	.	0			c.G681C						.						55.0	64.0	61.0					12																	48723755		2189	4294	6483	SO:0001819	synonymous_variant	341567	exon1			CACGCCGAGGTCA	AY302593	CCDS8762.1	12q13.11	2011-01-27				ENSG00000187166		"""Histones / Replication-independent"""	24893	protein-coding gene	gene with protein product						15710904	Standard	NM_181788		Approved	HANP1, H1T2	uc001rrm.3	Q75WM6		ENST00000335017.1:c.681G>C	chr12.hg19:g.48723755G>C		51.0	1.0		37.0	8.0	NM_181788	Q147U8|Q5GKZ5|Q7Z694	Silent	SNP	ENST00000335017.1	hg19	CCDS8762.1																																																																																			.	.		0.657	H1FNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406516.1	NM_181788	
ADCY6	112	hgsc.bcm.edu	37	12	49168824	49168824	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:49168824A>G	ENST00000307885.4	-	11	2688	c.1994T>C	c.(1993-1995)gTg>gCg	p.V665A	ADCY6_ENST00000357869.3_Missense_Mutation_p.V665A|ADCY6_ENST00000552090.1_5'UTR|ADCY6_ENST00000550422.1_Missense_Mutation_p.V665A	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	665					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)|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)|dopamine receptor signaling pathway (GO:0007212)|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)|negative regulation of neuron projection development (GO:0010977)|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)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						GCGGGGATCCACCTTCCGGGA	0.597																																					p.V665A		Atlas-SNP	.											.	ADCY6	81	.	0			c.T1994C						.						65.0	56.0	59.0					12																	49168824		2181	4268	6449	SO:0001583	missense	112	exon12			GGATCCACCTTCC		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"""Adenylate cyclases"""	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.1994T>C	chr12.hg19:g.49168824A>G	ENSP00000311405:p.Val665Ala	100.0	0.0		85.0	5.0	NM_020983	Q9NR75|Q9UDB0	Missense_Mutation	SNP	ENST00000307885.4	hg19	CCDS8767.1	.	.	.	.	.	.	.	.	.	.	A	14.28	2.489498	0.44249	.	.	ENSG00000174233	ENST00000357869;ENST00000550422;ENST00000307885	T;T;T	0.34859	1.34;1.34;1.34	4.63	4.63	0.57726	.	0.074628	0.52532	D	0.000072	T	0.41465	0.1160	L	0.58101	1.795	0.58432	D	0.999994	P;P	0.40681	0.486;0.727	B;P	0.45660	0.356;0.489	T	0.20638	-1.0269	10	0.28530	T	0.3	.	13.7149	0.62691	1.0:0.0:0.0:0.0	.	665;665	O43306-2;O43306	.;ADCY6_HUMAN	A	665	ENSP00000350536:V665A;ENSP00000446730:V665A;ENSP00000311405:V665A	ENSP00000311405:V665A	V	-	2	0	ADCY6	47455091	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.683000	0.91236	2.026000	0.59711	0.533000	0.62120	GTG	.	.		0.597	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983	
DDN	23109	hgsc.bcm.edu	37	12	49391772	49391772	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:49391772C>A	ENST00000421952.2	-	2	908	c.887G>T	c.(886-888)gGa>gTa	p.G296V	RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	296						cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	8						GCCTGGGGATCCCCCCAAGAG	0.657																																					p.G296V		Atlas-SNP	.											DDN_ENST00000421952,NS,carcinoma,0,2	DDN	54	.	0			c.G887T						.						52.0	61.0	57.0					12																	49391772		2203	4299	6502	SO:0001583	missense	23109	exon2			GGGGATCCCCCCA	AB018292	CCDS31791.2	12q13	2008-02-05			ENSG00000181418	ENSG00000181418			24458	protein-coding gene	gene with protein product		610588					Standard	NM_015086		Approved	KIAA0749	uc001rsv.1	O94850	OTTHUMG00000156183	ENST00000421952.2:c.887G>T	chr12.hg19:g.49391772C>A	ENSP00000390590:p.Gly296Val	100.0	0.0		54.0	3.0	NM_015086		Missense_Mutation	SNP	ENST00000421952.2	hg19	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	C	18.34	3.602955	0.66445	.	.	ENSG00000181418	ENST00000421952	T	0.64085	-0.08	4.09	4.09	0.47781	.	0.000000	0.44902	D	0.000409	T	0.67154	0.2863	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.69316	-0.5177	10	0.54805	T	0.06	-7.7903	14.2411	0.65956	0.0:1.0:0.0:0.0	.	296	O94850	DEND_HUMAN	V	296	ENSP00000390590:G296V	ENSP00000390590:G296V	G	-	2	0	DDN	47678039	0.099000	0.21834	0.995000	0.50966	0.996000	0.88848	2.370000	0.44240	2.583000	0.87209	0.561000	0.74099	GGA	.	.		0.657	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1		
PRPF40B	25766	hgsc.bcm.edu	37	12	50036726	50036726	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:50036726A>G	ENST00000380281.1	+	21	2133	c.2069A>G	c.(2068-2070)cAc>cGc	p.H690R	PRPF40B_ENST00000261897.1_Missense_Mutation_p.H677R|FMNL3_ENST00000335154.5_3'UTR|PRPF40B_ENST00000548825.2_Missense_Mutation_p.H711R			Q6NWY9	PR40B_HUMAN	PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)	690					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34						GAATGCCAGCACCTCCACACC	0.542																																					p.H711R		Atlas-SNP	.											.	PRPF40B	83	.	0			c.A2132G						.						125.0	103.0	110.0					12																	50036726		2203	4300	6503	SO:0001583	missense	25766	exon22			GCCAGCACCTCCA	AF049525	CCDS31796.1, CCDS31796.2	12q13.12	2014-09-17	2006-04-04			ENSG00000110844			25031	protein-coding gene	gene with protein product	"""Huntingtin interacting protein C"""		"""PRP40 pre-mRNA processing factor 40 homolog B (yeast)"""			9700202	Standard	NM_001031698		Approved	HYPC	uc001rus.2	Q6NWY9		ENST00000380281.1:c.2069A>G	chr12.hg19:g.50036726A>G	ENSP00000369634:p.His690Arg	138.0	0.0		120.0	5.0	NM_001031698	O75401|Q6PI09|Q6ZWB3|Q8NCZ1|Q9H5G4|Q9NT95	Missense_Mutation	SNP	ENST00000380281.1	hg19		.	.	.	.	.	.	.	.	.	.	A	22.7	4.323693	0.81580	.	.	ENSG00000110844	ENST00000261897;ENST00000380281	T;T	0.22945	1.95;1.93	4.63	4.63	0.57726	.	0.000000	0.64402	D	0.000007	T	0.51805	0.1696	M	0.85859	2.78	0.80722	D	1	D;D;D	0.61080	0.981;0.989;0.989	D;D;D	0.75020	0.966;0.985;0.985	T	0.53287	-0.8460	10	0.25751	T	0.34	-16.018	13.4498	0.61163	1.0:0.0:0.0:0.0	.	690;677;689	Q6NWY9;Q6NWY9-2;Q6NWY9-3	PR40B_HUMAN;.;.	R	677;690	ENSP00000261897:H677R;ENSP00000369634:H690R	ENSP00000261897:H677R	H	+	2	0	PRPF40B	48322993	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.871000	0.92346	2.092000	0.63282	0.459000	0.35465	CAC	.	.		0.542	PRPF40B-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000404838.1	NM_012272	
KRT84	3890	hgsc.bcm.edu	37	12	52779324	52779324	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:52779324T>C	ENST00000257951.3	-	1	112	c.46A>G	c.(46-48)Aac>Gac	p.N16D	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	16	Head.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GAGCTGAAGTTGCCCACCCGG	0.572																																					p.N16D		Atlas-SNP	.											.	KRT84	61	.	0			c.A46G						.						85.0	93.0	90.0					12																	52779324		2203	4300	6503	SO:0001583	missense	3890	exon1			TGAAGTTGCCCAC	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.46A>G	chr12.hg19:g.52779324T>C	ENSP00000257951:p.Asn16Asp	83.0	0.0		61.0	4.0	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	hg19	CCDS8825.1	.	.	.	.	.	.	.	.	.	.	T	10.47	1.358873	0.24598	.	.	ENSG00000161849	ENST00000257951	T	0.81078	-1.45	5.06	3.9	0.45041	.	0.448207	0.19373	N	0.115847	T	0.66197	0.2765	N	0.17631	0.505	0.09310	N	1	B	0.31125	0.309	B	0.25140	0.058	T	0.58853	-0.7563	10	0.51188	T	0.08	.	11.16	0.48509	0.0:0.0727:0.0:0.9273	.	16	Q9NSB2	KRT84_HUMAN	D	16	ENSP00000257951:N16D	ENSP00000257951:N16D	N	-	1	0	KRT84	51065591	0.051000	0.20477	0.884000	0.34674	0.415000	0.31203	1.240000	0.32731	1.053000	0.40415	0.443000	0.29094	AAC	.	.		0.572	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
RDH16	8608	hgsc.bcm.edu	37	12	57351246	57351246	+	Start_Codon_SNP	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:57351246T>C	ENST00000398138.3	-	1	857	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	RDH16_ENST00000360752.4_5'UTR	NM_003708.3	NP_003699.3	O75452	RDH16_HUMAN	retinol dehydrogenase 16 (all-trans)	1					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						TAGAGCCACATGGCTTTGCAG	0.547																																					p.M1V	GBM(179;741 2921 43105 45298)	Atlas-SNP	.											.	RDH16	33	.	0			c.A1G						.						57.0	60.0	59.0					12																	57351246		2203	4300	6503	SO:0001582	initiator_codon_variant	8608	exon1			GCCACATGGCTTT		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.1A>G	chr12.hg19:g.57351246T>C	ENSP00000381206:p.Met1Val	113.0	0.0		79.0	9.0	NM_003708	Q9UNV2	Missense_Mutation	SNP	ENST00000398138.3	hg19	CCDS41797.1	.	.	.	.	.	.	.	.	.	.	T	15.33	2.802684	0.50315	.	.	ENSG00000139547	ENST00000398138	D	0.88124	-2.34	4.72	4.72	0.59763	.	0.000000	0.64402	D	0.000001	D	0.90283	0.6961	.	.	.	0.80722	D	1	P	0.49783	0.928	P	0.54100	0.742	D	0.91272	0.5045	9	0.66056	D	0.02	.	13.3137	0.60394	0.0:0.0:0.0:1.0	.	1	O75452	RDH16_HUMAN	V	1	ENSP00000381206:M1V	ENSP00000381206:M1V	M	-	1	0	RDH16	55637513	0.995000	0.38212	0.955000	0.39395	0.138000	0.21146	1.413000	0.34725	1.981000	0.57761	0.533000	0.62120	ATG	.	.		0.547	RDH16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410898.1	NM_003708	Missense_Mutation
NXPH4	11247	hgsc.bcm.edu	37	12	57619481	57619481	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:57619481A>G	ENST00000349394.5	+	2	1053	c.878A>G	c.(877-879)aAg>aGg	p.K293R	Y_RNA_ENST00000365197.1_RNA	NM_007224.3	NP_009155.1	O95158	NXPH4_HUMAN	neurexophilin 4	293	V (Cys-rich).				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)	10						CTGGTGCAGAAGGTGTGCCCA	0.572																																					p.K293R		Atlas-SNP	.											.	NXPH4	40	.	0			c.A878G						.						62.0	69.0	67.0					12																	57619481		2203	4300	6503	SO:0001583	missense	11247	exon2			TGCAGAAGGTGTG	AF043469	CCDS8933.1	12q13.3	2014-09-04			ENSG00000182379	ENSG00000182379			8078	protein-coding gene	gene with protein product		604637				9570794	Standard	NM_007224		Approved	NPH4	uc009zpj.4	O95158	OTTHUMG00000171241	ENST00000349394.5:c.878A>G	chr12.hg19:g.57619481A>G	ENSP00000333593:p.Lys293Arg	52.0	0.0		53.0	5.0	NM_007224	A8K4I4|Q7Z6L3|Q8N462	Missense_Mutation	SNP	ENST00000349394.5	hg19	CCDS8933.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.444454	0.83993	.	.	ENSG00000182379	ENST00000349394	.	.	.	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.69904	0.3163	L	0.52905	1.665	0.52099	D	0.999941	D	0.89917	1.0	D	0.87578	0.998	T	0.73164	-0.4069	9	0.87932	D	0	-21.6572	12.3172	0.54964	1.0:0.0:0.0:0.0	.	293	O95158	NXPH4_HUMAN	R	293	.	ENSP00000333593:K293R	K	+	2	0	NXPH4	55905748	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.859000	0.92264	1.744000	0.51775	0.460000	0.39030	AAG	.	.		0.572	NXPH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412474.1	NM_007224	
MON2	23041	hgsc.bcm.edu	37	12	62887709	62887709	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:62887709A>G	ENST00000393632.2	+	3	581	c.190A>G	c.(190-192)Agc>Ggc	p.S64G	MON2_ENST00000393630.3_Missense_Mutation_p.S64G|MON2_ENST00000549378.1_Intron|MON2_ENST00000280379.6_Missense_Mutation_p.S64G|MON2_ENST00000552738.1_Missense_Mutation_p.S64G|MON2_ENST00000552115.1_Missense_Mutation_p.S64G|MON2_ENST00000546600.1_Missense_Mutation_p.S64G|MON2_ENST00000393629.2_Missense_Mutation_p.S64G	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	64					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		GAAAGAGAACAGCTCAGAGGT	0.333																																					p.S64G		Atlas-SNP	.											.	MON2	160	.	0			c.A190G						.						79.0	67.0	71.0					12																	62887709		2202	4300	6502	SO:0001583	missense	23041	exon3			GAGAACAGCTCAG		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.190A>G	chr12.hg19:g.62887709A>G	ENSP00000377252:p.Ser64Gly	142.0	0.0		86.0	4.0	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	hg19	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	A	19.16	3.773486	0.69992	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629;ENST00000552115	T;T;T;T;T;T;T	0.66460	-0.2;-0.21;-0.21;-0.2;-0.2;-0.21;1.4	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.75012	0.3792	L	0.58810	1.83	0.80722	D	1	D;P;P;D	0.54047	0.964;0.776;0.544;0.963	P;P;B;P	0.56434	0.632;0.583;0.257;0.798	T	0.74728	-0.3567	9	.	.	.	-9.3819	15.8953	0.79329	1.0:0.0:0.0:0.0	.	64;64;64;64	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-4	.;.;.;.	G	64	ENSP00000377252:S64G;ENSP00000377250:S64G;ENSP00000280379:S64G;ENSP00000447407:S64G;ENSP00000449215:S64G;ENSP00000377249:S64G;ENSP00000446635:S64G	.	S	+	1	0	MON2	61173976	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.163000	0.67991	0.482000	0.46254	AGC	.	.		0.333	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
TBK1	29110	hgsc.bcm.edu	37	12	64878199	64878199	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:64878199T>C	ENST00000331710.5	+	9	1448	c.1109T>C	c.(1108-1110)tTc>tCc	p.F370S		NM_013254.3	NP_037386.1	Q9UHD2	TBK1_HUMAN	TANK-binding kinase 1	370	Ubiquitin-like.				defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of gene expression (GO:0010629)|negative regulation of type I interferon production (GO:0032480)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon production (GO:0032606)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)	ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)	20				GBM - Glioblastoma multiforme(28;0.0386)		GCACAACATTTCCCTAAAACT	0.363																																					p.F370S		Atlas-SNP	.											.	TBK1	149	.	0			c.T1109C						.						59.0	61.0	61.0					12																	64878199		2203	4300	6503	SO:0001583	missense	29110	exon9			AACATTTCCCTAA	AF191838	CCDS8968.1	12q14.2	2006-06-10			ENSG00000183735	ENSG00000183735			11584	protein-coding gene	gene with protein product		604834				10581243, 10783893	Standard	NM_013254		Approved	NAK	uc001ssc.2	Q9UHD2	OTTHUMG00000168796	ENST00000331710.5:c.1109T>C	chr12.hg19:g.64878199T>C	ENSP00000329967:p.Phe370Ser	141.0	0.0		98.0	4.0	NM_013254	A8K4S4|Q8IYV3|Q9NUJ5	Missense_Mutation	SNP	ENST00000331710.5	hg19	CCDS8968.1	.	.	.	.	.	.	.	.	.	.	T	19.37	3.814078	0.70912	.	.	ENSG00000183735	ENST00000331710	T	0.68331	-0.32	5.07	5.07	0.68467	.	0.094445	0.64402	D	0.000001	T	0.72779	0.3503	L	0.34521	1.04	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.71556	-0.4557	9	.	.	.	-2.3032	15.533	0.75980	0.0:0.0:0.0:1.0	.	370	Q9UHD2	TBK1_HUMAN	S	370	ENSP00000329967:F370S	.	F	+	2	0	TBK1	63164466	1.000000	0.71417	0.996000	0.52242	0.328000	0.28507	6.623000	0.74238	2.212000	0.71576	0.460000	0.39030	TTC	.	.		0.363	TBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401130.1	NM_013254	
CPM	1368	hgsc.bcm.edu	37	12	69326513	69326513	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:69326513A>G	ENST00000551568.1	-	2	165	c.105T>C	c.(103-105)gtT>gtC	p.V35V	CPM_ENST00000546373.1_Silent_p.V35V|CPM_ENST00000338356.3_Silent_p.V35V	NM_001005502.2|NM_198320.3	NP_001005502.1|NP_938079.1	P14384	CBPM_HUMAN	carboxypeptidase M	35					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)			AGTTTTGGGCAACAGTCTTCA	0.517																																					p.V35V		Atlas-SNP	.											.	CPM	30	.	0			c.T105C						.						137.0	130.0	133.0					12																	69326513		2203	4300	6503	SO:0001819	synonymous_variant	1368	exon2			TTGGGCAACAGTC	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.105T>C	chr12.hg19:g.69326513A>G		156.0	0.0		108.0	5.0	NM_001005502	B2R800|Q9H2K9	Silent	SNP	ENST00000551568.1	hg19	CCDS8987.1																																																																																			.	.		0.517	CPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403355.1	NM_198320	
FRS2	10818	hgsc.bcm.edu	37	12	69968235	69968235	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:69968235A>G	ENST00000550389.1	+	7	1273	c.1027A>G	c.(1027-1029)Aga>Gga	p.R343G	FRS2_ENST00000397997.2_Missense_Mutation_p.R343G|FRS2_ENST00000299293.2_Missense_Mutation_p.R343G|FRS2_ENST00000549921.1_Missense_Mutation_p.R343G	NM_001278353.1|NM_001278357.1	NP_001265282.1|NP_001265286.1	Q8WU20	FRS2_HUMAN	fibroblast growth factor receptor substrate 2	343					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification, embryo (GO:0008595)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation with mouth forming second (GO:0001702)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lens fiber cell development (GO:0070307)|neuroblast proliferation (GO:0007405)|neurotrophin TRK receptor signaling pathway (GO:0048011)|optic placode formation involved in camera-type eye formation (GO:0046619)|organ induction (GO:0001759)|phosphatidylinositol-mediated signaling (GO:0048015)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of apoptotic process (GO:0042981)|regulation of epithelial cell proliferation (GO:0050678)|regulation of ERK1 and ERK2 cascade (GO:0070372)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatase activator activity (GO:0019211)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			AGCTCAGAGAAGAACTGCATT	0.453																																					p.R343G		Atlas-SNP	.											.	FRS2	88	.	0			c.A1027G						.						66.0	65.0	65.0					12																	69968235		1894	4124	6018	SO:0001583	missense	10818	exon10			CAGAGAAGAACTG	AF036717	CCDS41809.1	12q15	2008-02-05				ENSG00000166225			16971	protein-coding gene	gene with protein product		607743				8761293, 9660748	Standard	NM_001278351		Approved	SNT-1, FRS2alpha, SNT1, FRS2A	uc001suz.3	Q8WU20		ENST00000550389.1:c.1027A>G	chr12.hg19:g.69968235A>G	ENSP00000447241:p.Arg343Gly	89.0	0.0		64.0	4.0	NM_001042555	B0LPF2|B2R684|O43558|Q7LDQ6	Missense_Mutation	SNP	ENST00000550389.1	hg19	CCDS41809.1	.	.	.	.	.	.	.	.	.	.	A	15.99	2.995471	0.54147	.	.	ENSG00000166225	ENST00000299293;ENST00000549921;ENST00000550389;ENST00000397997	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	6.04	6.04	0.98038	.	0.043348	0.85682	D	0.000000	T	0.51753	0.1693	L	0.42245	1.32	0.44771	D	0.997779	D	0.57899	0.981	D	0.67231	0.95	T	0.42085	-0.9472	9	.	.	.	-11.0668	16.6244	0.84952	1.0:0.0:0.0:0.0	.	343	Q8WU20	FRS2_HUMAN	G	343	ENSP00000299293:R343G;ENSP00000450048:R343G;ENSP00000447241:R343G;ENSP00000381083:R343G	.	R	+	1	2	FRS2	68254502	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.134000	0.57990	2.323000	0.78572	0.529000	0.55759	AGA	.	.		0.453	FRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403760.1	NM_006654	
PTPRB	5787	hgsc.bcm.edu	37	12	70989899	70989899	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:70989899T>C	ENST00000261266.5	-	3	563	c.534A>G	c.(532-534)aaA>aaG	p.K178K	PTPRB_ENST00000538708.1_Silent_p.K178K|PTPRB_ENST00000451516.2_Silent_p.K178K|PTPRB_ENST00000551525.1_Silent_p.K395K|PTPRB_ENST00000550857.1_Silent_p.K178K|PTPRB_ENST00000550358.1_Silent_p.K396K|PTPRB_ENST00000334414.6_Silent_p.K396K|PTPRB_ENST00000538174.2_5'UTR	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	178	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CAATATTGTATTTACTACCAG	0.333																																					p.K396K		Atlas-SNP	.											.	PTPRB	676	.	0			c.A1188G						.						69.0	67.0	68.0					12																	70989899		1843	4086	5929	SO:0001819	synonymous_variant	5787	exon5			ATTGTATTTACTA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.534A>G	chr12.hg19:g.70989899T>C		149.0	0.0		98.0	5.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	hg19	CCDS44944.1																																																																																			.	.		0.333	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75816822	75816822	+	Intron	SNP	A	A	G	rs75261424		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:75816822A>G	ENST00000550916.1	+	4	717				GLIPR1L2_ENST00000320460.4_Silent_p.K241K|GLIPR1L2_ENST00000441218.1_Intron|GLIPR1L2_ENST00000435775.1_Intron|GLIPR1L2_ENST00000378692.3_Intron	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2							integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						TGGACAAGAAAAATAAGCGAT	0.313																																					p.K241K		Atlas-SNP	.											.	GLIPR1L2	54	.	0			c.A723G						.						109.0	111.0	110.0					12																	75816822		2203	4300	6503	SO:0001627	intron_variant	144321	exon4			CAAGAAAAATAAG	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.670+53A>G	chr12.hg19:g.75816822A>G		124.0	0.0		113.0	7.0	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Silent	SNP	ENST00000550916.1	hg19	CCDS58258.1																																																																																			.	.		0.313	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436	
ATP2B1	490	hgsc.bcm.edu	37	12	90014010	90014010	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:90014010T>C	ENST00000428670.3	-	11	2051	c.1595A>G	c.(1594-1596)gAg>gGg	p.E532G	ATP2B1_ENST00000359142.3_Missense_Mutation_p.E532G|ATP2B1_ENST00000348959.3_Missense_Mutation_p.E532G|ATP2B1_ENST00000261173.2_Missense_Mutation_p.E532G|ATP2B1_ENST00000393164.2_Missense_Mutation_p.E275G			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	532					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						ACCCTCTTTCTCTGGTGGCTA	0.338																																					p.E532G		Atlas-SNP	.											.	ATP2B1	191	.	0			c.A1595G						.						63.0	63.0	63.0					12																	90014010		2203	4300	6503	SO:0001583	missense	490	exon10			TCTTTCTCTGGTG	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.1595A>G	chr12.hg19:g.90014010T>C	ENSP00000392043:p.Glu532Gly	139.0	0.0		96.0	4.0	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	ENST00000428670.3	hg19	CCDS9035.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.301762	0.81136	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.68961	0.3058	N	0.16307	0.4	0.80722	D	1	D;B;B	0.89917	1.0;0.189;0.092	D;B;B	0.80764	0.994;0.125;0.056	T	0.68857	-0.5298	9	.	.	.	-24.6541	15.5449	0.76090	0.0:0.0:0.0:1.0	.	532;532;532	P20020-3;P20020-2;P20020-6	.;.;.	G	532;532;532;532;275	ENSP00000261173:E532G;ENSP00000343599:E532G;ENSP00000352054:E532G;ENSP00000392043:E532G;ENSP00000376869:E275G	.	E	-	2	0	ATP2B1	88538141	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	8.008000	0.88588	2.070000	0.61991	0.383000	0.25322	GAG	.	.		0.338	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682	
CCER1	196477	hgsc.bcm.edu	37	12	91348403	91348403	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:91348403A>G	ENST00000358859.2	-	1	550	c.117T>C	c.(115-117)caT>caC	p.H39H	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	39																	GGCGCCTTCGATGGCAGGACG	0.662																																					p.H39H		Atlas-SNP	.											.	.	.	.	0			c.T117C						.						21.0	20.0	20.0					12																	91348403		2203	4300	6503	SO:0001819	synonymous_variant	196477	exon1			CCTTCGATGGCAG	BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651			28373	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 12"""	C12orf12		17967063	Standard	NM_152638		Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.117T>C	chr12.hg19:g.91348403A>G		34.0	0.0		47.0	5.0	NM_152638	Q8TC47	Silent	SNP	ENST00000358859.2	hg19	CCDS9036.1																																																																																			.	.		0.662	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638	
POLR3B	55703	hgsc.bcm.edu	37	12	106824062	106824062	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:106824062T>C	ENST00000228347.4	+	14	1497	c.1275T>C	c.(1273-1275)tcT>tcC	p.S425S	POLR3B_ENST00000539066.1_Silent_p.S367S	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	425					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						GAAATTGGTCTTTAAAGAGAT	0.443																																					p.S425S		Atlas-SNP	.											.	POLR3B	123	.	0			c.T1275C						.						101.0	111.0	108.0					12																	106824062		2203	4300	6503	SO:0001819	synonymous_variant	55703	exon14			TTGGTCTTTAAAG	AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"""RNA polymerase subunits"""	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.1275T>C	chr12.hg19:g.106824062T>C		76.0	0.0		92.0	4.0	NM_018082	A8K6H0|B3KV73|F5H1E6|Q9NW59	Silent	SNP	ENST00000228347.4	hg19	CCDS9105.1																																																																																			.	.		0.443	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082	
MYO1H	283446	hgsc.bcm.edu	37	12	109853345	109853345	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:109853345G>A	ENST00000431443.2	+	14	1499	c.1499G>A	c.(1498-1500)gGt>gAt	p.G500D	MYO1H_ENST00000310903.5_Missense_Mutation_p.G490D	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	500	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						AAGCTGGCTGGTCCAAAGGGC	0.517																																					p.G490D		Atlas-SNP	.											.	MYO1H	98	.	0			c.G1469A						.						47.0	48.0	48.0					12																	109853345		1938	4158	6096	SO:0001583	missense	283446	exon14			TGGCTGGTCCAAA		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"""Myosins / Myosin superfamily : Class I"""	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.1499G>A	chr12.hg19:g.109853345G>A	ENSP00000444076:p.Gly500Asp	71.0	0.0		80.0	4.0	NM_001101421	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	hg19		.	.	.	.	.	.	.	.	.	.	G	4.082	0.013064	0.07912	.	.	ENSG00000174527	ENST00000310903;ENST00000431443	T;T	0.71698	-0.59;-0.59	5.5	3.66	0.41972	.	.	.	.	.	T	0.27419	0.0673	N	0.00298	-1.69	0.36097	D	0.843858	B	0.15141	0.012	B	0.19946	0.027	T	0.43114	-0.9411	9	0.02654	T	1	.	5.9099	0.19023	0.3367:0.0:0.6633:0.0	.	490	F5H3C6	.	D	490;500	ENSP00000439182:G490D;ENSP00000444076:G500D	ENSP00000439182:G490D	G	+	2	0	MYO1H	108337728	1.000000	0.71417	0.097000	0.21041	0.916000	0.54674	5.495000	0.66912	1.310000	0.45006	0.655000	0.94253	GGT	.	.		0.517	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
ERP29	10961	hgsc.bcm.edu	37	12	112451275	112451275	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:112451275T>C	ENST00000261735.3	+	1	156	c.6T>C	c.(4-6)gcT>gcC	p.A2A	TMEM116_ENST00000552839.2_5'Flank|TMEM116_ENST00000552374.2_5'Flank|TMEM116_ENST00000355445.3_5'Flank|ERP29_ENST00000455836.1_Silent_p.A2A|TMEM116_ENST00000437003.2_5'Flank|TMEM116_ENST00000549537.2_5'Flank|TMEM116_ENST00000550831.3_5'Flank|TMEM116_ENST00000354825.3_5'Flank	NM_006817.3	NP_006808.1	P30040	ERP29_HUMAN	endoplasmic reticulum protein 29	2					intracellular protein transport (GO:0006886)|protein folding (GO:0006457)|protein secretion (GO:0009306)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	5						GCGATATGGCTGCCGCTGTGC	0.682																																					p.A2A		Atlas-SNP	.											.	ERP29	17	.	0			c.T6C						.						53.0	59.0	57.0					12																	112451275		2203	4298	6501	SO:0001819	synonymous_variant	10961	exon1			TATGGCTGCCGCT	X94910	CCDS9158.1, CCDS44977.1	12q24.13	2011-10-19	2005-10-05	2005-10-05		ENSG00000089248		"""Protein disulfide isomerases"""	13799	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 9"""	602287	"""chromosome 12 open reading frame 8"""	C12orf8		9738895, 9037184	Standard	NM_006817		Approved	ERp28, ERp31, ERp29, PDI-DB, PDIA9	uc001ttk.1	P30040	OTTHUMG00000169637	ENST00000261735.3:c.6T>C	chr12.hg19:g.112451275T>C		58.0	0.0		86.0	4.0	NM_001034025	C9J183|Q3MJC3|Q6FHT4	Silent	SNP	ENST00000261735.3	hg19	CCDS9158.1																																																																																			.	.		0.682	ERP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405200.1		
OAS1	4938	hgsc.bcm.edu	37	12	113357213	113357213	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:113357213A>G	ENST00000202917.5	+	6	1321	c.1058A>G	c.(1057-1059)gAc>gGc	p.D353G	OAS1_ENST00000445409.2_Intron|OAS1_ENST00000551241.1_Intron|RP1-71H24.1_ENST00000552784.1_RNA	NM_016816.2	NP_058132.2	P00973	OAS1_HUMAN	2'-5'-oligoadenylate synthetase 1, 40/46kDa	353					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						AACAGTGCAGACGATGAGACC	0.488																																					p.D353G		Atlas-SNP	.											.	OAS1	128	.	0			c.A1058G						.						87.0	86.0	87.0					12																	113357213		2203	4300	6503	SO:0001583	missense	4938	exon6			GTGCAGACGATGA	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.1058A>G	chr12.hg19:g.113357213A>G	ENSP00000202917:p.Asp353Gly	78.0	0.0		85.0	4.0	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	.	.	.	.	.	.	.	.	.	.	A	7.064	0.566970	0.13560	.	.	ENSG00000089127	ENST00000202917	T	0.05258	3.47	2.38	-0.113	0.13568	.	.	.	.	.	T	0.02649	0.0080	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48647	-0.9017	9	0.15066	T	0.55	.	4.3968	0.11367	0.6134:0.0:0.3866:0.0	.	353	P00973	OAS1_HUMAN	G	353	ENSP00000202917:D353G	ENSP00000202917:D353G	D	+	2	0	OAS1	111841596	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.513000	0.06305	-0.026000	0.13895	0.455000	0.32223	GAC	.	.		0.488	OAS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405896.2		
IQCD	115811	hgsc.bcm.edu	37	12	113633675	113633675	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:113633675T>C	ENST00000416617.2	-	5	1245	c.1055A>G	c.(1054-1056)gAc>gGc	p.D352G	IQCD_ENST00000299732.2_Missense_Mutation_p.D250G			Q96DY2	IQCD_HUMAN	IQ motif containing D	352										endometrium(2)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						GTGAACAGCGTCCAGATCCTC	0.632																																					p.D250G		Atlas-SNP	.											.	IQCD	32	.	0			c.A749G						.						51.0	47.0	48.0					12																	113633675		2203	4300	6503	SO:0001583	missense	115811	exon3			ACAGCGTCCAGAT	BC013151	CCDS9167.1	12q24.21	2014-07-18				ENSG00000166578			25168	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 10"""					23427265, 24804578	Standard	NM_138451		Approved	DRC10, CFAP84	uc001tuu.3	Q96DY2		ENST00000416617.2:c.1055A>G	chr12.hg19:g.113633675T>C	ENSP00000400669:p.Asp352Gly	98.0	0.0		81.0	4.0	NM_138451	Q6ZSU0	Missense_Mutation	SNP	ENST00000416617.2	hg19		.	.	.	.	.	.	.	.	.	.	T	8.935	0.964391	0.18583	.	.	ENSG00000166578	ENST00000299732;ENST00000416617	T;T	0.46451	2.98;0.87	4.29	4.29	0.51040	.	.	.	.	.	T	0.36853	0.0982	.	.	.	0.80722	D	1	B	0.27679	0.185	B	0.28553	0.091	T	0.31336	-0.9947	8	0.56958	D	0.05	-9.3408	12.5394	0.56161	0.0:0.0:0.0:1.0	.	250	Q96DY2-2	.	G	250;352	ENSP00000299732:D250G;ENSP00000400669:D352G	ENSP00000299732:D250G	D	-	2	0	IQCD	112118058	0.133000	0.22466	0.808000	0.32385	0.003000	0.03518	2.823000	0.48081	1.804000	0.52760	0.459000	0.35465	GAC	.	.		0.632	IQCD-004	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000405327.1	NM_138451	
VSIG10	54621	hgsc.bcm.edu	37	12	118533406	118533406	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:118533406T>C	ENST00000359236.5	-	2	569	c.293A>G	c.(292-294)gAg>gGg	p.E98G	VSIG10_ENST00000536905.1_5'UTR	NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	98	Ig-like C2-type 1.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						GTAGATTCCCTCATCTCCCAG	0.592																																					p.E98G		Atlas-SNP	.											.	VSIG10	41	.	0			c.A293G						.						88.0	96.0	93.0					12																	118533406		2116	4243	6359	SO:0001583	missense	54621	exon2			ATTCCCTCATCTC		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.293A>G	chr12.hg19:g.118533406T>C	ENSP00000352172:p.Glu98Gly	83.0	0.0		92.0	5.0	NM_019086	Q9NWQ7	Missense_Mutation	SNP	ENST00000359236.5	hg19	CCDS44992.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.712689	0.48517	.	.	ENSG00000176834	ENST00000359236;ENST00000538357	T;T	0.67698	-0.28;-0.28	4.99	2.46	0.29980	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.155706	0.30210	N	0.010146	T	0.75889	0.3911	M	0.73430	2.235	0.34189	D	0.67189	D	0.65815	0.995	D	0.63703	0.917	T	0.79725	-0.1683	10	0.32370	T	0.25	-18.387	10.1025	0.42513	0.0:0.0:0.3214:0.6786	.	98	Q8N0Z9	VSI10_HUMAN	G	98	ENSP00000352172:E98G;ENSP00000442861:E98G	ENSP00000352172:E98G	E	-	2	0	VSIG10	117017789	0.722000	0.28017	0.992000	0.48379	0.177000	0.22998	1.256000	0.32921	0.905000	0.36596	0.533000	0.62120	GAG	.	.		0.592	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086	
GPR133	283383	hgsc.bcm.edu	37	12	131616271	131616271	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:131616271T>C	ENST00000261654.5	+	21	2736	c.2177T>C	c.(2176-2178)gTc>gCc	p.V726A	GPR133_ENST00000535015.1_Splice_Site_p.V758A|GPR133_ENST00000376682.4_Splice_Site_p.V412A|GPR133_ENST00000543617.1_Splice_Site_p.V245A|GPR133_ENST00000540207.1_3'UTR	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	726					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		CTTGTGCAGGTCAACATTGGC	0.587																																					p.V726A		Atlas-SNP	.											.	GPR133	136	.	0			c.T2177C						.						153.0	116.0	129.0					12																	131616271		2203	4300	6503	SO:0001630	splice_region_variant	283383	exon21			TGCAGGTCAACAT	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"""-"", ""GPCR / Class B : Orphans"""	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.2176-1T>C	chr12.hg19:g.131616271T>C		140.0	0.0		167.0	7.0	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	hg19	CCDS9272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.02|17.02	3.282762|3.282762	0.59867|0.59867	.|.	.|.	ENSG00000111452|ENSG00000111452	ENST00000335486|ENST00000261654;ENST00000535015;ENST00000376682;ENST00000543617	.|T;T;T;T	.|0.55052	.|0.54;0.54;1.24;1.24	4.39|4.39	4.39|4.39	0.52855|0.52855	.|GPCR, family 2-like (1);	.|0.000000	.|0.64402	.|U	.|0.000001	T|T	0.64294|0.64294	0.2585|0.2585	L|L	0.55990|0.55990	1.75|1.75	0.80722|0.80722	D|D	1|1	.|P;D;P	.|0.61080	.|0.608;0.989;0.743	.|P;D;P	.|0.68039	.|0.852;0.955;0.613	T|T	0.64483|0.64483	-0.6397|-0.6397	5|10	.|0.45353	.|T	.|0.12	.|.	11.8298|11.8298	0.52288|0.52288	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|758;79;726	.|B7ZLF7;Q9NSM3;Q6QNK2	.|.;.;GP133_HUMAN	P|A	80|726;758;412;245	.|ENSP00000261654:V726A;ENSP00000444425:V758A;ENSP00000365872:V412A;ENSP00000438021:V245A	.|ENSP00000261654:V726A	S|V	+|+	1|2	0|0	GPR133|GPR133	130182224|130182224	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.837000|0.837000	0.47467|0.47467	4.951000|4.951000	0.63610|0.63610	1.721000|1.721000	0.51461|0.51461	0.402000|0.402000	0.26972|0.26972	TCA|GTC	.	.		0.587	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	Missense_Mutation
EP400	57634	hgsc.bcm.edu	37	12	132549247	132549247	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:132549247A>G	ENST00000333577.4	+	49	8586	c.8477A>G	c.(8476-8478)cAg>cGg	p.Q2826R	EP400_ENST00000332482.4_Missense_Mutation_p.Q2753R|EP400_ENST00000330386.6_Missense_Mutation_p.Q2709R|EP400_ENST00000389562.2_Missense_Mutation_p.Q2789R|EP400_ENST00000389561.2_Missense_Mutation_p.Q2790R			Q96L91	EP400_HUMAN	E1A binding protein p400	2826					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CAGAAACTGCAGATGCCCCCG	0.542																																					p.Q2790R		Atlas-SNP	.											.	EP400	370	.	0			c.A8369G						.						36.0	48.0	44.0					12																	132549247		2202	4300	6502	SO:0001583	missense	57634	exon48			AACTGCAGATGCC	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8477A>G	chr12.hg19:g.132549247A>G	ENSP00000333602:p.Gln2826Arg	64.0	0.0		64.0	4.0	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	hg19		.	.	.	.	.	.	.	.	.	.	A	15.49	2.848961	0.51164	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.90844	-2.74;-2.74;-2.71;-2.72;-2.71	4.83	4.83	0.62350	.	0.066245	0.64402	D	0.000009	D	0.91222	0.7234	L	0.29908	0.895	0.39818	D	0.972799	D;D;D;D	0.67145	0.985;0.996;0.996;0.996	P;D;D;D	0.75484	0.696;0.986;0.986;0.986	D	0.89729	0.3925	10	0.23302	T	0.38	.	14.0591	0.64788	1.0:0.0:0.0:0.0	.	2826;2790;2709;2789	Q96L91;Q96L91-2;Q96L91-4;Q96L91-5	EP400_HUMAN;.;.;.	R	2826;2790;2789;2753;2709;2790	ENSP00000333602:Q2826R;ENSP00000374212:Q2790R;ENSP00000374213:Q2789R;ENSP00000331737:Q2753R;ENSP00000330620:Q2709R	ENSP00000330620:Q2709R	Q	+	2	0	EP400	131115200	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	8.063000	0.89482	1.813000	0.52934	0.402000	0.26972	CAG	.	.		0.542	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
GALNT9	50614	hgsc.bcm.edu	37	12	132688051	132688051	+	Splice_Site	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:132688051G>A	ENST00000328957.8	-	7	1261	c.1262C>T	c.(1261-1263)tCg>tTg	p.S421L	GALNT9_ENST00000541995.1_Splice_Site_p.S55L|GALNT9_ENST00000535228.1_Splice_Site_p.S172L|GALNT9_ENST00000397325.2_Splice_Site_p.S55L	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	421					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.S421L(1)|p.S55L(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		GGGACTCACCGACATGGGGAT	0.682																																					p.S421L	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											GALNT9_ENST00000328957,NS,carcinoma,0,2	GALNT9	74	.	2	Substitution - Missense(2)	lung(2)	c.C1262T						.						43.0	46.0	45.0					12																	132688051		2073	4199	6272	SO:0001630	splice_region_variant	50614	exon7			CTCACCGACATGG	AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4131	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 9"""	606251	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"""			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.1263+1C>T	chr12.hg19:g.132688051G>A		65.0	0.0		74.0	4.0	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Missense_Mutation	SNP	ENST00000328957.8	hg19		.	.	.	.	.	.	.	.	.	.	g	12.27	1.887299	0.33348	.	.	ENSG00000182870	ENST00000397325;ENST00000328957;ENST00000535228;ENST00000541995;ENST00000538356	T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55	3.87	2.97	0.34412	.	0.220504	0.45126	D	0.000382	T	0.47728	0.1461	N	0.12182	0.205	0.21719	N	0.999571	B;B;B	0.20887	0.049;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.30268	-0.9984	10	0.30854	T	0.27	.	8.4984	0.33144	0.0883:0.1557:0.756:0.0	.	172;421;278	B3KNR7;Q9HCQ5;B3KP58	.;GALT9_HUMAN;.	L	55;421;172;55;55	ENSP00000380488:S55L;ENSP00000329846:S421L;ENSP00000439745:S172L;ENSP00000440544:S55L;ENSP00000444709:S55L	ENSP00000329846:S421L	S	-	2	0	GALNT9	131254004	0.998000	0.40836	0.565000	0.28409	0.375000	0.29983	2.717000	0.47227	0.714000	0.32081	0.448000	0.29417	TCG	.	.		0.682	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636	Missense_Mutation
FBRSL1	57666	hgsc.bcm.edu	37	12	133102339	133102339	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:133102339A>G	ENST00000434748.2	+	3	1529	c.509A>G	c.(508-510)aAa>aGa	p.K170R	FBRSL1_ENST00000261673.6_Missense_Mutation_p.K97R	NM_001142641.1	NP_001136113.1	Q9HCM7	FBSL_HUMAN	fibrosin-like 1	170							poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(1)|stomach(1)	4						ACCGTGTCCAAAGGGGGCGAC	0.672																																					p.K170R		Atlas-SNP	.											.	FBRSL1	47	.	0			c.A509G						.						53.0	64.0	60.0					12																	133102339		692	1591	2283	SO:0001583	missense	57666	exon3			TGTCCAAAGGGGG		CCDS45010.1	12q24.33	2008-12-09			ENSG00000112787	ENSG00000112787			29308	protein-coding gene	gene with protein product						10997877	Standard	NM_001142641		Approved	KIAA1545	uc001ukf.3	Q9HCM7	OTTHUMG00000167991	ENST00000434748.2:c.509A>G	chr12.hg19:g.133102339A>G	ENSP00000396160:p.Lys170Arg	58.0	0.0		80.0	4.0	NM_001142641	Q86XQ1	Missense_Mutation	SNP	ENST00000434748.2	hg19	CCDS45010.1	.	.	.	.	.	.	.	.	.	.	A	4.968	0.179734	0.09443	.	.	ENSG00000112787	ENST00000434748;ENST00000261673	T;T	0.30182	1.55;1.54	4.51	2.1	0.27182	.	.	.	.	.	T	0.06554	0.0168	N	0.00436	-1.5	0.21020	N	0.99981	B	0.06786	0.001	B	0.08055	0.003	T	0.38156	-0.9674	9	0.07644	T	0.81	.	4.2854	0.10853	0.4578:0.0:0.5422:0.0	.	170	Q9HCM7	FBSL_HUMAN	R	170;97	ENSP00000396160:K170R;ENSP00000261673:K97R	ENSP00000261673:K97R	K	+	2	0	FBRSL1	131612412	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.222000	0.32515	0.754000	0.32968	0.379000	0.24179	AAA	.	.		0.672	FBRSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397404.2		
POLE	5426	hgsc.bcm.edu	37	12	133218836	133218836	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr12:133218836A>G	ENST00000320574.5	-	38	5143	c.5100T>C	c.(5098-5100)gaT>gaC	p.D1700D	POLE_ENST00000434528.3_5'Flank|POLE_ENST00000535270.1_Silent_p.D1673D	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1700					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)	GACAGTTGTCATCAGCCTCCT	0.592								DNA polymerases (catalytic subunits)																													p.D1700D		Atlas-SNP	.											.	POLE	416	.	0			c.T5100C						.						135.0	123.0	127.0					12																	133218836		2203	4300	6503	SO:0001819	synonymous_variant	5426	exon38			GTTGTCATCAGCC		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.5100T>C	chr12.hg19:g.133218836A>G		114.0	0.0		99.0	4.0	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	hg19	CCDS9278.1																																																																																			.	.		0.592	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
SKA3	221150	hgsc.bcm.edu	37	13	21742126	21742126	+	Splice_Site	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:21742126C>A	ENST00000314759.5	-	4	868		c.e4+1		SKA3_ENST00000400018.3_Splice_Site	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3						chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						GAGCTGCTTACCTTTTATTAT	0.284																																					.		Atlas-SNP	.											.	SKA3	76	.	0			c.743+1G>T						.						63.0	58.0	60.0					13																	21742126		2203	4297	6500	SO:0001630	splice_region_variant	221150	exon5			TGCTTACCTTTTA	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.743+1G>T	chr13.hg19:g.21742126C>A		142.0	0.0		120.0	15.0	NM_001166017	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Splice_Site	SNP	ENST00000314759.5	hg19	CCDS31946.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.052163	0.36181	.	.	ENSG00000165480	ENST00000314759;ENST00000400018	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6803	0.77364	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SKA3	20640126	1.000000	0.71417	1.000000	0.80357	0.302000	0.27658	4.395000	0.59678	2.777000	0.95525	0.655000	0.94253	.	.	.		0.284	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	Intron
SACS	26278	hgsc.bcm.edu	37	13	23906630	23906630	+	Silent	SNP	A	A	G	rs148605896		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:23906630A>G	ENST00000382292.3	-	9	11658	c.11385T>C	c.(11383-11385)gcT>gcC	p.A3795A	SACS_ENST00000402364.1_Silent_p.A3045A|SACS_ENST00000382298.3_Silent_p.A3795A			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3795					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)		CCATCACAAAAGCAACCCCTC	0.368																																					p.A3795A		Atlas-SNP	.											.	SACS	871	.	0			c.T11385C						.						88.0	85.0	86.0					13																	23906630		2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			CACAAAAGCAACC	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.11385T>C	chr13.hg19:g.23906630A>G		120.0	0.0		110.0	5.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	hg19	CCDS9300.2																																																																																			.	A|0.999;C|0.001		0.368	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
SACS	26278	hgsc.bcm.edu	37	13	23911630	23911630	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:23911630C>T	ENST00000382292.3	-	9	6658	c.6385G>A	c.(6385-6387)Ggg>Agg	p.G2129R	SACS_ENST00000402364.1_Missense_Mutation_p.G1379R|SACS_ENST00000382298.3_Missense_Mutation_p.G2129R			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2129					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)		GGGAATCTCCCATCTTTAATA	0.378																																					p.G2129R		Atlas-SNP	.											.	SACS	871	.	0			c.G6385A						.						52.0	56.0	55.0					13																	23911630		2203	4297	6500	SO:0001583	missense	26278	exon10			ATCTCCCATCTTT	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.6385G>A	chr13.hg19:g.23911630C>T	ENSP00000371729:p.Gly2129Arg	131.0	0.0		94.0	4.0	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	15.11	2.737234	0.49045	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.88431	-2.24;-2.38;-2.24	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.93562	0.7945	L	0.54323	1.7	0.58432	D	0.999995	D	0.89917	1.0	D	0.87578	0.998	D	0.93466	0.6815	10	0.72032	D	0.01	.	20.1306	0.97998	0.0:1.0:0.0:0.0	.	2129	Q9NZJ4	SACS_HUMAN	R	2129;1379;2129	ENSP00000371729:G2129R;ENSP00000385844:G1379R;ENSP00000371735:G2129R	ENSP00000371729:G2129R	G	-	1	0	SACS	22809630	1.000000	0.71417	0.994000	0.49952	0.059000	0.15707	7.487000	0.81328	2.751000	0.94390	0.655000	0.94253	GGG	.	.		0.378	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
AMER2	219287	hgsc.bcm.edu	37	13	25744544	25744544	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:25744544T>C	ENST00000515384.1	-	1	1881	c.1214A>G	c.(1213-1215)aAg>aGg	p.K405R	AMER2_ENST00000381853.3_Missense_Mutation_p.K286R|AMER2-AS1_ENST00000413501.1_lincRNA|AMER2_ENST00000357816.2_Missense_Mutation_p.K286R			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	405					ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)										CAGAGCCGGCTTGCCTGGCCC	0.577																																					p.K405R		Atlas-SNP	.											.	.	.	.	0			c.A1214G						.						30.0	33.0	32.0					13																	25744544		2203	4300	6503	SO:0001583	missense	219287	exon1			GCCGGCTTGCCTG	AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"""-"""	26360	protein-coding gene	gene with protein product		614659	"""family with sequence similarity 123A"""	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.1214A>G	chr13.hg19:g.25744544T>C	ENSP00000426528:p.Lys405Arg	60.0	0.0		45.0	4.0	NM_152704	Q5RL80|Q5VX56|Q8N593|Q96NN5	Missense_Mutation	SNP	ENST00000515384.1	hg19	CCDS53859.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.867607	0.51588	.	.	ENSG00000165566	ENST00000357816;ENST00000381853;ENST00000515384	T;T;T	0.17528	2.27;2.27;2.27	4.42	4.42	0.53409	.	0.252962	0.36167	N	0.002741	T	0.16257	0.0391	L	0.46157	1.445	0.37051	D	0.89758	P;P	0.37914	0.611;0.557	B;B	0.35114	0.196;0.124	T	0.13124	-1.0521	10	0.44086	T	0.13	-18.2309	13.0064	0.58707	0.0:0.0:0.0:1.0	.	405;286	Q8N7J2;Q8N7J2-2	F123A_HUMAN;.	R	286;286;405	ENSP00000350469:K286R;ENSP00000371277:K286R;ENSP00000426528:K405R	ENSP00000350469:K286R	K	-	2	0	FAM123A	24642544	1.000000	0.71417	0.989000	0.46669	0.908000	0.53690	3.647000	0.54403	1.851000	0.53745	0.459000	0.35465	AAG	.	.		0.577	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704	
URAD	646625	hgsc.bcm.edu	37	13	28562605	28562605	+	Missense_Mutation	SNP	T	T	C	rs3897926	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:28562605T>C	ENST00000332715.5	-	1	186	c.170A>G	c.(169-171)cAg>cGg	p.Q57R	RN7SL272P_ENST00000487762.2_RNA	NM_001105577.1	NP_001099047.1	A6NGE7	URAD_HUMAN	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5-) decarboxylase	57			Q -> P (in dbSNP:rs3897926).		allantoin biosynthetic process (GO:0019428)|purine nucleobase metabolic process (GO:0006144)|urate catabolic process (GO:0019628)	peroxisome (GO:0005777)	carboxy-lyase activity (GO:0016831)	p.Q57P(1)									CTTACCTGACTGTGCAAGGGC	0.433																																					p.Q57R		Atlas-SNP	.											PRHOXNB,NS,carcinoma,0,1	PRHOXNB	6	.	1	Substitution - Missense(1)	stomach(1)	c.A170G						.						71.0	66.0	68.0					13																	28562605		1876	4114	5990	SO:0001583	missense	646625	exon1			CCTGACTGTGCAA		CCDS45020.1	13q12.2	2014-04-09	2013-06-18	2013-06-18	ENSG00000183463	ENSG00000183463	4.1.1.n1		17785	protein-coding gene	gene with protein product	"""OHCU decarboxylase"""	615804	"""parahox cluster neighbor"""	PRHOXNB		16462750	Standard	NM_001105577		Approved		uc010aan.1	A6NGE7	OTTHUMG00000186217	ENST00000332715.5:c.170A>G	chr13.hg19:g.28562605T>C	ENSP00000333490:p.Gln57Arg	82.0	0.0		68.0	3.0	NM_001105577		Missense_Mutation	SNP	ENST00000332715.5	hg19	CCDS45020.1	.	.	.	.	.	.	.	.	.	.	T	4.980	0.182035	0.09495	.	.	ENSG00000183463	ENST00000332715	T	0.39997	1.05	5.2	-2.01	0.07410	2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, type 1 (1);Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase (2);	0.537574	0.18843	N	0.129613	T	0.13286	0.0322	N	0.03903	-0.33	0.80722	P	0.0	B	0.10296	0.003	B	0.11329	0.006	T	0.18587	-1.0332	9	0.14656	T	0.56	-0.8652	3.3162	0.07034	0.405:0.168:0.0:0.427	.	57	A6NGE7	URAD_HUMAN	R	57	ENSP00000333490:Q57R	ENSP00000333490:Q57R	Q	-	2	0	PRHOXNB	27460605	0.000000	0.05858	0.016000	0.15963	0.713000	0.41058	-0.723000	0.04952	-0.313000	0.08728	0.482000	0.46254	CAG	.	T|0.723;G|0.277		0.433	URAD-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472432.1		
FLT1	2321	hgsc.bcm.edu	37	13	28913323	28913323	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:28913323G>A	ENST00000282397.4	-	17	2721	c.2470C>T	c.(2470-2472)Cgg>Tgg	p.R824W	FLT1_ENST00000540678.1_Missense_Mutation_p.R42W	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	824					blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGTCTCTCCCGGGCAAACTCC	0.418																																					p.R824W		Atlas-SNP	.											.	FLT1	393	.	0			c.C2470T						.						78.0	77.0	77.0					13																	28913323		2203	4300	6503	SO:0001583	missense	2321	exon17			TCTCCCGGGCAAA	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2470C>T	chr13.hg19:g.28913323G>A	ENSP00000282397:p.Arg824Trp	124.0	0.0		88.0	4.0	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	hg19	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	G	19.89	3.911144	0.72983	.	.	ENSG00000102755	ENST00000282397;ENST00000540678	D;D	0.89552	-2.53;-2.53	5.52	4.63	0.57726	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.94159	0.8126	M	0.79693	2.465	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94445	0.7662	10	0.87932	D	0	.	14.6701	0.68937	0.0:0.0:0.7069:0.2931	.	824	P17948	VGFR1_HUMAN	W	824;42	ENSP00000282397:R824W;ENSP00000443311:R42W	ENSP00000282397:R824W	R	-	1	2	FLT1	27811323	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.074000	0.41529	2.761000	0.94854	0.655000	0.94253	CGG	.	.		0.418	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1		
BRCA2	675	hgsc.bcm.edu	37	13	32914823	32914823	+	Missense_Mutation	SNP	A	A	G	rs397507369|rs80359574|rs587781470		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:32914823A>G	ENST00000380152.3	+	11	6564	c.6331A>G	c.(6331-6333)Aag>Gag	p.K2111E	BRCA2_ENST00000544455.1_Missense_Mutation_p.K2111E			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2111					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TCGTGTTGATAAGAGAAACCC	0.343			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.K2111E	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.A6331G						.						40.0	42.0	41.0					13																	32914823		2203	4297	6500	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	GTTGATAAGAGAA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.6331A>G	chr13.hg19:g.32914823A>G	ENSP00000369497:p.Lys2111Glu	102.0	0.0		96.0	4.0	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	6.836	0.523531	0.13066	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00705	5.81;5.81	5.49	-0.7	0.11273	.	0.904941	0.09578	N	0.783329	T	0.00754	0.0025	L	0.38838	1.175	0.09310	N	1	B	0.22276	0.067	B	0.18263	0.021	T	0.44128	-0.9348	10	0.10636	T	0.68	.	10.0594	0.42266	0.571:0.0:0.429:0.0	.	2111	P51587	BRCA2_HUMAN	E	2111	ENSP00000369497:K2111E;ENSP00000439902:K2111E	ENSP00000369497:K2111E	K	+	1	0	BRCA2	31812823	0.000000	0.05858	0.000000	0.03702	0.356000	0.29392	0.419000	0.21247	0.085000	0.17107	0.482000	0.46254	AAG	.	.		0.343	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
N4BP2L2	10443	hgsc.bcm.edu	37	13	33012840	33012840	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:33012840A>G	ENST00000504114.1	-	7	2230	c.2139T>C	c.(2137-2139)ctT>ctC	p.L713L	N4BP2L2_ENST00000380121.3_5'UTR|N4BP2L2_ENST00000357505.6_Silent_p.L713L|N4BP2L2_ENST00000399396.3_Silent_p.L728L|N4BP2L2_ENST00000446957.2_Silent_p.L631L			Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	0					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		TCTTCCAGTCAAGGGGAACCA	0.393																																					p.L728L		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.T2184C						.						101.0	101.0	101.0					13																	33012840		1952	4164	6116	SO:0001819	synonymous_variant	10443	exon8			CCAGTCAAGGGGA	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"""phosphonoformate immuno-associated protein 5"""	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000504114.1:c.2139T>C	chr13.hg19:g.33012840A>G		96.0	0.0		111.0	5.0	NM_033111	A3KME8	Silent	SNP	ENST00000504114.1	hg19																																																																																				.	.		0.393	N4BP2L2-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000361380.1	NM_014887	
NBEA	26960	hgsc.bcm.edu	37	13	36229065	36229065	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:36229065T>C	ENST00000400445.3	+	53	8580	c.8046T>C	c.(8044-8046)tgT>tgC	p.C2682C	NBEA_ENST00000379922.3_Silent_p.C260C|NBEA_ENST00000537702.1_Silent_p.C475C|NBEA_ENST00000540320.1_Silent_p.C2682C|NBEA_ENST00000310336.4_Silent_p.C2682C|NBEA_ENST00000379939.2_Silent_p.C2679C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2682					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)		ATGCACATTGTTTTGTGGTAA	0.358																																					p.C2682C		Atlas-SNP	.											.	NBEA	340	.	0			c.T8046C						.						110.0	103.0	105.0					13																	36229065		1863	4096	5959	SO:0001819	synonymous_variant	26960	exon53			ACATTGTTTTGTG	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.8046T>C	chr13.hg19:g.36229065T>C		127.0	0.0		92.0	4.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.		0.358	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
SUPT20H	55578	hgsc.bcm.edu	37	13	37586423	37586423	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:37586423T>C	ENST00000350612.6	-	24	2224	c.2004A>G	c.(2002-2004)caA>caG	p.Q668Q	SUPT20H_ENST00000360252.4_Silent_p.Q669Q|SUPT20H_ENST00000356185.3_Silent_p.Q669Q|SUPT20H_ENST00000475892.1_Silent_p.Q747Q|SUPT20H_ENST00000464744.1_Silent_p.Q669Q	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	668	Gln-rich.				autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										TGGTTGAACCTTGCTCAGAAC	0.368																																					p.Q669Q		Atlas-SNP	.											.	.	.	.	0			c.A2007G						.						138.0	139.0	139.0					13																	37586423		2203	4300	6503	SO:0001819	synonymous_variant	55578	exon24			TGAACCTTGCTCA	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.2004A>G	chr13.hg19:g.37586423T>C		53.0	0.0		50.0	5.0	NM_017569	E7ER46|Q71RF3|Q9Y6A6	Silent	SNP	ENST00000350612.6	hg19	CCDS31959.1	.	.	.	.	.	.	.	.	.	.	T	8.149	0.786994	0.16189	.	.	ENSG00000102710	ENST00000469488	.	.	.	5.64	3.17	0.36434	.	.	.	.	.	T	0.55130	0.1901	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45977	-0.9224	4	.	.	.	-1.3626	6.6608	0.23012	0.1353:0.0781:0.0:0.7866	.	.	.	.	R	211	.	.	K	-	2	0	FAM48A	36484423	1.000000	0.71417	0.995000	0.50966	0.957000	0.61999	3.227000	0.51262	0.400000	0.25396	0.379000	0.24179	AAG	.	.		0.368	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569	
VWA8	23078	hgsc.bcm.edu	37	13	42306265	42306265	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:42306265A>G	ENST00000379310.3	-	22	2521	c.2453T>C	c.(2452-2454)cTt>cCt	p.L818P	VWA8_ENST00000281496.6_Missense_Mutation_p.L818P	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	818						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										CGAAGGCTGAAGCGTAAGAGT	0.328																																					p.L818P		Atlas-SNP	.											.	.	.	.	0			c.T2453C						.						90.0	89.0	89.0					13																	42306265		2203	4300	6503	SO:0001583	missense	23078	exon22			GGCTGAAGCGTAA	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"""KIAA0564"""	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.2453T>C	chr13.hg19:g.42306265A>G	ENSP00000368612:p.Leu818Pro	51.0	0.0		32.0	4.0	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	hg19	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.534102	0.85812	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496	T;T	0.54866	0.55;0.55	5.94	5.94	0.96194	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.067028	0.64402	D	0.000013	T	0.72326	0.3446	M	0.74546	2.27	0.80722	D	1	D	0.61697	0.99	D	0.69142	0.962	T	0.75216	-0.3396	10	0.66056	D	0.02	.	16.4075	0.83691	1.0:0.0:0.0:0.0	.	818	A3KMH1	K0564_HUMAN	P	722;818;818	ENSP00000368612:L818P;ENSP00000281496:L818P	ENSP00000251030:L722P	L	-	2	0	KIAA0564	41204265	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.272000	0.72575	2.275000	0.75901	0.528000	0.53228	CTT	.	.		0.328	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058	
KPNA3	3839	hgsc.bcm.edu	37	13	50285129	50285129	+	Silent	SNP	T	T	C	rs370734199		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:50285129T>C	ENST00000261667.3	-	11	1215	c.801A>G	c.(799-801)tcA>tcG	p.S267S		NM_002267.3	NP_002258.2	O00505	IMA4_HUMAN	karyopherin alpha 3 (importin alpha 4)	267					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)|protein complex assembly (GO:0006461)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(4)	21		Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.42e-09)		CTGTCAAGTATGACAGAGCCC	0.398																																					p.S267S		Atlas-SNP	.											.	KPNA3	53	.	0			c.A801G						.						75.0	66.0	69.0					13																	50285129		2203	4300	6503	SO:0001819	synonymous_variant	3839	exon11			CAAGTATGACAGA	D89618	CCDS9421.1	13q14.3	2013-02-14			ENSG00000102753	ENSG00000102753		"""Importins"", ""Armadillo repeat containing"""	6396	protein-coding gene	gene with protein product		601892				9154134, 9435235	Standard	NM_002267		Approved	SRP1gamma, SRP4, hSRP1, IPOA4	uc001vdj.2	O00505	OTTHUMG00000016922	ENST00000261667.3:c.801A>G	chr13.hg19:g.50285129T>C		100.0	0.0		68.0	4.0	NM_002267	O00191|O43195|Q5JVM9|Q96AA7	Silent	SNP	ENST00000261667.3	hg19	CCDS9421.1																																																																																			.	.		0.398	KPNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044939.2	NM_002267	
PIBF1	10464	hgsc.bcm.edu	37	13	73401963	73401963	+	Silent	SNP	T	T	C	rs552358739	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:73401963T>C	ENST00000326291.6	+	8	1346	c.1008T>C	c.(1006-1008)caT>caC	p.H336H		NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	336						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)		GCTGTGCTCATGAAGAGGATC	0.398													T|||	2	0.000399361	0.0	0.0	5008	,	,		15434	0.002		0.0	False		,,,				2504	0.0				p.H336H		Atlas-SNP	.											.	PIBF1	65	.	0			c.T1008C						.						104.0	93.0	97.0					13																	73401963		2203	4300	6503	SO:0001819	synonymous_variant	10464	exon8			TGCTCATGAAGAG	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.1008T>C	chr13.hg19:g.73401963T>C		73.0	0.0		50.0	4.0	NM_006346	O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	Silent	SNP	ENST00000326291.6	hg19	CCDS31991.1																																																																																			.	.		0.398	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045255.1	NM_006346	
NALCN	259232	hgsc.bcm.edu	37	13	102047689	102047689	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:102047689C>A	ENST00000251127.6	-	3	217	c.136G>T	c.(136-138)Gcc>Tcc	p.A46S	NALCN_ENST00000376196.3_Missense_Mutation_p.A46S|NALCN_ENST00000470333.1_5'UTR|NALCN_ENST00000376200.5_Missense_Mutation_p.A46S	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	46					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CTGATGATGGCACAGATGCGC	0.423																																					p.A46S		Atlas-SNP	.											.	NALCN	431	.	0			c.G136T						.						129.0	105.0	113.0					13																	102047689		2203	4300	6503	SO:0001583	missense	259232	exon3			TGATGGCACAGAT	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.136G>T	chr13.hg19:g.102047689C>A	ENSP00000251127:p.Ala46Ser	89.0	0.0		64.0	4.0	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	hg19	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.843579	0.91197	.	.	ENSG00000102452	ENST00000251127;ENST00000376196;ENST00000376200;ENST00000449582	D;D;D	0.97404	-4.37;-4.37;-4.37	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.96358	0.8812	L	0.56769	1.78	0.80722	D	1	P;P	0.41929	0.765;0.765	B;B	0.43052	0.353;0.406	D	0.95560	0.8628	10	0.35671	T	0.21	.	19.7619	0.96323	0.0:1.0:0.0:0.0	.	46;46	F2Z323;Q8IZF0	.;NALCN_HUMAN	S	46	ENSP00000251127:A46S;ENSP00000365367:A46S;ENSP00000365373:A46S	ENSP00000251127:A46S	A	-	1	0	NALCN	100845690	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.487000	0.81328	2.681000	0.91329	0.561000	0.74099	GCC	.	.		0.423	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
TEX29	121793	hgsc.bcm.edu	37	13	111995257	111995257	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:111995257A>G	ENST00000283547.1	+	5	523	c.394A>G	c.(394-396)Agt>Ggt	p.S132G		NM_152324.1	NP_689537.1	Q8N6K0	TEX29_HUMAN	testis expressed 29	132						integral component of membrane (GO:0016021)											CTCGATGAAGAGTGACGAGGA	0.577																																					p.S132G		Atlas-SNP	.											.	.	.	.	0			c.A394G						.						84.0	80.0	81.0					13																	111995257		2203	4300	6503	SO:0001583	missense	121793	exon5			ATGAAGAGTGACG	BC029889	CCDS9522.1	13q34	2012-03-23	2012-02-07	2012-02-07	ENSG00000153495	ENSG00000153495			20370	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 16"""	C13orf16			Standard	NM_152324		Approved	bA474D23.1, MGC35169	uc001vsa.3	Q8N6K0	OTTHUMG00000017358	ENST00000283547.1:c.394A>G	chr13.hg19:g.111995257A>G	ENSP00000283547:p.Ser132Gly	68.0	0.0		52.0	4.0	NM_152324		Missense_Mutation	SNP	ENST00000283547.1	hg19	CCDS9522.1	.	.	.	.	.	.	.	.	.	.	A	6.325	0.428126	0.11987	.	.	ENSG00000153495	ENST00000283547	.	.	.	1.65	-3.3	0.05003	.	8.714320	0.00465	N	0.000116	T	0.19604	0.0471	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.04767	-1.0928	9	0.30078	T	0.28	0.0149	0.0801	0.00031	0.3194:0.241:0.201:0.2386	.	132	Q8N6K0	CM016_HUMAN	G	132	.	ENSP00000283547:S132G	S	+	1	0	C13orf16	110793258	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.432000	0.06956	-0.952000	0.03649	0.379000	0.24179	AGT	.	.		0.577	TEX29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045812.2	NM_152324	
LAMP1	3916	hgsc.bcm.edu	37	13	113973926	113973926	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr13:113973926C>T	ENST00000332556.4	+	5	899	c.705C>T	c.(703-705)agC>agT	p.S235S	LAMP1_ENST00000397181.3_Silent_p.S182S	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	235	Second lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			TGCTGGCCAGCATGGGGCTGC	0.677																																					p.S235S		Atlas-SNP	.											.	LAMP1	41	.	0			c.C705T						.						48.0	57.0	54.0					13																	113973926		2051	4174	6225	SO:0001819	synonymous_variant	3916	exon5			GGCCAGCATGGGG	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"""CD molecules"""	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.705C>T	chr13.hg19:g.113973926C>T		43.0	0.0		35.0	4.0	NM_005561	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Silent	SNP	ENST00000332556.4	hg19	CCDS41909.1																																																																																			.	.		0.677	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2		
OR4K14	122740	hgsc.bcm.edu	37	14	20482991	20482991	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:20482991T>C	ENST00000305045.2	-	1	361	c.362A>G	c.(361-363)tAt>tGt	p.Y121C		NM_001004712.1	NP_001004712.1	Q8NGD5	OR4KE_HUMAN	olfactory receptor, family 4, subfamily K, member 14	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(20)|skin(6)	37	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2e-06)	GBM - Glioblastoma multiforme(265;0.00124)		ATATCTGTCATAGGCCATGGA	0.468																																					p.Y121C		Atlas-SNP	.											.	OR4K14	86	.	0			c.A362G						.						96.0	93.0	94.0					14																	20482991		2203	4300	6503	SO:0001583	missense	122740	exon1			CTGTCATAGGCCA		CCDS32027.1	14q11.2	2013-09-23			ENSG00000169484	ENSG00000169484		"""GPCR / Class A : Olfactory receptors"""	15352	protein-coding gene	gene with protein product							Standard	NM_001004712		Approved		uc010tky.2	Q8NGD5	OTTHUMG00000170780	ENST00000305045.2:c.362A>G	chr14.hg19:g.20482991T>C	ENSP00000305011:p.Tyr121Cys	124.0	0.0		86.0	4.0	NM_001004712	Q6IEU1|Q96R71	Missense_Mutation	SNP	ENST00000305045.2	hg19	CCDS32027.1	.	.	.	.	.	.	.	.	.	.	.	16.16	3.044397	0.55110	.	.	ENSG00000169484	ENST00000305045	T	0.00490	7.03	4.04	4.04	0.47022	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40640	N	0.001053	T	0.01489	0.0048	M	0.89658	3.05	0.31676	N	0.643736	D	0.67145	0.996	P	0.60886	0.88	T	0.02654	-1.1128	10	0.72032	D	0.01	.	12.097	0.53761	0.0:0.0:0.0:1.0	.	121	Q8NGD5	OR4KE_HUMAN	C	121	ENSP00000305011:Y121C	ENSP00000305011:Y121C	Y	-	2	0	OR4K14	19552831	0.990000	0.36364	1.000000	0.80357	0.966000	0.64601	0.207000	0.17395	1.695000	0.51148	0.413000	0.27773	TAT	.	.		0.468	OR4K14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410343.1		
OR6S1	341799	hgsc.bcm.edu	37	14	21109228	21109228	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:21109228A>G	ENST00000320704.3	-	1	622	c.623T>C	c.(622-624)cTc>cCc	p.L208P		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		TACAATGACGAGGGAGGCCAG	0.577																																					p.L208P		Atlas-SNP	.											.	OR6S1	49	.	0			c.T623C						.						90.0	90.0	90.0					14																	21109228		2203	4300	6503	SO:0001583	missense	341799	exon1			ATGACGAGGGAGG	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.623T>C	chr14.hg19:g.21109228A>G	ENSP00000313110:p.Leu208Pro	67.0	0.0		46.0	4.0	NM_001001968	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	hg19	CCDS32038.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.826478	0.50739	.	.	ENSG00000181803	ENST00000320704	T	0.44881	0.91	5.62	5.62	0.85841	GPCR, rhodopsin-like superfamily (1);	0.349077	0.20846	N	0.084603	T	0.53883	0.1824	L	0.39245	1.2	0.21220	N	0.999757	D	0.63880	0.993	D	0.65323	0.934	T	0.50849	-0.8779	10	0.87932	D	0	-9.0646	13.7709	0.63023	1.0:0.0:0.0:0.0	.	208	Q8NH40	OR6S1_HUMAN	P	208	ENSP00000313110:L208P	ENSP00000313110:L208P	L	-	2	0	OR6S1	20179068	0.000000	0.05858	0.798000	0.32154	0.926000	0.56050	1.250000	0.32850	2.124000	0.65301	0.533000	0.62120	CTC	.	.		0.577	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
MMP14	4323	hgsc.bcm.edu	37	14	23310816	23310816	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:23310816A>G	ENST00000311852.6	+	2	486	c.225A>G	c.(223-225)caA>caG	p.Q75Q	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	75					angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	ACGGCTTGCAAGTAACAGGCA	0.567																																					p.Q75Q		Atlas-SNP	.											.	MMP14	40	.	0			c.A225G						.						96.0	73.0	81.0					14																	23310816		2203	4300	6503	SO:0001819	synonymous_variant	4323	exon2			CTTGCAAGTAACA		CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"""membrane type 1 metalloprotease"""	600754	"""matrix metalloproteinase 14 (membrane-inserted)"""			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.225A>G	chr14.hg19:g.23310816A>G		48.0	0.0		44.0	4.0	NM_004995	A8K5L0|Q6GSF3|Q92678	Silent	SNP	ENST00000311852.6	hg19	CCDS9577.1																																																																																			.	.		0.567	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995	
DHRS2	10202	hgsc.bcm.edu	37	14	24112421	24112421	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:24112421G>A	ENST00000250383.6	+	5	957	c.481G>A	c.(481-483)Gag>Aag	p.E161K	DHRS2_ENST00000344777.7_Missense_Mutation_p.E161K	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2	161					C21-steroid hormone metabolic process (GO:0008207)|cellular response to oxidative stress (GO:0034599)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	carbonyl reductase (NADPH) activity (GO:0004090)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		GCCCTACATGGAGAACAGGTA	0.582																																					p.E161K		Atlas-SNP	.											DHRS2_ENST00000344777,NS,carcinoma,0,2	DHRS2	78	.	0			c.G481A						.						139.0	137.0	138.0					14																	24112421		2203	4300	6503	SO:0001583	missense	10202	exon5			TACATGGAGAACA		CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18349	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 1"""	615194				7556196, 11944995, 16685466, 19027726	Standard	NM_182908		Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.481G>A	chr14.hg19:g.24112421G>A	ENSP00000250383:p.Glu161Lys	85.0	0.0		58.0	3.0	NM_182908	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Missense_Mutation	SNP	ENST00000250383.6	hg19	CCDS9604.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.56|12.56	1.974175|1.974175	0.34848|0.34848	.|.	.|.	ENSG00000100867|ENSG00000100867	ENST00000432832;ENST00000250383;ENST00000344777;ENST00000553600|ENST00000557535	T;T;T;T|.	0.19532|.	2.14;2.14;2.14;2.14|.	4.6|4.6	4.6|4.6	0.57074|0.57074	.|.	0.234355|.	0.42294|.	D|.	0.000722|.	T|T	0.32255|0.32255	0.0823|0.0823	N|N	0.04162|0.04162	-0.26|-0.26	0.47441|0.47441	D|D	0.999422|0.999422	B;B;B|.	0.33212|.	0.055;0.402;0.007|.	B;B;B|.	0.27380|.	0.035;0.079;0.013|.	T|T	0.15263|0.15263	-1.0443|-1.0443	10|5	0.05833|.	T|.	0.94|.	.|.	11.0392|11.0392	0.47820|0.47820	0.0:0.1884:0.8116:0.0|0.0:0.1884:0.8116:0.0	.|.	161;161;139|.	C9JZP6;D3DS54;Q13268-2|.	.;.;.|.	K|E	161;161;161;61|76	ENSP00000401213:E161K;ENSP00000250383:E161K;ENSP00000344674:E161K;ENSP00000451485:E61K|.	ENSP00000250383:E161K|.	E|G	+|+	1|2	0|0	DHRS2|DHRS2	23182261|23182261	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.574000|0.574000	0.36063|0.36063	4.151000|4.151000	0.58105|0.58105	2.533000|2.533000	0.85409|0.85409	0.563000|0.563000	0.77884|0.77884	GAG|GGA	.	.		0.582	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908	
LRRC16B	90668	hgsc.bcm.edu	37	14	24533482	24533482	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:24533482A>G	ENST00000342740.5	+	32	3161	c.3007A>G	c.(3007-3009)Aat>Gat	p.N1003D	LRRC16B_ENST00000334420.7_Missense_Mutation_p.N99D	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1003						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)		TCGTCAGGAGAATGGGATGGC	0.567																																					p.N1003D		Atlas-SNP	.											.	LRRC16B	120	.	0			c.A3007G						.						62.0	51.0	54.0					14																	24533482		2203	4300	6503	SO:0001583	missense	90668	exon32			CAGGAGAATGGGA	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.3007A>G	chr14.hg19:g.24533482A>G	ENSP00000340467:p.Asn1003Asp	51.0	0.0		56.0	4.0	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	hg19	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.328354	0.60743	.	.	ENSG00000186648	ENST00000342740;ENST00000334420	T;T	0.56941	0.43;0.43	5.28	5.28	0.74379	.	0.000000	0.45606	D	0.000343	T	0.61489	0.2351	L	0.46157	1.445	0.38364	D	0.944697	D;P	0.64830	0.994;0.882	D;B	0.68039	0.955;0.332	T	0.61158	-0.7119	10	0.24483	T	0.36	-18.0226	11.6259	0.51145	1.0:0.0:0.0:0.0	.	99;1003	Q8ND23-2;Q8ND23	.;LR16B_HUMAN	D	1003;99	ENSP00000340467:N1003D;ENSP00000334701:N99D	ENSP00000334701:N99D	N	+	1	0	LRRC16B	23603322	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.348000	0.52209	1.998000	0.58463	0.533000	0.62120	AAT	.	.		0.567	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
AKAP6	9472	hgsc.bcm.edu	37	14	33293955	33293955	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:33293955A>G	ENST00000280979.4	+	13	7106	c.6936A>G	c.(6934-6936)aaA>aaG	p.K2312K	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	2312					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TTCATGAAAAACGACATAGAA	0.418																																					p.K2312K	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.A6936G						.						65.0	69.0	68.0					14																	33293955		2146	4282	6428	SO:0001819	synonymous_variant	9472	exon13			TGAAAAACGACAT	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.6936A>G	chr14.hg19:g.33293955A>G		137.0	0.0		111.0	5.0	NM_004274	A7E242|A7E2D4|O15028	Silent	SNP	ENST00000280979.4	hg19	CCDS9644.1																																																																																			.	.		0.418	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
KIAA0391	9692	hgsc.bcm.edu	37	14	35596745	35596745	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:35596745T>C	ENST00000557565.1	+	4	1476	c.1095T>C	c.(1093-1095)taT>taC	p.Y365Y	KIAA0391_ENST00000603588.1_3'UTR|KIAA0391_ENST00000321130.10_Silent_p.Y349Y|KIAA0391_ENST00000604948.1_Silent_p.Y270Y|KIAA0391_ENST00000534898.4_Silent_p.Y365Y|KIAA0391_ENST00000605870.1_5'UTR|KIAA0391_ENST00000603544.1_Silent_p.Y349Y|KIAA0391_ENST00000250377.7_Silent_p.Y270Y	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	365					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		CAGAAGAATATGAATGTCTTA	0.358																																					p.Y365Y		Atlas-SNP	.											.	KIAA0391	35	.	0			c.T1095C						.						82.0	82.0	82.0					14																	35596745		2203	4300	6503	SO:0001819	synonymous_variant	9692	exon4			AGAATATGAATGT	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"""mitochondrial RNase P subunit 3"", ""proteinaceous RNase P"""	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.1095T>C	chr14.hg19:g.35596745T>C		110.0	0.0		92.0	4.0	NM_014672	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Silent	SNP	ENST00000557565.1	hg19	CCDS32063.1																																																																																			.	.		0.358	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672	
RALGAPA1	253959	hgsc.bcm.edu	37	14	36017712	36017712	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:36017712A>G	ENST00000389698.3	-	40	6525		c.e40+1		RALGAPA1_ENST00000307138.6_Intron|RALGAPA1_ENST00000382366.3_Splice_Site|RALGAPA1_ENST00000258840.6_Splice_Site	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)						activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						ACTTTGTCTTACCTTCAGATA	0.338																																					.		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.6134+2T>C						.						96.0	101.0	99.0					14																	36017712		2203	4299	6502	SO:0001630	splice_region_variant	253959	exon41			TGTCTTACCTTCA	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"""tuberin-like protein 1"", ""GAP-related interacting protein to E12"""	608884	"""GTPase activating RANGAP domain-like 1"", ""GTPase activating Rap/RanGAP domain-like 1"""	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.6108+1T>C	chr14.hg19:g.36017712A>G		120.0	0.0		91.0	4.0	NM_014990	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Splice_Site	SNP	ENST00000389698.3	hg19	CCDS32065.1																																																																																			.	.		0.338	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	Intron
CLEC14A	161198	hgsc.bcm.edu	37	14	38724408	38724408	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:38724408C>A	ENST00000342213.2	-	1	1166	c.820G>T	c.(820-822)Gct>Tct	p.A274S		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	274	EGF-like.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)		AAGCCCGTAGCACATTCGCAG	0.662																																					p.A274S		Atlas-SNP	.											CLEC14A,NS,carcinoma,0,1	CLEC14A	83	.	0			c.G820T						.						63.0	69.0	67.0					14																	38724408		2203	4300	6503	SO:0001583	missense	161198	exon1			CCGTAGCACATTC		CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"""C-type lectin domain containing"""	19832	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 27"""	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.820G>T	chr14.hg19:g.38724408C>A	ENSP00000353013:p.Ala274Ser	74.0	0.0		59.0	3.0	NM_175060	Q695G9|Q6PWT6|Q8N5V5	Missense_Mutation	SNP	ENST00000342213.2	hg19	CCDS9667.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.867327	0.32977	.	.	ENSG00000176435	ENST00000342213;ENST00000546356	D	0.95622	-3.76	3.91	3.91	0.45181	Epidermal growth factor-like (1);	0.127905	0.30101	N	0.010420	D	0.94142	0.8121	N	0.20986	0.625	0.32366	N	0.556535	D	0.64830	0.994	D	0.62955	0.909	D	0.92674	0.6152	10	0.32370	T	0.25	-9.0137	11.7127	0.51635	0.0:1.0:0.0:0.0	.	274	Q86T13	CLC14_HUMAN	S	274;39	ENSP00000353013:A274S	ENSP00000353013:A274S	A	-	1	0	CLEC14A	37794159	0.993000	0.37304	0.953000	0.39169	0.611000	0.37282	1.858000	0.39408	2.498000	0.84270	0.591000	0.81541	GCT	.	.		0.662	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060	
VCPKMT	79609	hgsc.bcm.edu	37	14	50583176	50583176	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:50583176T>C	ENST00000395860.2	-	1	99	c.95A>G	c.(94-96)cAg>cGg	p.Q32R	VCPKMT_ENST00000395859.2_Missense_Mutation_p.Q32R	NM_024558.2	NP_078834.2	Q9H867	MT21D_HUMAN	valosin containing protein lysine (K) methyltransferase	32					peptidyl-lysine trimethylation (GO:0018023)	cytoplasm (GO:0005737)	protein-lysine N-methyltransferase activity (GO:0016279)										GGAGCTATACTGCTGTAGTCG	0.597																																					p.Q32R		Atlas-SNP	.											.	METTL21D	11	.	0			c.A95G						.						59.0	63.0	62.0					14																	50583176		2203	4300	6503	SO:0001583	missense	79609	exon1			CTATACTGCTGTA	AK023982	CCDS9696.2, CCDS41951.1	14q21.3	2013-09-30	2013-09-30	2013-09-30	ENSG00000100483	ENSG00000100483			20352	protein-coding gene	gene with protein product		615260	"""chromosome 14 open reading frame 138"", ""methyltransferase like 21D"""	C14orf138, METTL21D		22948820	Standard	NR_049738		Approved	VCP-KMT	uc001wxo.1	Q9H867	OTTHUMG00000029531	ENST00000395860.2:c.95A>G	chr14.hg19:g.50583176T>C	ENSP00000379201:p.Gln32Arg	98.0	0.0		84.0	4.0	NM_024558	B7ZLA3|B7ZLA4|Q2M2X3|Q86T12	Missense_Mutation	SNP	ENST00000395860.2	hg19	CCDS9696.2	.	.	.	.	.	.	.	.	.	.	T	29.1	4.975096	0.92919	.	.	ENSG00000100483	ENST00000395859;ENST00000395860	T;T	0.07688	3.17;3.17	6.06	4.93	0.64822	.	0.050670	0.85682	D	0.000000	T	0.32496	0.0831	M	0.88310	2.945	0.54753	D	0.999982	D;D	0.76494	0.999;0.997	D;D	0.69307	0.963;0.927	T	0.18429	-1.0337	10	0.72032	D	0.01	-4.084	12.113	0.53850	0.0:0.0665:0.0:0.9335	.	32;32	B7ZLA4;Q9H867	.;MT21D_HUMAN	R	32	ENSP00000379200:Q32R;ENSP00000379201:Q32R	ENSP00000379200:Q32R	Q	-	2	0	METTL21D	49652926	1.000000	0.71417	0.997000	0.53966	0.970000	0.65996	7.115000	0.77110	1.122000	0.41944	0.528000	0.53228	CAG	.	.		0.597	VCPKMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276877.1	NM_024558	
DHRS7	51635	hgsc.bcm.edu	37	14	60619873	60619873	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:60619873A>G	ENST00000216500.5	-	5	872	c.417T>C	c.(415-417)ggT>ggC	p.G139G	DHRS7_ENST00000536410.2_Silent_p.G89G|PCNXL4_ENST00000553898.1_Intron|DHRS7_ENST00000557185.1_Silent_p.G139G|DHRS7_ENST00000553986.1_5'UTR|PCNXL4_ENST00000406949.1_Intron			Q9Y394	DHRS7_HUMAN	dehydrogenase/reductase (SDR family) member 7	139						membrane (GO:0016020)	oxidoreductase activity (GO:0016491)			endometrium(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	5				OV - Ovarian serous cystadenocarcinoma(108;0.121)		GGGACATTCCACCATTGTTGA	0.428																																					p.G139G		Atlas-SNP	.											.	DHRS7	31	.	0			c.T417C						.						96.0	87.0	90.0					14																	60619873		2203	4300	6503	SO:0001819	synonymous_variant	51635	exon4			CATTCCACCATTG	AF151844	CCDS9743.1	14q23.1	2011-09-20			ENSG00000100612	ENSG00000100612		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	21524	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 4"", ""short chain dehydrogenase/reductase family 34C, member 1"""	612833				10800688, 10810093, 19027726	Standard	NM_016029		Approved	retDSR4, SDR34C1	uc001xes.3	Q9Y394	OTTHUMG00000140331	ENST00000216500.5:c.417T>C	chr14.hg19:g.60619873A>G		123.0	0.0		102.0	5.0	NM_016029	B2R896|Q9UKU2	Silent	SNP	ENST00000216500.5	hg19	CCDS9743.1	.	.	.	.	.	.	.	.	.	.	A	4.680	0.126440	0.08931	.	.	ENSG00000100612	ENST00000557751;ENST00000554101	.	.	.	5.95	0.798	0.18660	.	.	.	.	.	T	0.45216	0.1331	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21999	-1.0229	4	.	.	.	.	3.5656	0.07899	0.4401:0.0:0.1984:0.3614	.	.	.	.	A	7;134	.	.	V	-	2	0	DHRS7	59689626	0.932000	0.31603	0.984000	0.44739	0.402000	0.30811	0.172000	0.16704	-0.090000	0.12462	-0.371000	0.07208	GTG	.	.		0.428	DHRS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276947.2	NM_016029	
SYNE2	23224	hgsc.bcm.edu	37	14	64630170	64630170	+	Silent	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:64630170C>A	ENST00000344113.4	+	89	16562	c.16350C>A	c.(16348-16350)tcC>tcA	p.S5450S	SYNE2_ENST00000357395.3_Silent_p.S1835S|SYNE2_ENST00000555002.1_Silent_p.S2084S|SYNE2_ENST00000358025.3_Silent_p.S5450S|SYNE2_ENST00000394768.2_Silent_p.S1835S|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000554584.1_Silent_p.S5367S	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5450					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)		TCCAAAATTCCAGTGTCCTGG	0.522																																					p.S5450S		Atlas-SNP	.											.	SYNE2	577	.	0			c.C16350A						.						76.0	79.0	78.0					14																	64630170		2203	4300	6503	SO:0001819	synonymous_variant	23224	exon89			AAATTCCAGTGTC	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.16350C>A	chr14.hg19:g.64630170C>A		106.0	0.0		97.0	4.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.		0.522	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
YLPM1	56252	hgsc.bcm.edu	37	14	75301993	75301993	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:75301993A>G	ENST00000552421.1	+	19	4326	c.4202A>G	c.(4201-4203)aAg>aGg	p.K1401R	YLPM1_ENST00000325680.7_Missense_Mutation_p.K2107R			P49750	YLPM1_HUMAN	YLP motif containing 1	1912					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		CTGGAAGAGAAGAAGGATGCA	0.468																																					p.K2107R		Atlas-SNP	.											.	YLPM1	298	.	0			c.A6320G						.						102.0	101.0	101.0					14																	75301993		1883	4121	6004	SO:0001583	missense	56252	exon20			AAGAGAAGAAGGA	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 169"""		"""chromosome 14 open reading frame 170"""	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.4202A>G	chr14.hg19:g.75301993A>G	ENSP00000447921:p.Lys1401Arg	106.0	0.0		100.0	4.0	NM_019589	P49752|Q96I64|Q9P1V7	Missense_Mutation	SNP	ENST00000552421.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.66	2.602157	0.46423	.	.	ENSG00000119596	ENST00000552421;ENST00000325680	.	.	.	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000001	T	0.49338	0.1551	N	0.04203	-0.255	0.80722	D	1	D	0.63880	0.993	D	0.63488	0.915	T	0.57585	-0.7786	9	0.33940	T	0.23	-13.4137	15.8972	0.79344	1.0:0.0:0.0:0.0	.	2107	P49750-4	.	R	1401;2107	.	ENSP00000324463:K2107R	K	+	2	0	YLPM1	74371746	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.157000	0.67596	0.460000	0.39030	AAG	.	.		0.468	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589	
POMT2	29954	hgsc.bcm.edu	37	14	77765880	77765880	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:77765880C>T	ENST00000261534.4	-	7	1043	c.841G>A	c.(841-843)Gct>Act	p.A281T		NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	281						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)		AGGACACGAGCAGTCAGGTGT	0.507																																					p.A281T		Atlas-SNP	.											.	POMT2	47	.	0			c.G841A						.						137.0	111.0	119.0					14																	77765880		2203	4300	6503	SO:0001583	missense	29954	exon7			CACGAGCAGTCAG	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.841G>A	chr14.hg19:g.77765880C>T	ENSP00000261534:p.Ala281Thr	95.0	0.0		124.0	5.0	NM_013382	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	hg19	CCDS9857.1	.	.	.	.	.	.	.	.	.	.	C	36	5.598825	0.96614	.	.	ENSG00000009830	ENST00000261534	D	0.86769	-2.17	5.41	5.41	0.78517	Glycosyl transferase, family 39 (1);	0.000000	0.85682	D	0.000000	D	0.93933	0.8058	M	0.83692	2.655	0.80722	D	1	D	0.76494	0.999	D	0.73708	0.981	D	0.93826	0.7123	10	0.51188	T	0.08	-9.8709	19.187	0.93648	0.0:1.0:0.0:0.0	.	281	Q9UKY4	POMT2_HUMAN	T	281	ENSP00000261534:A281T	ENSP00000261534:A281T	A	-	1	0	POMT2	76835633	1.000000	0.71417	0.996000	0.52242	0.890000	0.51754	7.036000	0.76524	2.515000	0.84797	0.655000	0.94253	GCT	.	.		0.507	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382	
FOXN3	1112	hgsc.bcm.edu	37	14	89878687	89878687	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:89878687A>G	ENST00000345097.4	-	2	250	c.134T>C	c.(133-135)cTg>cCg	p.L45P	FOXN3_ENST00000555353.1_Missense_Mutation_p.L45P|RP11-33N16.3_ENST00000555070.1_RNA|RP11-33N16.2_ENST00000556383.1_RNA|FOXN3_ENST00000261302.5_Missense_Mutation_p.L45P|FOXN3_ENST00000557258.1_Missense_Mutation_p.L45P	NM_001085471.1	NP_001078940.1	O00409	FOXN3_HUMAN	forkhead box N3	45					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GATGTCAGGCAGAGAAAAGTC	0.532																																					p.L45P		Atlas-SNP	.											.	FOXN3	78	.	0			c.T134C						.						90.0	84.0	86.0					14																	89878687		2203	4300	6503	SO:0001583	missense	1112	exon2			TCAGGCAGAGAAA		CCDS32138.1, CCDS41977.1	14q32.11	2012-04-17	2007-05-02	2007-05-02	ENSG00000053254	ENSG00000053254		"""Forkhead boxes"""	1928	protein-coding gene	gene with protein product		602628	"""chromosome 14 open reading frame 116"", ""checkpoint suppressor 1"""	C14orf116, CHES1		9154802	Standard	NM_005197		Approved		uc001xxo.4	O00409	OTTHUMG00000170898	ENST00000345097.4:c.134T>C	chr14.hg19:g.89878687A>G	ENSP00000343288:p.Leu45Pro	92.0	0.0		83.0	4.0	NM_005197	Q96II7|Q9UIE7	Missense_Mutation	SNP	ENST00000345097.4	hg19	CCDS41977.1	.	.	.	.	.	.	.	.	.	.	A	10.09	1.253771	0.22965	.	.	ENSG00000053254	ENST00000345097;ENST00000261302;ENST00000557258;ENST00000555353;ENST00000555855;ENST00000555034;ENST00000553904	T;T;T;T;D	0.95724	-0.03;-0.03;-0.03;-0.03;-3.79	5.29	5.29	0.74685	.	0.000000	0.64402	D	0.000007	D	0.91703	0.7377	L	0.43152	1.355	0.80722	D	1	B;B	0.14805	0.009;0.011	B;B	0.16289	0.004;0.015	D	0.87527	0.2450	10	0.30078	T	0.28	.	9.7105	0.40243	0.9226:0.0:0.0774:0.0	.	45;45	O00409;O00409-2	FOXN3_HUMAN;.	P	45	ENSP00000343288:L45P;ENSP00000261302:L45P;ENSP00000452005:L45P;ENSP00000452227:L45P;ENSP00000451135:L45P	ENSP00000261302:L45P	L	-	2	0	FOXN3	88948440	1.000000	0.71417	0.936000	0.37596	0.329000	0.28539	4.205000	0.58466	2.012000	0.59069	0.528000	0.53228	CTG	.	.		0.532	FOXN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410902.2	NM_005197	
RPS6KA5	9252	hgsc.bcm.edu	37	14	91369167	91369167	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:91369167A>G	ENST00000261991.3	-	9	1277	c.1104T>C	c.(1102-1104)tcT>tcC	p.S368S	RPS6KA5_ENST00000536315.2_Silent_p.S289S|RPS6KA5_ENST00000418736.2_Silent_p.S368S	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	368	AGC-kinase C-terminal.				axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|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 cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|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)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		ACAGCTTCTCAGAACTCTGGG	0.413																																					p.S368S		Atlas-SNP	.											.	RPS6KA5	135	.	0			c.T1104C						.						82.0	75.0	77.0					14																	91369167		2203	4300	6503	SO:0001819	synonymous_variant	9252	exon9			CTTCTCAGAACTC	AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"""ribosomal protein S6 kinase, 90kD, polypeptide 5"""			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.1104T>C	chr14.hg19:g.91369167A>G		168.0	0.0		125.0	5.0	NM_182398	O95316|Q96AF7	Silent	SNP	ENST00000261991.3	hg19	CCDS9893.1																																																																																			.	.		0.413	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755	
GPR68	8111	hgsc.bcm.edu	37	14	91700443	91700443	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:91700443C>T	ENST00000531499.2	-	2	1291	c.952G>A	c.(952-954)Gag>Aag	p.E318K	GPR68_ENST00000238699.3_Missense_Mutation_p.E328K|GPR68_ENST00000529300.1_5'Flank|GPR68_ENST00000535815.1_Missense_Mutation_p.E318K			Q15743	OGR1_HUMAN	G protein-coupled receptor 68	318					cellular response to pH (GO:0071467)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of osteoclast development (GO:2001206)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	8		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)		GGGTAGGCCTCCCTGGCCCGG	0.731																																					p.E318K		Atlas-SNP	.											.	GPR68	32	.	0			c.G952A						.						7.0	10.0	9.0					14																	91700443		1923	3691	5614	SO:0001583	missense	8111	exon2			AGGCCTCCCTGGC	U48405	CCDS9894.1, CCDS9894.2	14q31	2012-08-21				ENSG00000119714		"""GPCR / Class A : Orphans"""	4519	protein-coding gene	gene with protein product		601404				8661159	Standard	NM_001177676		Approved	OGR1	uc001xzg.3	Q15743		ENST00000531499.2:c.952G>A	chr14.hg19:g.91700443C>T	ENSP00000434045:p.Glu318Lys	18.0	0.0		23.0	6.0	NM_001177676	Q13334|Q4VBB4|Q6IX34	Missense_Mutation	SNP	ENST00000531499.2	hg19	CCDS9894.2	.	.	.	.	.	.	.	.	.	.	C	12.55	1.972256	0.34754	.	.	ENSG00000119714	ENST00000531499;ENST00000238699;ENST00000535815;ENST00000529102	T;T;T;T	0.62498	0.03;0.02;0.03;0.04	5.26	3.39	0.38822	.	0.192813	0.31092	N	0.008273	T	0.44932	0.1317	L	0.27053	0.805	0.27758	N	0.943931	B;B	0.19200	0.034;0.034	B;B	0.20577	0.03;0.03	T	0.28299	-1.0048	10	0.22706	T	0.39	.	8.9293	0.35661	0.0:0.7721:0.149:0.0789	.	318;318	Q6NWR5;Q15743	.;OGR1_HUMAN	K	318;328;318;318	ENSP00000434045:E318K;ENSP00000238699:E328K;ENSP00000440797:E318K;ENSP00000432740:E318K	ENSP00000238699:E328K	E	-	1	0	GPR68	90770196	0.992000	0.36948	0.887000	0.34795	0.603000	0.37013	1.735000	0.38176	0.572000	0.29383	0.555000	0.69702	GAG	.	.		0.731	GPR68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395245.2		
SERPINA11	256394	hgsc.bcm.edu	37	14	94914957	94914957	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:94914957G>A	ENST00000334708.3	-	2	219	c.155C>T	c.(154-156)cCc>cTc	p.P52L	RP11-349I1.2_ENST00000536735.1_RNA	NM_001080451.1	NP_001073920.1	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	52					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(14)|skin(1)|upper_aerodigestive_tract(1)	24				COAD - Colon adenocarcinoma(157;0.211)		GGTAATGGTGGGTGTGATTCT	0.567																																					p.P52L		Atlas-SNP	.											.	SERPINA11	53	.	0			c.C155T						.						122.0	134.0	130.0					14																	94914957		2203	4300	6503	SO:0001583	missense	256394	exon2			ATGGTGGGTGTGA	BX248259	CCDS32149.1	14q32.13	2014-02-18	2005-08-18		ENSG00000186910	ENSG00000186910		"""Serine (or cysteine) peptidase inhibitors"""	19193	protein-coding gene	gene with protein product			"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11"""			15014966, 24172014	Standard	NM_001080451		Approved		uc001ydd.1	Q86U17	OTTHUMG00000171348	ENST00000334708.3:c.155C>T	chr14.hg19:g.94914957G>A	ENSP00000335024:p.Pro52Leu	96.0	0.0		92.0	4.0	NM_001080451	B2RV07	Missense_Mutation	SNP	ENST00000334708.3	hg19	CCDS32149.1	.	.	.	.	.	.	.	.	.	.	G	18.43	3.622231	0.66787	.	.	ENSG00000186910	ENST00000334708	D	0.87256	-2.23	4.85	4.85	0.62838	Serpin domain (1);	0.000000	0.64402	D	0.000009	D	0.91643	0.7359	M	0.72894	2.215	0.48830	D	0.999715	D	0.63046	0.992	D	0.63597	0.916	D	0.91936	0.5559	10	0.59425	D	0.04	.	13.5049	0.61479	0.0773:0.0:0.9227:0.0	.	52	Q86U17	SPA11_HUMAN	L	52	ENSP00000335024:P52L	ENSP00000335024:P52L	P	-	2	0	SERPINA11	93984710	1.000000	0.71417	0.999000	0.59377	0.528000	0.34623	5.441000	0.66569	2.516000	0.84829	0.655000	0.94253	CCC	.	.		0.567	SERPINA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413091.1	NM_001080451	
TCL1B	9623	hgsc.bcm.edu	37	14	96157133	96157133	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:96157133T>C	ENST00000340722.7	+	2	274	c.223T>C	c.(223-225)Tcc>Ccc	p.S75P	RP11-1070N10.6_ENST00000461160.1_RNA	NM_004918.3	NP_004909.1	O95988	TCL1B_HUMAN	T-cell leukemia/lymphoma 1B	75										cervix(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		GGAGCTACTCTCCTCCGGCCA	0.582																																					p.S75P		Atlas-SNP	.											.	TCL1B	30	.	0			c.T223C						.						106.0	105.0	105.0					14																	96157133		2203	4300	6503	SO:0001583	missense	9623	exon2			CTACTCTCCTCCG	AB018563	CCDS32151.1	14q32.1	2008-09-05			ENSG00000213231	ENSG00000213231			11649	protein-coding gene	gene with protein product		603769				10077617	Standard	NM_004918		Approved	TML1	uc001yez.3	O95988	OTTHUMG00000028912	ENST00000340722.7:c.223T>C	chr14.hg19:g.96157133T>C	ENSP00000343223:p.Ser75Pro	76.0	0.0		95.0	6.0	NM_004918	A6NEK7|Q6IAR7|Q9UBQ4	Missense_Mutation	SNP	ENST00000340722.7	hg19	CCDS32151.1	.	.	.	.	.	.	.	.	.	.	T	10.42	1.345544	0.24426	.	.	ENSG00000213231	ENST00000340722;ENST00000538038	T	0.28895	1.59	3.0	-2.93	0.05598	.	.	.	.	.	T	0.17152	0.0412	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.25187	-1.0139	9	0.30854	T	0.27	-0.8758	7.98	0.30177	0.0:0.6107:0.0:0.3893	.	75	O95988	TCL1B_HUMAN	P	75	ENSP00000343223:S75P	ENSP00000343223:S75P	S	+	1	0	TCL1B	95226886	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.504000	0.00964	-0.558000	0.06118	0.379000	0.24179	TCC	.	.		0.582	TCL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315123.2		
HSP90AA1	3320	hgsc.bcm.edu	37	14	102551266	102551266	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:102551266T>C	ENST00000216281.8	-	5	938	c.733A>G	c.(733-735)Aaa>Gaa	p.K245E	HSP90AA1_ENST00000441629.2_Missense_Mutation_p.K66E|HSP90AA1_ENST00000334701.7_Missense_Mutation_p.K367E	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	245					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)	p.E366fs*72(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	tctttttctttttcttcttct	0.378																																					p.K367E		Atlas-SNP	.											.,1	HSP90AA1	65	.	1	Deletion - Frameshift(1)	ovary(1)	c.A1099G						.						54.0	51.0	52.0					14																	102551266		2203	4300	6503	SO:0001583	missense	3320	exon6			TTTCTTTTTCTTC	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"""Heat shock proteins / HSPC"""	5253	protein-coding gene	gene with protein product		140571	"""heat shock 90kD protein 1, alpha"", ""heat shock 90kDa protein 1, alpha"""	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.733A>G	chr14.hg19:g.102551266T>C	ENSP00000216281:p.Lys245Glu	249.0	0.0		189.0	9.0	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Missense_Mutation	SNP	ENST00000216281.8	hg19	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	t	2.275	-0.366010	0.05069	.	.	ENSG00000080824	ENST00000216281;ENST00000334701;ENST00000441629	T;T;T	0.57107	0.42;0.42;0.42	4.37	3.22	0.36961	.	0.557487	0.16271	N	0.221780	T	0.23649	0.0572	N	0.04162	-0.26	0.19775	N	0.999954	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.18871	-1.0323	10	0.02654	T	1	-22.5825	9.1829	0.37152	0.0:0.089:0.0:0.911	.	66;367;245	Q86U12;P07900-2;P07900	.;.;HS90A_HUMAN	E	245;367;66	ENSP00000216281:K245E;ENSP00000335153:K367E;ENSP00000396189:K66E	ENSP00000216281:K245E	K	-	1	0	HSP90AA1	101621019	0.810000	0.29049	0.390000	0.26220	0.768000	0.43524	1.460000	0.35244	1.748000	0.51833	0.482000	0.46254	AAA	.	.		0.378	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348	
HSP90AA1	3320	hgsc.bcm.edu	37	14	102551269	102551269	+	Missense_Mutation	SNP	C	C	T	rs3208444		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:102551269C>T	ENST00000216281.8	-	5	935	c.730G>A	c.(730-732)Gaa>Aaa	p.E244K	HSP90AA1_ENST00000441629.2_Missense_Mutation_p.E65K|HSP90AA1_ENST00000334701.7_Missense_Mutation_p.E366K	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	244					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)	p.E366fs*72(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	ttttctttttcttcttctttg	0.383																																					p.E366K		Atlas-SNP	.											.	HSP90AA1	65	.	1	Deletion - Frameshift(1)	ovary(1)	c.G1096A						.						53.0	50.0	51.0					14																	102551269		2203	4300	6503	SO:0001583	missense	3320	exon6			CTTTTTCTTCTTC	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"""Heat shock proteins / HSPC"""	5253	protein-coding gene	gene with protein product		140571	"""heat shock 90kD protein 1, alpha"", ""heat shock 90kDa protein 1, alpha"""	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.730G>A	chr14.hg19:g.102551269C>T	ENSP00000216281:p.Glu244Lys	246.0	0.0		186.0	11.0	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Missense_Mutation	SNP	ENST00000216281.8	hg19	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	c	11.92	1.781836	0.31502	.	.	ENSG00000080824	ENST00000216281;ENST00000334701;ENST00000441629	T;T;T	0.59083	0.29;0.29;0.29	4.37	3.4	0.38934	.	0.579755	0.15072	U	0.282125	T	0.40498	0.1119	N	0.20766	0.605	0.53005	D	0.999964	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.09377	0.003;0.004;0.003	T	0.18713	-1.0328	10	0.15952	T	0.53	-12.6218	13.6002	0.62015	0.0:0.8432:0.1568:0.0	rs3208444	65;366;244	Q86U12;P07900-2;P07900	.;.;HS90A_HUMAN	K	244;366;65	ENSP00000216281:E244K;ENSP00000335153:E366K;ENSP00000396189:E65K	ENSP00000216281:E244K	E	-	1	0	HSP90AA1	101621022	0.009000	0.17119	0.449000	0.26957	0.672000	0.39443	1.078000	0.30754	2.152000	0.67230	0.591000	0.81541	GAA	.	.		0.383	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348	
GPR132	29933	hgsc.bcm.edu	37	14	105517339	105517339	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr14:105517339A>G	ENST00000329797.3	-	4	2046	c.1135T>C	c.(1135-1137)Tcc>Ccc	p.S379P	GPR132_ENST00000392585.2_Missense_Mutation_p.S370P|GPR132_ENST00000546679.1_5'Flank|GPR132_ENST00000539291.2_Missense_Mutation_p.S379P	NM_001278694.1|NM_001278696.1|NM_013345.2	NP_001265623.1|NP_001265625.1|NP_037477.1	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	379					G1/S transition of mitotic cell cycle (GO:0000082)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	18		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		GCTCAGCAGGACTCCTCAATC	0.647																																					p.S379P		Atlas-SNP	.											.	GPR132	40	.	0			c.T1135C						.						58.0	52.0	54.0					14																	105517339		2203	4300	6503	SO:0001583	missense	29933	exon4			AGCAGGACTCCTC	AF083955	CCDS9997.1, CCDS61567.1	14q32.3	2012-08-21			ENSG00000183484	ENSG00000183484		"""GPCR / Class A : Orphans"""	17482	protein-coding gene	gene with protein product	"""G2 accumulation"""	606167				12086852	Standard	NM_013345		Approved	G2A	uc001yqd.3	Q9UNW8	OTTHUMG00000140173	ENST00000329797.3:c.1135T>C	chr14.hg19:g.105517339A>G	ENSP00000328818:p.Ser379Pro	124.0	0.0		99.0	5.0	NM_013345	A8K7X7|B4E144|Q9BSU2	Missense_Mutation	SNP	ENST00000329797.3	hg19	CCDS9997.1	.	.	.	.	.	.	.	.	.	.	A	11.91	1.780763	0.31502	.	.	ENSG00000183484	ENST00000329797;ENST00000392585;ENST00000539291	T;T;T	0.38887	1.11;1.14;1.11	2.56	-2.83	0.05769	.	1.607050	0.04698	N	0.415371	T	0.24044	0.0582	N	0.19112	0.55	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.08055	0.003;0.003	T	0.11792	-1.0573	10	0.33141	T	0.24	.	3.4172	0.07380	0.3461:0.0:0.4416:0.2122	.	370;379	B4E144;Q9UNW8	.;GP132_HUMAN	P	379;370;379	ENSP00000328818:S379P;ENSP00000376364:S370P;ENSP00000438094:S379P	ENSP00000328818:S379P	S	-	1	0	GPR132	104588384	0.000000	0.05858	0.003000	0.11579	0.558000	0.35554	-1.056000	0.03489	-0.692000	0.05128	0.379000	0.24179	TCC	.	.		0.647	GPR132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409278.1	NM_013345	
MKRN3	7681	hgsc.bcm.edu	37	15	23811668	23811668	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:23811668G>A	ENST00000314520.3	+	1	1215	c.739G>A	c.(739-741)Gct>Act	p.A247T	MKRN3_ENST00000568252.1_Intron|MKRN3_ENST00000568945.1_3'UTR|RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000564592.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	247					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		TTGCTATTATGCTTCCAGGGG	0.577																																					p.A247T		Atlas-SNP	.											MKRN3,right_upper_lobe,carcinoma,0,1	MKRN3	155	.	0			c.G739A						.						99.0	105.0	103.0					15																	23811668		2203	4300	6503	SO:0001583	missense	7681	exon1			TATTATGCTTCCA	U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"""RING-type (C3HC4) zinc fingers"""	7114	protein-coding gene	gene with protein product	"""zinc finger protein 127"""	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.739G>A	chr15.hg19:g.23811668G>A	ENSP00000313881:p.Ala247Thr	69.0	0.0		66.0	3.0	NM_005664		Missense_Mutation	SNP	ENST00000314520.3	hg19	CCDS10013.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.653168	0.47362	.	.	ENSG00000179455	ENST00000314520	T	0.41758	0.99	4.07	3.14	0.36123	Zinc finger, CCCH-type (2);	0.241045	0.40222	N	0.001143	T	0.66973	0.2844	M	0.91717	3.235	0.58432	D	0.999992	D	0.89917	1.0	D	0.72075	0.976	T	0.70447	-0.4869	10	0.33141	T	0.24	.	11.4389	0.50086	0.0:0.0:0.8184:0.1815	.	247	Q13064	MKRN3_HUMAN	T	247	ENSP00000313881:A247T	ENSP00000313881:A247T	A	+	1	0	MKRN3	21362761	1.000000	0.71417	0.024000	0.17045	0.005000	0.04900	7.156000	0.77453	1.288000	0.44600	-0.182000	0.12963	GCT	.	.		0.577	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664	
HERC2	8924	hgsc.bcm.edu	37	15	28493786	28493786	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:28493786A>G	ENST00000261609.7	-	21	3255	c.3147T>C	c.(3145-3147)gcT>gcC	p.A1049A		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		AATCCAATGAAGCAGATCTTT	0.388																																					p.A1049A		Atlas-SNP	.											.	HERC2	501	.	0			c.T3147C						.						104.0	94.0	98.0					15																	28493786		2203	4300	6503	SO:0001819	synonymous_variant	8924	exon21			CAATGAAGCAGAT	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.3147T>C	chr15.hg19:g.28493786A>G		125.0	0.0		82.0	4.0	NM_004667		Silent	SNP	ENST00000261609.7	hg19	CCDS10021.1																																																																																			.	.		0.388	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
FAM189A1	23359	hgsc.bcm.edu	37	15	29488731	29488731	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:29488731T>C	ENST00000261275.4	-	4	424	c.425A>G	c.(424-426)gAg>gGg	p.E142G		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	142						integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						GTGCTGCAGCTCACAGCAGAC	0.577																																					p.E142G		Atlas-SNP	.											FAM189A1,colon,carcinoma,0,1	FAM189A1	20	.	0			c.A425G						.						115.0	95.0	101.0					15																	29488731		692	1591	2283	SO:0001583	missense	23359	exon4			TGCAGCTCACAGC		CCDS45198.1	15q12	2014-02-12				ENSG00000104059			29075	protein-coding gene	gene with protein product	"""transmembrane protein 228"""					9628581	Standard	NM_015307		Approved	KIAA0574, TMEM228	uc010azk.1	O60320		ENST00000261275.4:c.425A>G	chr15.hg19:g.29488731T>C	ENSP00000261275:p.Glu142Gly	111.0	1.0		109.0	5.0	NM_015307	A0PK09	Missense_Mutation	SNP	ENST00000261275.4	hg19	CCDS45198.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.815317	0.90790	.	.	ENSG00000104059	ENST00000261275	T	0.03580	3.88	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.13543	0.0328	L	0.50333	1.59	0.54753	D	0.999981	D	0.89917	1.0	D	0.83275	0.996	T	0.00453	-1.1730	10	0.59425	D	0.04	-19.7164	13.6478	0.62292	0.0:0.0:0.0:1.0	.	142	O60320	F1891_HUMAN	G	142	ENSP00000261275:E142G	ENSP00000261275:E142G	E	-	2	0	FAM189A1	27276023	1.000000	0.71417	0.939000	0.37840	0.976000	0.68499	7.058000	0.76676	2.104000	0.64026	0.533000	0.62120	GAG	.	.		0.577	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
FMN1	342184	hgsc.bcm.edu	37	15	33359640	33359640	+	Intron	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:33359640T>C	ENST00000559047.1	-	3	2043				FMN1_ENST00000334528.9_Missense_Mutation_p.D149G|FMN1_ENST00000558197.1_Missense_Mutation_p.D149G|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000561249.1_Intron			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		ATCATCAGAGTCAGAATCACT	0.517																																					p.D149G		Atlas-SNP	.											.	FMN1	174	.	0			c.A446G						.						74.0	75.0	75.0					15																	33359640		2019	4180	6199	SO:0001627	intron_variant	342184	exon1			TCAGAGTCAGAAT	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-2365A>G	chr15.hg19:g.33359640T>C		124.0	0.0		94.0	5.0	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.79	2.343388	0.41498	.	.	ENSG00000248905	ENST00000334528	T	0.41400	1.0	5.66	4.48	0.54585	.	.	.	.	.	T	0.60117	0.2244	.	.	.	.	.	.	D;D	0.76494	0.999;0.961	D;P	0.65443	0.935;0.616	T	0.71076	-0.4697	7	0.56958	D	0.05	.	12.455	0.55700	0.0:0.0:0.1398:0.8602	.	149;149	Q68DA7-3;Q68DA7-5	.;.	G	149	ENSP00000333950:D149G	ENSP00000333950:D149G	D	-	2	0	FMN1	31146932	0.921000	0.31238	0.797000	0.32132	0.676000	0.39594	2.169000	0.42434	2.157000	0.67596	0.533000	0.62120	GAC	.	.		0.517	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
PGBD4	161779	hgsc.bcm.edu	37	15	34395101	34395101	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:34395101A>G	ENST00000397766.2	+	1	828	c.369A>G	c.(367-369)gaA>gaG	p.E123E	EMC7_ENST00000256545.4_5'Flank|EMC7_ENST00000532113.1_5'Flank	NM_152595.4	NP_689808.2	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	123										breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)|prostate(1)	16		all_lung(180;1.76e-08)		all cancers(64;1.22e-17)|GBM - Glioblastoma multiforme(113;1.78e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0242)		TTACTAGAGAAACAAATGCCC	0.428																																					p.E123E		Atlas-SNP	.											.	PGBD4	58	.	0			c.A369G						.						53.0	55.0	54.0					15																	34395101		2201	4298	6499	SO:0001819	synonymous_variant	161779	exon1			TAGAGAAACAAAT	AK057200	CCDS10033.1	15q13.1	2002-10-25			ENSG00000182405	ENSG00000182405			19401	protein-coding gene	gene with protein product							Standard	NM_152595		Approved	FLJ32638, FLJ37497	uc001zho.3	Q96DM1	OTTHUMG00000129370	ENST00000397766.2:c.369A>G	chr15.hg19:g.34395101A>G		118.0	0.0		78.0	4.0	NM_152595	A1L487|A8K0C6|Q8N9E8	Silent	SNP	ENST00000397766.2	hg19	CCDS10033.1																																																																																			.	.		0.428	PGBD4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251522.1		
NUTM1	256646	hgsc.bcm.edu	37	15	34640689	34640689	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:34640689G>A	ENST00000333756.4	+	2	691	c.536G>A	c.(535-537)tGg>tAg	p.W179*	NUTM1_ENST00000537011.1_Nonsense_Mutation_p.W207*|NUTM1_ENST00000438749.3_Nonsense_Mutation_p.W197*	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	179	Pro-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)											GAAAAAGCTTGGCCAGGGCCA	0.587																																					p.W179X		Atlas-SNP	.											.	C15orf55	110	.	0			c.G536A						.						32.0	32.0	32.0					15																	34640689		2201	4298	6499	SO:0001587	stop_gained	256646	exon2			AAGCTTGGCCAGG	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"""nuclear protein in testis"""	608963	"""chromosome 15 open reading frame 55"""	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.536G>A	chr15.hg19:g.34640689G>A	ENSP00000329448:p.Trp179*	63.0	0.0		56.0	4.0	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Nonsense_Mutation	SNP	ENST00000333756.4	hg19	CCDS32190.1	.	.	.	.	.	.	.	.	.	.	G	36	5.907219	0.97093	.	.	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000354999;ENST00000333756	.	.	.	5.69	3.83	0.44106	.	0.000000	0.53938	D	0.000044	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	9.4628	0.38796	0.0767:0.1425:0.7808:0.0	.	.	.	.	X	207;197;179;179	.	ENSP00000329448:W179X	W	+	2	0	C15orf55	32427981	1.000000	0.71417	0.995000	0.50966	0.099000	0.18886	2.375000	0.44283	0.775000	0.33450	-0.126000	0.14955	TGG	.	.		0.587	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741	
C15orf41	84529	hgsc.bcm.edu	37	15	37001438	37001438	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:37001438C>A	ENST00000566621.1	+	9	809	c.559C>A	c.(559-561)Cgt>Agt	p.R187S	C15orf41_ENST00000565792.1_3'UTR|C15orf41_ENST00000562489.1_Missense_Mutation_p.R11S|C15orf41_ENST00000567389.1_Missense_Mutation_p.R89S|C15orf41_ENST00000437989.2_Missense_Mutation_p.R187S|C15orf41_ENST00000562877.1_Missense_Mutation_p.R89S|C15orf41_ENST00000338183.4_Missense_Mutation_p.R89S|C15orf41_ENST00000569302.1_Missense_Mutation_p.R187S	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	187										kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		AGATCAGCTTCGTGCAAAGGG	0.299																																					p.R187S		Atlas-SNP	.											.	C15orf41	24	.	0			c.C559A						.						100.0	97.0	98.0					15																	37001438		1821	4075	5896	SO:0001583	missense	84529	exon9			CAGCTTCGTGCAA	BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.559C>A	chr15.hg19:g.37001438C>A	ENSP00000455397:p.Arg187Ser	153.0	0.0		93.0	4.0	NM_001130010	B2RD87	Missense_Mutation	SNP	ENST00000566621.1	hg19	CCDS45215.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.484981	0.63962	.	.	ENSG00000186073	ENST00000437989;ENST00000338183	T	0.68025	-0.3	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.84727	0.5536	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86020	0.1506	10	0.72032	D	0.01	-11.6817	20.0359	0.97557	0.0:1.0:0.0:0.0	.	187	Q9Y2V0	CO041_HUMAN	S	187;89	ENSP00000401362:R187S	ENSP00000342433:R89S	R	+	1	0	C15orf41	34788730	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.933000	0.70130	2.805000	0.96524	0.655000	0.94253	CGT	.	.		0.299	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499	
EXD1	161829	hgsc.bcm.edu	37	15	41482300	41482300	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:41482300T>C	ENST00000314992.5	-	9	907	c.717A>G	c.(715-717)cgA>cgG	p.R239R	EXD1_ENST00000458580.2_Silent_p.R297R|RN7SL497P_ENST00000476341.2_RNA	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	239							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						GTGAAACAGGTCGGATGAACC	0.428																																					p.R239R		Atlas-SNP	.											.	EXD1	52	.	0			c.A717G						.						118.0	119.0	119.0					15																	41482300		2203	4300	6503	SO:0001819	synonymous_variant	161829	exon9			AACAGGTCGGATG	BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"""exonuclease 3'-5' domain-like 1"""	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.717A>G	chr15.hg19:g.41482300T>C		98.0	0.0		90.0	4.0	NM_152596	A8K909|B7Z839|Q6ZW94	Silent	SNP	ENST00000314992.5	hg19	CCDS10072.1																																																																																			.	.		0.428	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596	
RPAP1	26015	hgsc.bcm.edu	37	15	41819624	41819624	+	Silent	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:41819624G>T	ENST00000304330.4	-	12	1724	c.1608C>A	c.(1606-1608)atC>atA	p.I536I	RPAP1_ENST00000561603.1_Silent_p.I536I|RPAP1_ENST00000568413.1_5'Flank	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	536						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CCTTTACCTTGATGACATCAT	0.542																																					p.I536I		Atlas-SNP	.											.	RPAP1	111	.	0			c.C1608A						.						89.0	90.0	90.0					15																	41819624		2203	4300	6503	SO:0001819	synonymous_variant	26015	exon12			TACCTTGATGACA	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.1608C>A	chr15.hg19:g.41819624G>T		117.0	0.0		96.0	4.0	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Silent	SNP	ENST00000304330.4	hg19	CCDS10079.1																																																																																			.	.		0.542	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
SPTBN5	51332	hgsc.bcm.edu	37	15	42167762	42167762	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:42167762A>G	ENST00000320955.6	-	22	4408	c.4181T>C	c.(4180-4182)cTt>cCt	p.L1394P		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1394					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CAGGCCTTGAAGCCTGGTCTG	0.587																																					p.L1359P		Atlas-SNP	.											.	SPTBN5	171	.	0			c.T4076C						.						49.0	53.0	52.0					15																	42167762		2097	4212	6309	SO:0001583	missense	51332	exon22			CCTTGAAGCCTGG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.4181T>C	chr15.hg19:g.42167762A>G	ENSP00000317790:p.Leu1394Pro	117.0	0.0		97.0	4.0	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	12.15	1.850211	0.32699	.	.	ENSG00000137877	ENST00000320955	T	0.56611	0.45	5.48	5.48	0.80851	.	0.374643	0.23228	N	0.050497	T	0.73337	0.3574	M	0.81942	2.565	0.18873	N	0.999982	D	0.89917	1.0	D	0.75020	0.985	T	0.68704	-0.5338	10	0.87932	D	0	.	14.5835	0.68308	1.0:0.0:0.0:0.0	.	1394	Q9NRC6	SPTN5_HUMAN	P	1394	ENSP00000317790:L1394P	ENSP00000317790:L1394P	L	-	2	0	SPTBN5	39955054	0.166000	0.22962	0.053000	0.19242	0.005000	0.04900	2.641000	0.46587	2.073000	0.62155	0.529000	0.55759	CTT	.	.		0.587	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
TMEM87A	25963	hgsc.bcm.edu	37	15	42531866	42531866	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:42531866A>G	ENST00000389834.4	-	8	949		c.e8+1		TMEM87A_ENST00000448392.1_Splice_Site	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A							integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		AAAGTCACTTACAATCATCAA	0.368																																					.		Atlas-SNP	.											.	TMEM87A	56	.	0			c.684+2T>C						.						122.0	122.0	122.0					15																	42531866		2203	4298	6501	SO:0001630	splice_region_variant	25963	exon9			TCACTTACAATCA	AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.684+1T>C	chr15.hg19:g.42531866A>G		99.0	0.0		82.0	4.0	NM_015497	Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Splice_Site	SNP	ENST00000389834.4	hg19	CCDS32205.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.531829	0.85706	.	.	ENSG00000103978	ENST00000389834;ENST00000448392;ENST00000535305	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1026	0.72292	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM87A	40319158	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.557000	0.90700	2.140000	0.66376	0.482000	0.46254	.	.	.		0.368	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2	NM_015497	Intron
HYPK	25764	hgsc.bcm.edu	37	15	44093963	44093963	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:44093963A>G	ENST00000406925.1	+	5	4460	c.349A>G	c.(349-351)Atg>Gtg	p.M117V	SERINC4_ENST00000249714.3_5'Flank|SERINC4_ENST00000319327.6_5'Flank|SERF2_ENST00000594896.1_Missense_Mutation_p.M163V|HYPK_ENST00000442995.2_Missense_Mutation_p.M117V|SERF2_ENST00000600633.1_Missense_Mutation_p.M117V|RP11-296A16.1_ENST00000417761.2_5'Flank|HYPK_ENST00000458412.1_3'UTR|SERINC4_ENST00000299969.6_5'Flank			Q9NX55	HYPK_HUMAN	huntingtin interacting protein K	117						cytoplasm (GO:0005737)|nucleus (GO:0005634)							all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		GBM - Glioblastoma multiforme(94;8.1e-07)		GCGGGAACACATGGGCAACGT	0.418																																					p.M117V		Atlas-SNP	.											.	.	.	.	0			c.A349G						.						97.0	90.0	92.0					15																	44093963		2198	4298	6496	SO:0001583	missense	25764	exon4			GAACACATGGGCA	AF049613	CCDS10104.1	15q14	2012-10-08	2012-10-08	2012-10-08	ENSG00000242028	ENSG00000242028			18418	protein-coding gene	gene with protein product	"""Huntingtin yeast partner K"""	612784	"""chromosome 15 open reading frame 63"""	C15orf63		9700202, 20154145	Standard	NM_016400		Approved	HSPC136, FLJ20431	uc001ztf.3	Q9NX55	OTTHUMG00000060146	ENST00000406925.1:c.349A>G	chr15.hg19:g.44093963A>G	ENSP00000384474:p.Met117Val	81.0	0.0		97.0	4.0	NM_016400	C9JKJ0|O75408|Q8WUW8|Q9P024	Missense_Mutation	SNP	ENST00000406925.1	hg19	CCDS10104.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.494575	0.64186	.	.	ENSG00000242028	ENST00000406925;ENST00000442995	T;T	0.43688	0.94;0.94	5.34	5.34	0.76211	.	0.071805	0.85682	D	0.000000	T	0.34279	0.0892	L	0.36672	1.1	0.80722	D	1	B	0.27117	0.168	B	0.22386	0.039	T	0.09100	-1.0690	10	0.31617	T	0.26	-26.6856	15.4877	0.75578	1.0:0.0:0.0:0.0	.	117	Q9NX55	HYPK_HUMAN	V	117	ENSP00000384474:M117V;ENSP00000401155:M117V	ENSP00000384474:M117V	M	+	1	0	C15orf63	41881255	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.919000	0.70005	2.248000	0.74166	0.533000	0.62120	ATG	.	.		0.418	HYPK-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133876.3	NM_016400	
SHF	90525	hgsc.bcm.edu	37	15	45467612	45467612	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:45467612A>G	ENST00000560734.1	-	3	652	c.652T>C	c.(652-654)Tcc>Ccc	p.S218P	SHF_ENST00000560540.1_Missense_Mutation_p.S218P|SHF_ENST00000561091.1_5'UTR|SHF_ENST00000318390.6_Missense_Mutation_p.S210P|SHF_ENST00000290894.8_Missense_Mutation_p.S153P|SHF_ENST00000458022.2_Missense_Mutation_p.S16P|RP11-519G16.2_ENST00000560034.1_RNA|SHF_ENST00000560471.1_Missense_Mutation_p.S218P					Src homology 2 domain containing F											endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		GTCTCCTTGGAGCCCCGGATC	0.637																																					p.S153P		Atlas-SNP	.											.	SHF	27	.	0			c.T457C						.						35.0	28.0	31.0					15																	45467612		2195	4296	6491	SO:0001583	missense	90525	exon4			CCTTGGAGCCCCG	BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606		"""SH2 domain containing"""	25116	protein-coding gene	gene with protein product						11095946	Standard	NM_138356		Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000560734.1:c.652T>C	chr15.hg19:g.45467612A>G	ENSP00000453168:p.Ser218Pro	75.0	0.0		75.0	4.0	NM_138356		Missense_Mutation	SNP	ENST00000560734.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.94	1.492540	0.26774	.	.	ENSG00000138606	ENST00000290894;ENST00000361989;ENST00000318390;ENST00000458022;ENST00000413198	T;T;T	0.30448	1.53;1.53;1.53	5.25	5.25	0.73442	.	0.201227	0.44483	D	0.000455	T	0.47303	0.1438	L	0.58510	1.815	0.34878	D	0.744315	D;D;B;B;B	0.71674	0.983;0.998;0.023;0.039;0.023	P;P;B;B;B	0.62649	0.791;0.905;0.007;0.028;0.017	T	0.58885	-0.7557	10	0.36615	T	0.2	-10.114	13.1129	0.59283	1.0:0.0:0.0:0.0	.	16;153;143;210;153	Q8N9I8;E7EV73;E7EWB7;F8W6K9;Q7M4L6	.;.;.;.;SHF_HUMAN	P	153;153;210;16;143	ENSP00000290894:S153P;ENSP00000315978:S210P;ENSP00000411530:S16P	ENSP00000290894:S153P	S	-	1	0	SHF	43254904	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.330000	0.52068	1.981000	0.57761	0.402000	0.26972	TCC	.	.		0.637	SHF-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000416338.1	NM_138356	
SQRDL	58472	hgsc.bcm.edu	37	15	45965905	45965905	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:45965905A>G	ENST00000260324.7	+	5	946	c.560A>G	c.(559-561)gAg>gGg	p.E187G	SQRDL_ENST00000568606.1_Missense_Mutation_p.E187G|RP11-96O20.4_ENST00000564080.1_Missense_Mutation_p.E187G	NM_021199.3	NP_067022.1	Q9Y6N5	SQRD_HUMAN	sulfide quinone reductase-like (yeast)	187					cellular nitrogen compound metabolic process (GO:0034641)|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)	mitochondrial inner membrane (GO:0005743)	sulfide:quinone oxidoreductase activity (GO:0070224)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	11		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		GACTTCAAAGAGGGCAATGCC	0.453																																					p.E187G		Atlas-SNP	.											.	SQRDL	27	.	0			c.A560G						.						140.0	128.0	132.0					15																	45965905		2198	4297	6495	SO:0001583	missense	58472	exon5			TCAAAGAGGGCAA	AF042284	CCDS10127.1	15q21.1	2010-08-05			ENSG00000137767	ENSG00000137767			20390	protein-coding gene	gene with protein product						10810093, 10224084	Standard	NM_021199		Approved	CGI-44	uc001zvu.4	Q9Y6N5	OTTHUMG00000131476	ENST00000260324.7:c.560A>G	chr15.hg19:g.45965905A>G	ENSP00000260324:p.Glu187Gly	130.0	0.0		109.0	5.0	NM_021199	Q9UQM8	Missense_Mutation	SNP	ENST00000260324.7	hg19	CCDS10127.1	.	.	.	.	.	.	.	.	.	.	A	6.130	0.392133	0.11581	.	.	ENSG00000137767	ENST00000260324	T	0.45276	0.9	5.62	5.62	0.85841	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.094126	0.64402	D	0.000001	T	0.16385	0.0394	N	0.01576	-0.805	0.51012	D	0.999908	B	0.02656	0.0	B	0.11329	0.006	T	0.20672	-1.0268	10	0.02654	T	1	-10.0801	14.6676	0.68921	1.0:0.0:0.0:0.0	.	187	Q9Y6N5	SQRD_HUMAN	G	187	ENSP00000260324:E187G	ENSP00000260324:E187G	E	+	2	0	SQRDL	43753197	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	7.338000	0.79269	2.146000	0.66826	0.460000	0.39030	GAG	.	.		0.453	SQRDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254319.2		
DTWD1	56986	hgsc.bcm.edu	37	15	49935632	49935632	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:49935632C>T	ENST00000251250.6	+	6	979	c.772C>T	c.(772-774)Ctg>Ttg	p.L258L	DTWD1_ENST00000403028.3_Silent_p.L258L|DTWD1_ENST00000415425.1_Silent_p.L171L|DTWD1_ENST00000558653.1_Silent_p.L258L	NM_020234.5	NP_064619.2	Q8N5C7	DTWD1_HUMAN	DTW domain containing 1	258										endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;0.0384)		all cancers(107;3.27e-08)|GBM - Glioblastoma multiforme(94;7.6e-05)		TTACTACTTTCTGGTAGACTA	0.323																																					p.L258L		Atlas-SNP	.											.	DTWD1	22	.	0			c.C772T						.						57.0	63.0	61.0					15																	49935632		2194	4293	6487	SO:0001819	synonymous_variant	56986	exon5			TACTTTCTGGTAG	BC032535	CCDS10132.1	15q21.2	2005-08-09			ENSG00000104047	ENSG00000104047			30926	protein-coding gene	gene with protein product							Standard	NM_020234		Approved	MDS009, MGC111207	uc001zxs.3	Q8N5C7	OTTHUMG00000131567	ENST00000251250.6:c.772C>T	chr15.hg19:g.49935632C>T		255.0	0.0		220.0	13.0	NM_001144955	Q567Q3|Q8WVG9|Q9NRU6	Silent	SNP	ENST00000251250.6	hg19	CCDS10132.1																																																																																			.	.		0.323	DTWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254431.2	NM_020234	
UNC13C	440279	hgsc.bcm.edu	37	15	54529885	54529885	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:54529885A>G	ENST00000260323.11	+	6	3225	c.3225A>G	c.(3223-3225)gaA>gaG	p.E1075E	UNC13C_ENST00000537900.1_Silent_p.E1073E|UNC13C_ENST00000545554.1_Silent_p.E1075E	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1075					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)		ATAATGAGGAACTGGTAAGTA	0.388																																					p.E1075E		Atlas-SNP	.											.	UNC13C	674	.	0			c.A3225G						.						77.0	73.0	74.0					15																	54529885		1885	4093	5978	SO:0001819	synonymous_variant	440279	exon5			TGAGGAACTGGTA	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.3225A>G	chr15.hg19:g.54529885A>G		112.0	0.0		82.0	4.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.		0.388	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
UNC13C	440279	hgsc.bcm.edu	37	15	54707196	54707196	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:54707196A>T	ENST00000260323.11	+	18	4864	c.4864A>T	c.(4864-4866)Aac>Tac	p.N1622Y	UNC13C_ENST00000537900.1_Missense_Mutation_p.N1620Y|UNC13C_ENST00000545554.1_Missense_Mutation_p.N1622Y	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1622					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)		TCAAGAGCTGAACATGGGAAA	0.303																																					p.N1622Y		Atlas-SNP	.											.	UNC13C	674	.	0			c.A4864T						.						101.0	100.0	100.0					15																	54707196		1815	4066	5881	SO:0001583	missense	440279	exon17			GAGCTGAACATGG	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.4864A>T	chr15.hg19:g.54707196A>T	ENSP00000260323:p.Asn1622Tyr	125.0	0.0		111.0	5.0	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	hg19	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.330404	0.81690	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.82081	-1.57;-1.57;-1.57	5.61	5.61	0.85477	Calcium-dependent secretion activator (1);	0.092243	0.64402	D	0.000001	D	0.91509	0.7319	M	0.85945	2.785	0.54753	D	0.999988	D;D	0.89917	1.0;1.0	D;D	0.91635	0.99;0.999	D	0.92734	0.6202	10	0.87932	D	0	.	13.7525	0.62917	1.0:0.0:0.0:0.0	.	1622;1622	F5H090;Q8NB66	.;UN13C_HUMAN	Y	1622;1622;1620	ENSP00000260323:N1622Y;ENSP00000438156:N1622Y;ENSP00000442569:N1620Y	ENSP00000260323:N1622Y	N	+	1	0	UNC13C	52494488	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.489000	0.90461	2.138000	0.66242	0.533000	0.62120	AAC	.	.		0.303	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
TPM1	7168	hgsc.bcm.edu	37	15	63349281	63349281	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:63349281T>C	ENST00000403994.3	+	3	418	c.338T>C	c.(337-339)cTg>cCg	p.L113P	TPM1_ENST00000317516.7_Missense_Mutation_p.L77P|TPM1_ENST00000334895.5_Missense_Mutation_p.L77P|TPM1_ENST00000560959.1_Missense_Mutation_p.L77P|TPM1_ENST00000288398.6_Missense_Mutation_p.L113P|TPM1_ENST00000559397.1_Missense_Mutation_p.L113P|TPM1_ENST00000404484.4_Missense_Mutation_p.L77P|TPM1_ENST00000559281.1_Missense_Mutation_p.L77P|TPM1_ENST00000357980.4_Missense_Mutation_p.L155P|TPM1_ENST00000358278.3_Missense_Mutation_p.L113P|TPM1_ENST00000267996.7_Missense_Mutation_p.L113P|TPM1_ENST00000559556.1_Missense_Mutation_p.L113P|TPM1_ENST00000560445.1_Intron	NM_001018005.1	NP_001018005.1	P09493	TPM1_HUMAN	tropomyosin 1 (alpha)	113					cardiac muscle contraction (GO:0060048)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|negative regulation of cell migration (GO:0030336)|positive regulation of ATPase activity (GO:0032781)|positive regulation of cell adhesion (GO:0045785)|positive regulation of heart rate by epinephrine (GO:0003065)|positive regulation of stress fiber assembly (GO:0051496)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|ruffle organization (GO:0031529)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|wound healing (GO:0042060)	bleb (GO:0032059)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|muscle thin filament tropomyosin (GO:0005862)|ruffle membrane (GO:0032587)|sarcomere (GO:0030017)|stress fiber (GO:0001725)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(1)|large_intestine(1)|lung(2)	4						TTGCAGAAGCTGGAGGAAGCT	0.547																																					p.L113P		Atlas-SNP	.											.	TPM1	59	.	0			c.T338C						.						103.0	97.0	99.0					15																	63349281		2203	4300	6503	SO:0001583	missense	7168	exon3			AGAAGCTGGAGGA	AB209041	CCDS10181.1, CCDS32262.1, CCDS32263.1, CCDS32264.1, CCDS45273.1, CCDS58368.1, CCDS58369.1	15q22.1	2014-09-17			ENSG00000140416	ENSG00000140416		"""Tropomyosins"""	12010	protein-coding gene	gene with protein product		191010	"""chromosome 15 open reading frame 13"", ""cardiomyopathy, hypertrophic 3"""	C15orf13, CMH3		10343096, 8205619	Standard	XM_005254637		Approved		uc002all.3	P09493	OTTHUMG00000132803	ENST00000403994.3:c.338T>C	chr15.hg19:g.63349281T>C	ENSP00000385107:p.Leu113Pro	86.0	0.0		84.0	4.0	NM_001018007	B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	Missense_Mutation	SNP	ENST00000403994.3	hg19	CCDS45273.1	.	.	.	.	.	.	.	.	.	.	T	18.60	3.658219	0.67586	.	.	ENSG00000140416	ENST00000288398;ENST00000267996;ENST00000358278;ENST00000403994;ENST00000357980;ENST00000404484;ENST00000334895;ENST00000317516	D;D;D;D;D;D	0.99194	-5.54;-5.54;-5.54;-5.54;-5.54;-5.54	5.72	5.72	0.89469	.	0.000000	0.41001	D	0.000979	D	0.99641	0.9868	H	0.99299	4.505	0.80722	D	1	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;0.998;1.0;1.0;0.998;0.998;1.0;1.0;0.998	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;0.995;1.0;1.0;1.0;0.994;1.0;0.998;0.991;0.997;0.996;1.0;0.994	D	0.97366	0.9973	10	0.87932	D	0	-11.1461	15.1809	0.72956	0.0:0.0:0.0:1.0	.	77;77;113;79;77;77;113;155;113;113;113;113;113;113	B7Z722;B7Z596;P09493-6;F5H7S3;D9YZV7;Q1ZYL5;D9YZV4;Q6ZN40;D9YZV8;D9YZV5;Q9Y427;D9YZV3;D9YZV2;P09493	.;.;.;.;.;.;.;.;.;.;.;.;.;TPM1_HUMAN	P	113;113;113;113;155;135;77;79	ENSP00000288398:L113P;ENSP00000267996:L113P;ENSP00000351022:L113P;ENSP00000385107:L113P;ENSP00000350667:L155P;ENSP00000334624:L77P	ENSP00000267996:L113P	L	+	2	0	TPM1	61136334	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.040000	0.89188	2.187000	0.69744	0.482000	0.46254	CTG	.	.		0.547	TPM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000417083.2	NM_001018004	
ANKDD1A	348094	hgsc.bcm.edu	37	15	65219192	65219192	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:65219192A>G	ENST00000380230.3	+	6	593	c.564A>G	c.(562-564)aaA>aaG	p.K188K	ANKDD1A_ENST00000357698.3_Silent_p.K188K|ANKDD1A_ENST00000496660.1_Silent_p.K97K|ANKDD1A_ENST00000491145.1_3'UTR|ANKDD1A_ENST00000319580.8_3'UTR|AC069368.3_ENST00000437723.1_Intron|ANKDD1A_ENST00000395720.1_Silent_p.K188K|ANKDD1A_ENST00000395723.1_Silent_p.K97K	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	188					signal transduction (GO:0007165)					NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						ACAATGTCAAAGACAAGGTAC	0.617																																					p.K188K		Atlas-SNP	.											.	ANKDD1A	47	.	0			c.A564G						.						111.0	93.0	99.0					15																	65219192		2202	4299	6501	SO:0001819	synonymous_variant	348094	exon6			TGTCAAAGACAAG		CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"""Ankyrin repeat domain containing"""	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.564A>G	chr15.hg19:g.65219192A>G		112.0	0.0		63.0	4.0	NM_182703	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Silent	SNP	ENST00000380230.3	hg19	CCDS10197.2																																																																																			.	.		0.617	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703	
CILP	8483	hgsc.bcm.edu	37	15	65499173	65499173	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:65499173T>C	ENST00000261883.4	-	4	537	c.371A>G	c.(370-372)cAg>cGg	p.Q124R		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	124					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						GCCAGGCCGCTGCTCCCTGTT	0.642																																					p.Q124R		Atlas-SNP	.											.	CILP	124	.	0			c.A371G						.						56.0	59.0	58.0					15																	65499173		2201	4299	6500	SO:0001583	missense	8483	exon4			GGCCGCTGCTCCC	AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.371A>G	chr15.hg19:g.65499173T>C	ENSP00000261883:p.Gln124Arg	60.0	0.0		45.0	4.0	NM_003613	B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	hg19	CCDS10203.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.190444	0.78789	.	.	ENSG00000138615	ENST00000261883	T	0.22743	1.94	5.3	5.3	0.74995	.	0.246394	0.43747	D	0.000532	T	0.44932	0.1317	M	0.94101	3.495	0.58432	D	0.999996	D	0.53312	0.959	P	0.50109	0.631	T	0.57619	-0.7780	10	0.45353	T	0.12	-4.0081	13.2541	0.60068	0.0:0.0:0.0:1.0	.	124	O75339	CILP1_HUMAN	R	124	ENSP00000261883:Q124R	ENSP00000261883:Q124R	Q	-	2	0	CILP	63286226	1.000000	0.71417	0.997000	0.53966	0.550000	0.35303	7.756000	0.85195	2.231000	0.72958	0.459000	0.35465	CAG	.	.		0.642	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613	
ITGA11	22801	hgsc.bcm.edu	37	15	68599732	68599732	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:68599732T>C	ENST00000315757.7	-	28	3421	c.3335A>G	c.(3334-3336)cAg>cGg	p.Q1112R	ITGA11_ENST00000423218.2_Missense_Mutation_p.Q1113R	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	1112					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						GCTGTGGAACTGCCTCTGCAA	0.572											OREG0023219	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q1112R		Atlas-SNP	.											.	ITGA11	110	.	0			c.A3335G						.						37.0	48.0	44.0					15																	68599732		1967	4109	6076	SO:0001583	missense	22801	exon28			TGGAACTGCCTCT	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.3335A>G	chr15.hg19:g.68599732T>C	ENSP00000327290:p.Gln1112Arg	88.0	0.0	1108	86.0	6.0	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	hg19	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	T	12.86	2.063102	0.36373	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.41400	1.0;1.0	4.73	4.73	0.59995	.	0.429079	0.27558	N	0.018823	T	0.30727	0.0774	N	0.25647	0.755	0.28611	N	0.908682	B;B	0.09022	0.0;0.002	B;B	0.06405	0.001;0.002	T	0.15009	-1.0452	10	0.34782	T	0.22	.	13.3728	0.60723	0.0:0.0:0.0:1.0	.	1112;1112	A8K8T0;Q9UKX5	.;ITA11_HUMAN	R	1112;1113;747	ENSP00000327290:Q1112R;ENSP00000403392:Q1113R	ENSP00000327290:Q1112R	Q	-	2	0	ITGA11	66386786	0.997000	0.39634	1.000000	0.80357	0.990000	0.78478	1.690000	0.37711	1.903000	0.55091	0.454000	0.30748	CAG	.	.		0.572	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
MYO9A	4649	hgsc.bcm.edu	37	15	72119321	72119321	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:72119321C>T	ENST00000356056.5	-	42	7719	c.7247G>A	c.(7246-7248)cGa>cAa	p.R2416Q	MYO9A_ENST00000424560.1_Missense_Mutation_p.R2487Q|MYO9A_ENST00000444904.1_Missense_Mutation_p.R2397Q|MYO9A_ENST00000564571.1_3'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	2416	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						AAGTTGCTTTCGCAACTTGCT	0.438																																					p.R2416Q		Atlas-SNP	.											.	MYO9A	203	.	0			c.G7247A						.						60.0	62.0	61.0					15																	72119321		2199	4297	6496	SO:0001583	missense	4649	exon42			TGCTTTCGCAACT	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.7247G>A	chr15.hg19:g.72119321C>T	ENSP00000348349:p.Arg2416Gln	59.0	0.0		59.0	7.0	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.254107	0.39896	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.90563	-2.64;-2.69;-2.63	5.55	2.66	0.31614	.	.	.	.	.	D	0.85986	0.5825	L	0.51422	1.61	0.22424	N	0.999114	B;B	0.25312	0.123;0.052	B;B	0.14023	0.01;0.008	T	0.74321	-0.3703	9	0.44086	T	0.13	.	8.7956	0.34876	0.0:0.712:0.0:0.288	.	2416;2180	B2RTY4;B2RTY4-5	MYO9A_HUMAN;.	Q	2416;2487;2397	ENSP00000348349:R2416Q;ENSP00000399162:R2487Q;ENSP00000398250:R2397Q	ENSP00000348349:R2416Q	R	-	2	0	MYO9A	69906375	0.032000	0.19561	0.123000	0.21794	0.825000	0.46686	0.720000	0.25896	0.303000	0.22785	-0.137000	0.14449	CGA	.	.		0.438	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
ZNF592	9640	hgsc.bcm.edu	37	15	85327556	85327556	+	Silent	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:85327556G>T	ENST00000560079.2	+	4	1938	c.1650G>T	c.(1648-1650)ctG>ctT	p.L550L	ZNF592_ENST00000299927.3_Silent_p.L550L	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	550					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)			CTGCCCCACTGATTGTAGAGG	0.582																																					p.L550L		Atlas-SNP	.											ZNF592,NS,carcinoma,0,1	ZNF592	95	.	0			c.G1650T						.						88.0	89.0	89.0					15																	85327556		2203	4299	6502	SO:0001819	synonymous_variant	9640	exon4			CCCACTGATTGTA	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.1650G>T	chr15.hg19:g.85327556G>T		103.0	0.0		63.0	3.0	NM_014630	Q2M1T2|Q504Y9	Silent	SNP	ENST00000560079.2	hg19	CCDS32317.1																																																																																			.	.		0.582	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630	
SLC28A1	9154	hgsc.bcm.edu	37	15	85476374	85476374	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:85476374A>G	ENST00000286749.3	+	12	1173		c.e12-1		SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000394573.1_Splice_Site|SLC28A1_ENST00000537624.1_Splice_Site|SLC28A1_ENST00000537216.1_Splice_Site			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1						nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	TCACTCTTGCAGATCGATGCC	0.582																																					.		Atlas-SNP	.											.	SLC28A1	118	.	0			c.1084-2A>G						.						194.0	168.0	177.0					15																	85476374		2203	4299	6502	SO:0001630	splice_region_variant	9154	exon13			TCTTGCAGATCGA	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.1084-1A>G	chr15.hg19:g.85476374A>G		173.0	0.0		121.0	5.0	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Splice_Site	SNP	ENST00000286749.3	hg19	CCDS10334.1	.	.	.	.	.	.	.	.	.	.	A	18.70	3.679187	0.68042	.	.	ENSG00000156222	ENST00000537216;ENST00000537624;ENST00000286749;ENST00000394573	.	.	.	4.4	4.4	0.53042	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6471	0.51267	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC28A1	83277378	1.000000	0.71417	0.973000	0.42090	0.803000	0.45373	8.204000	0.89741	1.840000	0.53500	0.460000	0.39030	.	.	.		0.582	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		Intron
NTRK3	4916	hgsc.bcm.edu	37	15	88423565	88423565	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:88423565C>T	ENST00000360948.2	-	18	2431	c.2270G>A	c.(2269-2271)gGg>gAg	p.G757E	NTRK3_ENST00000557856.1_Missense_Mutation_p.G735E|NTRK3_ENST00000355254.2_Missense_Mutation_p.G743E|NTRK3_ENST00000357724.2_Missense_Mutation_p.G749E|NTRK3_ENST00000394480.2_Missense_Mutation_p.G743E	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	757	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			GAGGATCACCCCGAAGCTCCA	0.512			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)																											p.G757E		Atlas-SNP	.		Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	.	NTRK3	587	.	0			c.G2270A						.						131.0	115.0	120.0					15																	88423565		2201	4299	6500	SO:0001583	missense	4916	exon19			ATCACCCCGAAGC	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.2270G>A	chr15.hg19:g.88423565C>T	ENSP00000354207:p.Gly757Glu	167.0	0.0		131.0	6.0	NM_001012338	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.966557	0.92855	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254	D;D;D;D	0.99158	-5.5;-5.5;-5.5;-5.5	5.34	5.34	0.76211	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99677	0.9879	H	0.99545	4.62	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	0.97157	0.9835	10	0.87932	D	0	.	17.5974	0.88016	0.0:1.0:0.0:0.0	.	735;743;757	B7Z4C5;Q16288-3;Q16288	.;.;NTRK3_HUMAN	E	743;757;749;743	ENSP00000377990:G743E;ENSP00000354207:G757E;ENSP00000350356:G749E;ENSP00000347397:G743E	ENSP00000347397:G743E	G	-	2	0	NTRK3	86224569	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.514000	0.81750	2.482000	0.83794	0.655000	0.94253	GGG	.	.		0.512	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding			
BLM	641	hgsc.bcm.edu	37	15	91328233	91328233	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:91328233T>C	ENST00000355112.3	+	14	2863	c.2745T>C	c.(2743-2745)gcT>gcC	p.A915A	BLM_ENST00000560509.1_Silent_p.A915A|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	915	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			GGCTCGCTGCTCTTGCTTACC	0.468			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.A915A		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	BLM	122	.	0			c.T2745C						.						102.0	91.0	95.0					15																	91328233		2198	4298	6496	SO:0001819	synonymous_variant	641	exon14	Familial Cancer Database		CGCTGCTCTTGCT	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.2745T>C	chr15.hg19:g.91328233T>C		99.0	0.0		84.0	4.0	NM_000057	Q52M96	Silent	SNP	ENST00000355112.3	hg19	CCDS10363.1																																																																																			.	.		0.468	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
FES	2242	hgsc.bcm.edu	37	15	91434318	91434318	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:91434318A>G	ENST00000328850.3	+	11	1569	c.1427A>G	c.(1426-1428)cAc>cGc	p.H476R	FES_ENST00000444422.2_Intron|FES_ENST00000414248.2_Intron|FES_ENST00000394300.3_Missense_Mutation_p.H418R|FES_ENST00000450438.2_Intron|FES_ENST00000394302.1_Intron	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	476	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of mast cell degranulation (GO:0043304)|regulation of vesicle-mediated transport (GO:0060627)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule cytoskeleton (GO:0015630)	ATP binding (GO:0005524)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol binding (GO:0035091)|protein tyrosine kinase activity (GO:0004713)			lung(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			CTGCTGGTGCACTCTGGGGAC	0.647																																					p.H476R		Atlas-SNP	.											.	FES	102	.	0			c.A1427G						.						96.0	73.0	81.0					15																	91434318		2195	4293	6488	SO:0001583	missense	2242	exon11			TGGTGCACTCTGG	X52192	CCDS10365.1, CCDS45349.1, CCDS45350.1, CCDS45351.1	15q26.1	2014-06-26	2014-06-26		ENSG00000182511	ENSG00000182511	2.7.10.1	"""SH2 domain containing"""	3657	protein-coding gene	gene with protein product	"""Oncogene FES, feline sarcoma virus"", ""c-fes/fps protein"""	190030	"""feline sarcoma (Snyder-Theilen) viral (v-fes)/Fujinami avian sarcoma (PRCII) viral (v-fps) oncogene homolog"", ""feline sarcoma oncogene"""			1870997	Standard	NM_002005		Approved	FPS	uc002bpv.3	P07332	OTTHUMG00000044456	ENST00000328850.3:c.1427A>G	chr15.hg19:g.91434318A>G	ENSP00000331504:p.His476Arg	91.0	0.0		104.0	5.0	NM_002005	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Missense_Mutation	SNP	ENST00000328850.3	hg19	CCDS10365.1	.	.	.	.	.	.	.	.	.	.	A	4.210	0.037720	0.08148	.	.	ENSG00000182511	ENST00000328850;ENST00000394300	T;T	0.61510	0.1;0.1	4.63	3.51	0.40186	SH2 motif (4);	0.269317	0.38959	N	0.001518	T	0.30885	0.0779	N	0.03881	-0.34	0.21861	N	0.999507	B;B;B	0.15473	0.007;0.01;0.013	B;B;B	0.15870	0.014;0.006;0.01	T	0.18335	-1.0340	10	0.44086	T	0.13	-20.1774	8.0094	0.30344	0.8162:0.0:0.1838:0.0	.	458;418;476	B4DUD9;P07332-3;P07332	.;.;FES_HUMAN	R	476;418	ENSP00000331504:H476R;ENSP00000377837:H418R	ENSP00000331504:H476R	H	+	2	0	FES	89235322	0.036000	0.19791	0.013000	0.15412	0.184000	0.23303	3.041000	0.49807	0.817000	0.34445	0.392000	0.25879	CAC	.	.		0.647	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005	
UNC45A	55898	hgsc.bcm.edu	37	15	91491925	91491925	+	Silent	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:91491925G>A	ENST00000418476.2	+	13	1819	c.1779G>A	c.(1777-1779)ctG>ctA	p.L593L	UNC45A_ENST00000394275.2_Silent_p.L578L	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	593					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CCTCAGCGCTGGTGAACTGCA	0.587																																					p.L593L		Atlas-SNP	.											.	UNC45A	57	.	0			c.G1779A						.						74.0	60.0	65.0					15																	91491925		2198	4298	6496	SO:0001819	synonymous_variant	55898	exon13			AGCGCTGGTGAAC		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"""smooth muscle cell associated protein-1"""	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.1779G>A	chr15.hg19:g.91491925G>A		88.0	0.0		93.0	4.0	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Silent	SNP	ENST00000418476.2	hg19	CCDS10367.1																																																																																			.	.		0.587	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671	
ARRDC4	91947	hgsc.bcm.edu	37	15	98512600	98512600	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr15:98512600T>C	ENST00000268042.6	+	5	1037	c.873T>C	c.(871-873)taT>taC	p.Y291Y	ARRDC4_ENST00000538249.1_Silent_p.Y204Y	NM_183376.2	NP_899232.2	Q8NCT1	ARRD4_HUMAN	arrestin domain containing 4	291					positive regulation of ubiquitin-protein transferase activity (GO:0051443)	endosome (GO:0005768)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|skin(3)	16	Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222)		OV - Ovarian serous cystadenocarcinoma(32;0.0417)			GAGTGGACTATTCCTTAGCTG	0.393																																					p.Y291Y		Atlas-SNP	.											.	ARRDC4	30	.	0			c.T873C						.						91.0	82.0	85.0					15																	98512600		2197	4298	6495	SO:0001819	synonymous_variant	91947	exon5			GGACTATTCCTTA	BC028704	CCDS10377.1	15q26.2	2005-08-16			ENSG00000140450	ENSG00000140450			28087	protein-coding gene	gene with protein product						12477932	Standard	NM_183376		Approved	FLJ36045	uc010bom.3	Q8NCT1	OTTHUMG00000149849	ENST00000268042.6:c.873T>C	chr15.hg19:g.98512600T>C		121.0	0.0		89.0	4.0	NM_183376	Q6NSI9	Silent	SNP	ENST00000268042.6	hg19	CCDS10377.1																																																																																			.	.		0.393	ARRDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313535.1	NM_183376	
CCNF	899	hgsc.bcm.edu	37	16	2503452	2503452	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:2503452A>G	ENST00000397066.4	+	15	1717	c.1629A>G	c.(1627-1629)acA>acG	p.T543T	RP11-715J22.3_ENST00000561653.1_RNA|RP11-715J22.4_ENST00000566085.1_lincRNA	NM_001761.2	NP_001752.2	P41002	CCNF_HUMAN	cyclin F	543					mitotic nuclear division (GO:0007067)|negative regulation of centrosome duplication (GO:0010826)|placenta development (GO:0001890)|protein ubiquitination (GO:0016567)|re-entry into mitotic cell cycle (GO:0000320)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	centriole (GO:0005814)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(2)|lung(5)|prostate(4)|skin(1)	20		Ovarian(90;0.17)				TAGGAGTGACACAAGACAGCC	0.627																																					p.T543T		Atlas-SNP	.											.	CCNF	110	.	0			c.A1629G						.						90.0	83.0	85.0					16																	2503452		2198	4300	6498	SO:0001819	synonymous_variant	899	exon15			AGTGACACAAGAC	Z36714	CCDS10467.1	16p13.3	2008-02-05			ENSG00000162063	ENSG00000162063		"""F-boxes /  ""other"""""	1591	protein-coding gene	gene with protein product		600227				7896286	Standard	NM_001761		Approved	FBX1, FBXO1	uc002cqd.1	P41002	OTTHUMG00000128858	ENST00000397066.4:c.1629A>G	chr16.hg19:g.2503452A>G		70.0	0.0		65.0	4.0	NM_001761	B2R8H3|Q96EG9	Silent	SNP	ENST00000397066.4	hg19	CCDS10467.1																																																																																			.	.		0.627	CCNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250801.1	NM_001761	
CREBBP	1387	hgsc.bcm.edu	37	16	3799678	3799678	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:3799678A>G	ENST00000262367.5	-	21	4595	c.3786T>C	c.(3784-3786)atT>atC	p.I1262I	CREBBP_ENST00000382070.3_Silent_p.I1224I	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1262	Cys/His-rich.				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)		GATCCTTTGAAATTGTCCTTG	0.284			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.I1262I		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.T3786C						.						83.0	78.0	80.0					16																	3799678		2194	4298	6492	SO:0001819	synonymous_variant	1387	exon21			CTTTGAAATTGTC	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.3786T>C	chr16.hg19:g.3799678A>G		114.0	0.0		123.0	5.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	hg19	CCDS10509.1																																																																																			.	.		0.284	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
ADCY9	115	hgsc.bcm.edu	37	16	4164949	4164949	+	Silent	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:4164949G>T	ENST00000294016.3	-	2	1033	c.495C>A	c.(493-495)acC>acA	p.T165T		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	165					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)|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)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CGTACAGCTTGGTGAAGGTAA	0.592																																					p.T165T		Atlas-SNP	.											.	ADCY9	151	.	0			c.C495A						.						86.0	84.0	85.0					16																	4164949		2197	4300	6497	SO:0001819	synonymous_variant	115	exon2			CAGCTTGGTGAAG	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.495C>A	chr16.hg19:g.4164949G>T		70.0	0.0		50.0	4.0	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	hg19	CCDS32382.1																																																																																			.	.		0.592	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
VASN	114990	hgsc.bcm.edu	37	16	4432547	4432547	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:4432547C>T	ENST00000304735.3	+	2	1824	c.1669C>T	c.(1669-1671)Cca>Tca	p.P557S	CORO7_ENST00000539968.1_Intron|CORO7_ENST00000251166.4_Intron|CORO7_ENST00000537233.2_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000423908.2_Intron|CORO7_ENST00000574025.1_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	557	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|cellular response to redox state (GO:0071461)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	transforming growth factor beta binding (GO:0050431)			breast(1)|lung(3)|prostate(1)|skin(1)	6						CCATACACCCCCAGCCGTCCA	0.736																																					p.P557S		Atlas-SNP	.											.	VASN	21	.	0			c.C1669T						.						11.0	17.0	15.0					16																	4432547		2153	4249	6402	SO:0001583	missense	114990	exon2			ACACCCCCAGCCG	AY358299	CCDS10514.1	16p13.3	2008-02-05	2006-03-30	2006-03-30	ENSG00000168140	ENSG00000168140			18517	protein-coding gene	gene with protein product		608843	"""slit-like 2 (Drosophila)"""	SLITL2		15247411	Standard	NM_138440		Approved		uc002cwj.1	Q6EMK4	OTTHUMG00000129469	ENST00000304735.3:c.1669C>T	chr16.hg19:g.4432547C>T	ENSP00000306864:p.Pro557Ser	34.0	0.0		46.0	4.0	NM_138440	Q6UXL4|Q6UXL5|Q96CX1	Missense_Mutation	SNP	ENST00000304735.3	hg19	CCDS10514.1	.	.	.	.	.	.	.	.	.	.	C	11.42	1.632559	0.29068	.	.	ENSG00000168140	ENST00000304735	T	0.55930	0.49	5.22	3.22	0.36961	.	0.609808	0.16478	N	0.212668	T	0.36524	0.0970	N	0.24115	0.695	0.09310	N	1	B	0.26081	0.141	B	0.31016	0.123	T	0.19160	-1.0314	10	0.06625	T	0.88	-6.3503	12.9558	0.58427	0.0:0.6888:0.3112:0.0	.	557	Q6EMK4	VASN_HUMAN	S	557	ENSP00000306864:P557S	ENSP00000306864:P557S	P	+	1	0	VASN	4372548	0.000000	0.05858	0.010000	0.14722	0.892000	0.51952	1.115000	0.31209	0.569000	0.29329	0.655000	0.94253	CCA	.	.		0.736	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440	
PPL	5493	hgsc.bcm.edu	37	16	4942072	4942072	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:4942072T>C	ENST00000345988.2	-	15	1882	c.1793A>G	c.(1792-1794)gAg>gGg	p.E598G	PPL_ENST00000590782.2_Missense_Mutation_p.E596G	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	598					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CAGGAGGTGCTCGTATTTCCG	0.677																																					p.E598G		Atlas-SNP	.											.	PPL	168	.	0			c.A1793G						.						63.0	62.0	62.0					16																	4942072		2197	4300	6497	SO:0001583	missense	5493	exon15			AGGTGCTCGTATT	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.1793A>G	chr16.hg19:g.4942072T>C	ENSP00000340510:p.Glu598Gly	105.0	0.0		88.0	4.0	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	hg19	CCDS10526.1	.	.	.	.	.	.	.	.	.	.	T	11.95	1.791649	0.31685	.	.	ENSG00000118898	ENST00000345988	T	0.37584	1.19	5.35	5.35	0.76521	.	0.573319	0.17738	N	0.163672	T	0.30947	0.0781	L	0.44542	1.39	0.34790	D	0.735676	B	0.32245	0.361	B	0.21708	0.036	T	0.42515	-0.9447	10	0.40728	T	0.16	.	15.3443	0.74324	0.0:0.0:0.0:1.0	.	598	O60437	PEPL_HUMAN	G	598	ENSP00000340510:E598G	ENSP00000340510:E598G	E	-	2	0	PPL	4882073	1.000000	0.71417	1.000000	0.80357	0.222000	0.24845	5.499000	0.66937	2.038000	0.60285	0.448000	0.29417	GAG	.	.		0.677	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
TXNDC11	51061	hgsc.bcm.edu	37	16	11785663	11785663	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:11785663T>C	ENST00000356957.3	-	9	1571	c.1464A>G	c.(1462-1464)ccA>ccG	p.P488P	TXNDC11_ENST00000570917.1_5'Flank|TXNDC11_ENST00000283033.5_Silent_p.P461P			Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	488					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			endometrium(3)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						AGCTGCACTGTGGCACGCTGA	0.532																																					p.P461P		Atlas-SNP	.											.	TXNDC11	75	.	0			c.A1383G						.						52.0	53.0	53.0					16																	11785663		2197	4300	6497	SO:0001819	synonymous_variant	51061	exon8			GCACTGTGGCACG	BC013727	CCDS32387.1	16p13.13	2008-09-29				ENSG00000153066			28030	protein-coding gene	gene with protein product	"""EF-hand binding protein 1"""					8619474, 9110174	Standard	XM_005255346		Approved	EFP1	uc002dbg.1	Q6PKC3		ENST00000356957.3:c.1464A>G	chr16.hg19:g.11785663T>C		77.0	0.0		93.0	4.0	NM_015914	O95887|Q6PJA6|Q8N2Q4|Q96K45|Q96K53	Silent	SNP	ENST00000356957.3	hg19																																																																																				.	.		0.532	TXNDC11-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000437057.1	NM_015914	
SMG1	23049	hgsc.bcm.edu	37	16	18849391	18849391	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:18849391T>C	ENST00000446231.2	-	45	7770	c.7358A>G	c.(7357-7359)gAg>gGg	p.E2453G	SMG1_ENST00000389467.3_Missense_Mutation_p.E2453G			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2453	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				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						TCGCTCCATCTCTCTCTTGCT	0.527																																					p.E2453G		Atlas-SNP	.											.	SMG1	401	.	0			c.A7358G						.						38.0	41.0	40.0					16																	18849391		2069	4205	6274	SO:0001583	missense	23049	exon45			TCCATCTCTCTCT	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.7358A>G	chr16.hg19:g.18849391T>C	ENSP00000402515:p.Glu2453Gly	144.0	0.0		123.0	5.0	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.295773	0.81025	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01185	5.21;5.21	5.72	5.72	0.89469	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3-/4-kinase, catalytic (2);	0.000000	0.64402	D	0.000001	T	0.02418	0.0074	L	0.31420	0.93	0.51012	D	0.999901	D	0.55172	0.97	P	0.51895	0.683	T	0.66716	-0.5853	10	0.56958	D	0.05	.	16.2988	0.82793	0.0:0.0:0.0:1.0	.	2453	Q96Q15	SMG1_HUMAN	G	2453	ENSP00000402515:E2453G;ENSP00000374118:E2453G	ENSP00000374118:E2453G	E	-	2	0	SMG1	18756892	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.243000	0.72384	2.311000	0.77944	0.533000	0.62120	GAG	.	.		0.527	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
HS3ST2	9956	hgsc.bcm.edu	37	16	22926348	22926348	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:22926348G>T	ENST00000261374.3	+	2	1003	c.569G>T	c.(568-570)cGc>cTc	p.R190L		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	190					carbohydrate metabolic process (GO:0005975)|circadian rhythm (GO:0007623)|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 2 activity (GO:0033871)|sulfotransferase activity (GO:0008146)			breast(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(2)|skin(1)	19				GBM - Glioblastoma multiforme(48;0.0299)		GCTCCTCGACGCATCTTCAAC	0.577																																					p.R190L		Atlas-SNP	.											HS3ST2,colon,carcinoma,0,1	HS3ST2	59	.	0			c.G569T						.						110.0	100.0	103.0					16																	22926348		2197	4300	6497	SO:0001583	missense	9956	exon2			CTCGACGCATCTT	AF105374	CCDS10606.1	16p12	2008-02-05			ENSG00000122254	ENSG00000122254	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5195	protein-coding gene	gene with protein product		604056				9988767	Standard	NM_006043		Approved	3OST2	uc002dli.3	Q9Y278	OTTHUMG00000094785	ENST00000261374.3:c.569G>T	chr16.hg19:g.22926348G>T	ENSP00000261374:p.Arg190Leu	80.0	0.0		64.0	3.0	NM_006043	Q52LZ1	Missense_Mutation	SNP	ENST00000261374.3	hg19	CCDS10606.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.015657	0.54468	.	.	ENSG00000122254	ENST00000261374;ENST00000540146	T	0.48522	0.81	5.25	4.3	0.51218	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.72203	0.3431	M	0.89478	3.035	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78109	-0.2332	10	0.87932	D	0	.	13.1286	0.59369	0.0769:0.0:0.9231:0.0	.	190	Q9Y278	HS3S2_HUMAN	L	190;198	ENSP00000261374:R190L	ENSP00000261374:R190L	R	+	2	0	HS3ST2	22833849	1.000000	0.71417	0.066000	0.19879	0.279000	0.26890	7.863000	0.87023	1.225000	0.43566	0.561000	0.74099	CGC	.	.		0.577	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043	
ZNF689	115509	hgsc.bcm.edu	37	16	30615611	30615611	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:30615611A>G	ENST00000287461.3	-	3	1814	c.1477T>C	c.(1477-1479)Tcc>Ccc	p.S493P	ZNF689_ENST00000566673.1_5'Flank|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	493					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			CTCTGACTGGAGCCCCCGATA	0.582																																					p.S493P		Atlas-SNP	.											.	ZNF689	48	.	0			c.T1477C						.						31.0	31.0	31.0					16																	30615611		2197	4300	6497	SO:0001583	missense	115509	exon3			GACTGGAGCCCCC	BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"""Zinc fingers, C2H2-type"", ""-"""	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.1477T>C	chr16.hg19:g.30615611A>G	ENSP00000287461:p.Ser493Pro	85.0	0.0		84.0	4.0	NM_138447	Q658J5	Missense_Mutation	SNP	ENST00000287461.3	hg19	CCDS10686.1	.	.	.	.	.	.	.	.	.	.	a	0.921	-0.715753	0.03206	.	.	ENSG00000156853	ENST00000287461;ENST00000443190	T	0.06933	3.24	4.38	-4.12	0.03916	.	0.589368	0.15468	N	0.260742	T	0.02610	0.0079	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36432	-0.9748	10	0.27082	T	0.32	-3.2162	1.1893	0.01862	0.3564:0.2821:0.2294:0.1321	.	493	Q96CS4	ZN689_HUMAN	P	493;491	ENSP00000287461:S493P	ENSP00000287461:S493P	S	-	1	0	ZNF689	30523112	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	0.088000	0.14979	-0.729000	0.04875	-0.384000	0.06662	TCC	.	.		0.582	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447	
RNF40	9810	hgsc.bcm.edu	37	16	30783507	30783507	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:30783507A>G	ENST00000324685.6	+	19	3260	c.2825A>G	c.(2824-2826)tAc>tGc	p.Y942C	RNF40_ENST00000357890.5_Missense_Mutation_p.Y842C|RNF40_ENST00000402121.3_Missense_Mutation_p.Y634C|RNF40_ENST00000563683.1_Missense_Mutation_p.Y902C|RNF40_ENST00000567365.1_3'UTR	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	942					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			ATCAAGGAGTACAAGGTGGGG	0.557																																					p.Y942C		Atlas-SNP	.											.	RNF40	83	.	0			c.A2825G						.						65.0	40.0	48.0					16																	30783507		2104	4119	6223	SO:0001583	missense	9810	exon19			AGGAGTACAAGGT	AB014561	CCDS10691.1, CCDS55994.1	16p11.2-p11.1	2012-02-23	2012-02-23		ENSG00000103549	ENSG00000103549		"""RING-type (C3HC4) zinc fingers"""	16867	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog B (S. cerevisiae)"""	607700	"""ring finger protein 40"""			9734811, 10944455, 12121982	Standard	NM_014771		Approved	KIAA0661, RBP95, BRE1B, STARING	uc002dzq.3	O75150	OTTHUMG00000132394	ENST00000324685.6:c.2825A>G	chr16.hg19:g.30783507A>G	ENSP00000325677:p.Tyr942Cys	101.0	0.0		88.0	4.0	NM_014771	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Missense_Mutation	SNP	ENST00000324685.6	hg19	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.983542	0.74474	.	.	ENSG00000103549	ENST00000324685;ENST00000357890;ENST00000402121;ENST00000538323	T;T;T	0.36520	1.25;1.27;1.27	5.58	5.58	0.84498	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.60818	0.2298	M	0.73598	2.24	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.984;1.0;1.0;1.0	D;D;D;D;D	0.83275	0.996;0.924;0.983;0.987;0.987	T	0.65327	-0.6195	10	0.87932	D	0	-15.1456	14.741	0.69455	1.0:0.0:0.0:0.0	.	274;634;842;941;942	F6SYU7;F8W8Z4;O75150-4;A8K6K1;O75150	.;.;.;.;BRE1B_HUMAN	C	942;842;634;274	ENSP00000325677:Y942C;ENSP00000350563:Y842C;ENSP00000384942:Y634C	ENSP00000325677:Y942C	Y	+	2	0	RNF40	30691008	1.000000	0.71417	1.000000	0.80357	0.775000	0.43874	8.952000	0.93031	2.135000	0.66039	0.533000	0.62120	TAC	.	.		0.557	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771	
ITGAX	3687	hgsc.bcm.edu	37	16	31384577	31384577	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:31384577T>C	ENST00000268296.4	+	20	2495	c.2374T>C	c.(2374-2376)Tcc>Ccc	p.S792P	ITGAX_ENST00000562522.1_Missense_Mutation_p.S792P	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	792					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						CAGCTTGAAGTCCCTGCTGGT	0.537																																					p.S792P		Atlas-SNP	.											.	ITGAX	198	.	0			c.T2374C						.						107.0	88.0	94.0					16																	31384577		2197	4300	6497	SO:0001583	missense	3687	exon20			TTGAAGTCCCTGC	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.2374T>C	chr16.hg19:g.31384577T>C	ENSP00000268296:p.Ser792Pro	128.0	0.0		99.0	4.0	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	hg19	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	A	18.89	3.719230	0.68844	.	.	ENSG00000140678	ENST00000268296	T	0.47177	0.85	4.89	4.89	0.63831	Integrin alpha-2 (1);	.	.	.	.	T	0.27241	0.0668	N	0.08118	0	0.19300	N	0.999972	B	0.24533	0.105	B	0.15484	0.013	T	0.15206	-1.0445	9	0.42905	T	0.14	.	9.2372	0.37473	0.8385:0.0:0.0:0.1615	.	792	P20702	ITAX_HUMAN	P	792	ENSP00000268296:S792P	ENSP00000268296:S792P	S	+	1	0	ITGAX	31292078	0.986000	0.35501	0.463000	0.27130	0.471000	0.32888	2.459000	0.45023	1.003000	0.39130	-0.336000	0.08194	TCC	.	.		0.537	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
ZNF843	283933	hgsc.bcm.edu	37	16	31447207	31447207	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:31447207A>G	ENST00000315678.5	-	2	1688	c.964T>C	c.(964-966)Tcg>Ccg	p.S322P	ZNF843_ENST00000564218.1_Intron	NM_001136509.1	NP_001129981.1	Q8N446	ZN843_HUMAN	zinc finger protein 843	322							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|large_intestine(1)|prostate(1)	4						TGTGGGTTCGAGGGCGGTGGA	0.687																																					p.S322P		Atlas-SNP	.											.	ZNF843	14	.	0			c.T964C						.						7.0	9.0	8.0					16																	31447207		687	1586	2273	SO:0001583	missense	283933	exon2			GGTTCGAGGGCGG	BC036762	CCDS45471.1	16p11.2	2013-01-11			ENSG00000176723	ENSG00000176723		"""Zinc fingers, C2H2-type"""	28710	protein-coding gene	gene with protein product						12477932	Standard	NM_001136509		Approved	MGC46336	uc010vfm.1	Q8N446		ENST00000315678.5:c.964T>C	chr16.hg19:g.31447207A>G	ENSP00000322899:p.Ser322Pro	83.0	0.0		81.0	6.0	NM_001136509	A8K4U8	Missense_Mutation	SNP	ENST00000315678.5	hg19	CCDS45471.1	.	.	.	.	.	.	.	.	.	.	A	10.91	1.483565	0.26598	.	.	ENSG00000176723	ENST00000315678	T	0.01272	5.07	2.14	-4.29	0.03721	.	.	.	.	.	T	0.00754	0.0025	N	0.08118	0	0.09310	N	1	B	0.18741	0.03	B	0.15052	0.012	T	0.48468	-0.9033	9	0.87932	D	0	.	0.8985	0.01269	0.2337:0.3046:0.2933:0.1684	.	322	Q8N446	ZN843_HUMAN	P	322	ENSP00000322899:S322P	ENSP00000322899:S322P	S	-	1	0	ZNF843	31354708	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.984000	0.03755	-0.826000	0.04284	0.397000	0.26171	TCG	.	.		0.687	ZNF843-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432843.1	NM_001136509	
ZNF267	10308	hgsc.bcm.edu	37	16	31927484	31927484	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:31927484C>T	ENST00000300870.10	+	4	2123	c.1914C>T	c.(1912-1914)ggC>ggT	p.G638G		NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267	638					multicellular organismal development (GO:0007275)|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(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						AAGAATGTGGCAAAGCCTTCA	0.413																																					p.G638G		Atlas-SNP	.											.	ZNF267	94	.	0			c.C1914T						.						73.0	75.0	74.0					16																	31927484		2197	4300	6497	SO:0001819	synonymous_variant	10308	exon4			ATGTGGCAAAGCC	X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"""Zinc fingers, C2H2-type"", ""-"""	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.1914C>T	chr16.hg19:g.31927484C>T		92.0	0.0		69.0	4.0	NM_003414	A0JNZ9|Q8NE41|Q9NRJ0	Silent	SNP	ENST00000300870.10	hg19	CCDS32440.1																																																																																			.	.		0.413	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432446.2	NM_003414	
CYLD	1540	hgsc.bcm.edu	37	16	50818357	50818357	+	Silent	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:50818357G>A	ENST00000427738.3	+	11	2149	c.1944G>A	c.(1942-1944)ctG>ctA	p.L648L	CYLD_ENST00000566206.1_Silent_p.L645L|CYLD_ENST00000569418.1_Silent_p.L645L|CYLD_ENST00000564326.1_Silent_p.L645L|CYLD_ENST00000311559.9_Silent_p.L648L|CYLD_ENST00000540145.1_Silent_p.L648L|RP11-327F22.4_ENST00000564510.1_RNA|RP11-327F22.4_ENST00000575917.1_RNA|CYLD_ENST00000398568.2_Silent_p.L645L|CYLD_ENST00000568704.2_Silent_p.L463L			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	648	USP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				TTAATCCTCTGAGAATGTAAG	0.333			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.L648L		Atlas-SNP	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	CYLD,right_upper_lobe,carcinoma,0,1	CYLD	150	.	0			c.G1944A						.						95.0	88.0	90.0					16																	50818357		1834	4086	5920	SO:0001819	synonymous_variant	1540	exon13	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	TCCTCTGAGAATG	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.1944G>A	chr16.hg19:g.50818357G>A		62.0	0.0		47.0	2.0	NM_015247	O94934|Q7L3N6|Q96EH0|Q9NZX9	Silent	SNP	ENST00000427738.3	hg19	CCDS45482.1																																																																																			.	.		0.333	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2		
SLC12A3	6559	hgsc.bcm.edu	37	16	56924197	56924197	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:56924197A>G	ENST00000563236.1	+	19	2322	c.2297A>G	c.(2296-2298)gAt>gGt	p.D766G	SLC12A3_ENST00000438926.2_Missense_Mutation_p.D766G|SLC12A3_ENST00000262502.5_Missense_Mutation_p.D765G|SLC12A3_ENST00000566786.1_Missense_Mutation_p.D765G			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	766				D -> E (in Ref. 1; AAC50355). {ECO:0000305}.	chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	GATGCCTTTGATTTCAACTAT	0.562																																					p.D766G		Atlas-SNP	.											.	SLC12A3	99	.	0			c.A2297G						.						206.0	145.0	165.0					16																	56924197		2198	4300	6498	SO:0001583	missense	6559	exon19			CCTTTGATTTCAA		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"""Solute carriers"""	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.2297A>G	chr16.hg19:g.56924197A>G	ENSP00000456149:p.Asp766Gly	91.0	0.0		89.0	4.0	NM_001126108	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	hg19	CCDS58464.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.674030	0.88445	.	.	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	5.63	5.63	0.86233	.	0.150659	0.64402	D	0.000017	D	0.85296	0.5664	M	0.93106	3.38	0.80722	D	1	B;D;D	0.76494	0.338;0.999;0.999	B;D;D	0.71414	0.211;0.94;0.973	D	0.88846	0.3316	9	0.72032	D	0.01	.	15.0231	0.71647	1.0:0.0:0.0:0.0	.	765;766;766	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	G	765;766	.	ENSP00000262502:D766G	D	+	2	0	SLC12A3	55481698	1.000000	0.71417	0.998000	0.56505	0.794000	0.44872	9.281000	0.95811	2.137000	0.66172	0.533000	0.62120	GAT	.	.		0.562	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1		
NLRC5	84166	hgsc.bcm.edu	37	16	57067552	57067552	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:57067552A>G	ENST00000262510.6	+	12	2739	c.2514A>G	c.(2512-2514)aaA>aaG	p.K838K	NLRC5_ENST00000436936.1_Silent_p.K838K|NLRC5_ENST00000308149.7_Silent_p.K838K|NLRC5_ENST00000539144.1_Silent_p.K838K	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	838					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				GCCAGAGGAAAGGGGCTCAGA	0.557																																					p.K838K		Atlas-SNP	.											.	NLRC5	186	.	0			c.A2514G						.						101.0	93.0	96.0					16																	57067552		2198	4300	6498	SO:0001819	synonymous_variant	84166	exon11			GAGGAAAGGGGCT	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.2514A>G	chr16.hg19:g.57067552A>G		67.0	0.0		70.0	4.0	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	hg19	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	A	0.049	-1.255598	0.01457	.	.	ENSG00000140853	ENST00000538805	.	.	.	3.98	1.45	0.22620	.	.	.	.	.	T	0.25568	0.0622	.	.	.	0.20196	N	0.99993	.	.	.	.	.	.	T	0.23404	-1.0189	4	.	.	.	.	5.2672	0.15605	0.6982:0.0:0.3018:0.0	.	.	.	.	G	591	.	.	R	+	1	2	NLRC5	55625053	0.931000	0.31567	0.018000	0.16275	0.053000	0.15095	0.013000	0.13310	0.264000	0.21851	-0.274000	0.10170	AGG	.	.		0.557	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
CNGB1	1258	hgsc.bcm.edu	37	16	57998104	57998104	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:57998104T>C	ENST00000251102.8	-	4	280	c.220A>G	c.(220-222)Acc>Gcc	p.T74A	CNGB1_ENST00000564448.1_Missense_Mutation_p.T74A|CNGB1_ENST00000311183.4_Missense_Mutation_p.T74A	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	74					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						GCCTCCTTGGTCTCTGGAAAA	0.557																																					p.T74A	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.A220G						.						68.0	73.0	72.0					16																	57998104		1899	4114	6013	SO:0001583	missense	1258	exon4			CCTTGGTCTCTGG	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.220A>G	chr16.hg19:g.57998104T>C	ENSP00000251102:p.Thr74Ala	83.0	0.0		89.0	4.0	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	hg19	CCDS42169.1	.	.	.	.	.	.	.	.	.	.	T	11.64	1.699215	0.30142	.	.	ENSG00000070729	ENST00000251102;ENST00000311183	D;T	0.96587	-4.06;0.92	3.9	3.9	0.45041	.	0.197173	0.25233	N	0.032152	D	0.94321	0.8175	L	0.27053	0.805	0.20821	N	0.999842	D;P	0.56035	0.974;0.884	P;B	0.54499	0.754;0.268	D	0.88495	0.3078	10	0.56958	D	0.05	.	9.4298	0.38604	0.0:0.0:0.0:1.0	.	74;74	Q14028-3;Q14028	.;CNGB1_HUMAN	A	74	ENSP00000251102:T74A;ENSP00000311670:T74A	ENSP00000251102:T74A	T	-	1	0	CNGB1	56555605	0.857000	0.29778	0.998000	0.56505	0.410000	0.31052	1.028000	0.30128	1.998000	0.58463	0.533000	0.62120	ACC	.	.		0.557	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
LRRC29	26231	hgsc.bcm.edu	37	16	67241508	67241508	+	Nonstop_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:67241508T>C	ENST00000409037.1	-	4	1568	c.672A>G	c.(670-672)tgA>tgG	p.*224W	LRRC29_ENST00000393992.1_Nonstop_Mutation_p.*224W|LRRC29_ENST00000341546.3_Nonstop_Mutation_p.*224W|LRRC29_ENST00000462169.1_5'Flank|LRRC29_ENST00000409509.1_Nonstop_Mutation_p.*224W			Q8WV35	LRC29_HUMAN	leucine rich repeat containing 29	0										autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(1)|lung(2)|urinary_tract(1)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		TGACCTGGCCTCAGAGTGTTA	0.627																																					p.X224W		Atlas-SNP	.											.	LRRC29	13	.	0			c.A672G						.						44.0	39.0	40.0					16																	67241508		2198	4299	6497	SO:0001578	stop_lost	26231	exon6			CTGGCCTCAGAGT	AF176701	CCDS32465.1	16q22.1	2008-02-05	2004-08-23	2004-08-26	ENSG00000125122	ENSG00000125122			13605	protein-coding gene	gene with protein product			"""F-box and leucine-rich repeat protein 9"""	FBXL9		10531037	Standard	NM_012163		Approved	FBL9	uc002esf.3	Q8WV35	OTTHUMG00000154403	ENST00000409037.1:c.672A>G	chr16.hg19:g.67241508T>C	ENSP00000387318:p.*224Cysext*5	61.0	0.0		53.0	4.0	NM_001004055	B2RE92|Q9UKA0	Missense_Mutation	SNP	ENST00000409037.1	hg19	CCDS32465.1	.	.	.	.	.	.	.	.	.	.	T	16.43	3.120864	0.56613	.	.	ENSG00000125122	ENST00000409509;ENST00000393992;ENST00000409037;ENST00000341546	.	.	.	4.68	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.6818	0.45819	0.0:0.0:0.0:1.0	.	.	.	.	W	224	.	.	X	-	3	0	LRRC29	65799009	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	2.561000	0.45905	2.096000	0.63516	0.533000	0.62120	TGA	.	.		0.627	LRRC29-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335073.1	NM_012163	
CTCF	10664	hgsc.bcm.edu	37	16	67644896	67644896	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:67644896T>C	ENST00000264010.4	+	3	605	c.161T>C	c.(160-162)gTc>gCc	p.V54A	CTCF_ENST00000401394.1_Intron	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	54					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		GTCCAGGATGTCAACAGCAGT	0.557																																					p.V54A	Colon(175;1200 1966 6945 23069 27405)	Atlas-SNP	.											.	CTCF	193	.	0			c.T161C						.						89.0	87.0	88.0					16																	67644896		2198	4300	6498	SO:0001583	missense	10664	exon3			AGGATGTCAACAG	U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"""Zinc fingers, C2H2-type"""	13723	protein-coding gene	gene with protein product	"""11 zinc finger transcriptional repressor"""	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.161T>C	chr16.hg19:g.67644896T>C	ENSP00000264010:p.Val54Ala	80.0	0.0		56.0	4.0	NM_006565	B5MC38|Q53XI7|Q59EL8	Missense_Mutation	SNP	ENST00000264010.4	hg19	CCDS10841.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.898288	0.52227	.	.	ENSG00000102974	ENST00000264010	T	0.08984	3.03	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000009	T	0.15003	0.0362	N	0.24115	0.695	0.80722	D	1	P	0.49447	0.924	P	0.59424	0.857	T	0.03413	-1.1039	10	0.49607	T	0.09	-1.9744	15.2015	0.73142	0.0:0.0:0.0:1.0	.	54	P49711	CTCF_HUMAN	A	54	ENSP00000264010:V54A	ENSP00000264010:V54A	V	+	2	0	CTCF	66202397	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.381000	0.44336	2.178000	0.69098	0.533000	0.62120	GTC	.	.		0.557	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268870.2	NM_006565	
EDC4	23644	hgsc.bcm.edu	37	16	67918040	67918040	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:67918040A>G	ENST00000358933.5	+	29	4434	c.4195A>G	c.(4195-4197)Agc>Ggc	p.S1399G	CTC-479C5.10_ENST00000572067.1_lincRNA|NRN1L_ENST00000576147.1_5'Flank|NRN1L_ENST00000339176.3_5'Flank	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	1399					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)		p.S1399C(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		CGTGACCCCCAGCCTCCCTTA	0.622											OREG0023890	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1399G		Atlas-SNP	.											EDC4,NS,carcinoma,0,1	EDC4	101	.	1	Substitution - Missense(1)	lung(1)	c.A4195G						.						49.0	37.0	41.0					16																	67918040		2198	4300	6498	SO:0001583	missense	23644	exon29			ACCCCCAGCCTCC	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.4195A>G	chr16.hg19:g.67918040A>G	ENSP00000351811:p.Ser1399Gly	36.0	0.0	1103	39.0	2.0	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	hg19	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	A	14.31	2.497317	0.44455	.	.	ENSG00000038358	ENST00000358933	.	.	.	4.94	2.7	0.31948	.	0.303191	0.32901	N	0.005501	T	0.11196	0.0273	N	0.00926	-1.1	0.24490	N	0.994307	B	0.06786	0.001	B	0.01281	0.0	T	0.17806	-1.0357	9	0.35671	T	0.21	-3.2229	6.4914	0.22117	0.7283:0.1506:0.121:0.0	.	1399	Q6P2E9	EDC4_HUMAN	G	1399	.	ENSP00000351811:S1399G	S	+	1	0	EDC4	66475541	0.998000	0.40836	0.994000	0.49952	0.980000	0.70556	3.776000	0.55356	0.992000	0.38840	0.528000	0.53228	AGC	.	.		0.622	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329	
NFATC3	4775	hgsc.bcm.edu	37	16	68208375	68208375	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:68208375T>C	ENST00000346183.3	+	6	1897	c.1873T>C	c.(1873-1875)Ttt>Ctt	p.F625L	NFATC3_ENST00000349223.5_Missense_Mutation_p.F625L|NFATC3_ENST00000329524.4_Missense_Mutation_p.F625L|NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Missense_Mutation_p.F625L	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	625					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		TGGATCTAATTTTCTTCCAGA	0.358																																					p.F625L		Atlas-SNP	.											.	NFATC3	190	.	0			c.T1873C						.						153.0	160.0	157.0					16																	68208375		2198	4300	6498	SO:0001583	missense	4775	exon6			TCTAATTTTCTTC	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"""Nuclear factor of activated T-cells"""	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.1873T>C	chr16.hg19:g.68208375T>C	ENSP00000300659:p.Phe625Leu	104.0	0.0		74.0	4.0	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	hg19	CCDS10860.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.462054	0.43736	.	.	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524;ENST00000535127	T;T;T	0.15372	2.43;2.43;2.44	5.62	4.53	0.55603	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.048303	0.85682	D	0.000000	T	0.41465	0.1160	M	0.80183	2.485	0.80722	D	1	D;D;D;D	0.71674	0.998;0.961;0.998;0.998	D;B;D;D	0.70716	0.97;0.253;0.97;0.97	T	0.31806	-0.9930	10	0.56958	D	0.05	-16.6876	11.4406	0.50094	0.0:0.0703:0.0:0.9297	.	625;625;625;625	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	L	625;625;625;146	ENSP00000264008:F625L;ENSP00000300659:F625L;ENSP00000331324:F625L	ENSP00000331324:F625L	F	+	1	0	NFATC3	66765876	1.000000	0.71417	1.000000	0.80357	0.006000	0.05464	5.030000	0.64128	0.980000	0.38523	-0.353000	0.07706	TTT	.	.		0.358	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555	
CHTF8	54921	hgsc.bcm.edu	37	16	69154536	69154536	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:69154536A>G	ENST00000448552.2	-	4	279	c.158T>C	c.(157-159)aTc>aCc	p.I53T	CHTF8_ENST00000574807.1_5'Flank|CHTF8_ENST00000520529.1_3'UTR|CHTF8_ENST00000522091.1_3'UTR|CHTF8_ENST00000518041.1_Intron|CHTF8_ENST00000306585.6_5'UTR|CHTF8_ENST00000519520.1_3'UTR|CHTF8_ENST00000398235.2_Missense_Mutation_p.I53T|CHTF8_ENST00000523421.1_Intron	NM_001039690.3|NM_001040146.3	NP_001034779.1|NP_001035236.1	P0CG13	CTF8_HUMAN	CTF8, chromosome transmission fidelity factor 8 homolog (S. cerevisiae)	53					cell cycle (GO:0007049)|DNA replication (GO:0006260)	nucleus (GO:0005634)	DNA binding (GO:0003677)										ATGCCCCACGATCAGCACAGG	0.522																																					p.I53T		Atlas-SNP	.											.	CHTF8	5	.	0			c.T158C						.						96.0	95.0	95.0					16																	69154536		1963	4150	6113	SO:0001583	missense	54921	exon4			CCCACGATCAGCA		CCDS42185.1	16q22.1	2009-01-14				ENSG00000168802			24353	protein-coding gene	gene with protein product		613202				12766176	Standard	NM_001039690		Approved	FLJ20400, CTF8, DERPC	uc002ewo.2	P0CG12		ENST00000448552.2:c.158T>C	chr16.hg19:g.69154536A>G	ENSP00000408367:p.Ile53Thr	90.0	0.0		79.0	4.0	NM_001039690	A8MYX8|Q71E72|Q8NDH8|Q8WV66|Q9NX73	Missense_Mutation	SNP	ENST00000448552.2	hg19	CCDS42185.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.410696	0.42817	.	.	ENSG00000168802	ENST00000448552;ENST00000398235	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	T	0.48589	0.1508	L	0.37850	1.14	0.80722	D	1	P	0.34684	0.463	B	0.34180	0.177	T	0.45440	-0.9261	8	0.30078	T	0.28	.	15.2868	0.73833	1.0:0.0:0.0:0.0	.	53	P0CG13	CTF8_HUMAN	T	53	.	ENSP00000381290:I53T	I	-	2	0	CHTF8	67712037	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.499000	0.90494	2.144000	0.66660	0.533000	0.62120	ATC	.	.		0.522	CHTF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376352.2	NM_017804	
NIP7	51388	hgsc.bcm.edu	37	16	69375544	69375544	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:69375544A>G	ENST00000254940.5	+	5	932	c.532A>G	c.(532-534)Acg>Gcg	p.T178A	RP11-343C2.7_ENST00000564737.1_Intron|COG8_ENST00000562081.1_5'Flank|COG8_ENST00000306875.4_5'Flank|RP11-343C2.9_ENST00000563634.1_Intron|NIP7_ENST00000254941.6_Missense_Mutation_p.T131A	NM_016101.4	NP_057185.1	Q9Y221	NIP7_HUMAN	NIP7, nucleolar pre-rRNA processing protein	178	C-terminal domain.				ribosome assembly (GO:0042255)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Ovarian(137;0.101)				GCATGAAGAGACGTTGACTTA	0.468																																					p.T178A		Atlas-SNP	.											.	NIP7	20	.	0			c.A532G						.						146.0	143.0	144.0					16																	69375544		2198	4300	6498	SO:0001583	missense	51388	exon5			GAAGAGACGTTGA	AB112439	CCDS10877.1, CCDS56003.1	16q22.1	2013-03-04	2013-03-04		ENSG00000132603	ENSG00000132603			24328	protein-coding gene	gene with protein product			"""nuclear import 7 homolog (S. cerevisiae)"""			14660641, 22195017	Standard	NM_016101		Approved	CGI-37, FLJ10296, HSPC031, KD93	uc002exa.3	Q9Y221	OTTHUMG00000137568	ENST00000254940.5:c.532A>G	chr16.hg19:g.69375544A>G	ENSP00000254940:p.Thr178Ala	137.0	0.0		84.0	5.0	NM_016101	B2RD04|Q9NZZ0	Missense_Mutation	SNP	ENST00000254940.5	hg19	CCDS10877.1	.	.	.	.	.	.	.	.	.	.	A	13.94	2.386563	0.42308	.	.	ENSG00000132603	ENST00000254940;ENST00000254941	.	.	.	5.44	5.44	0.79542	.	0.047928	0.85682	D	0.000000	T	0.60287	0.2257	L	0.59436	1.845	0.80722	D	1	B;B	0.09022	0.002;0.0	B;B	0.14578	0.011;0.003	T	0.57195	-0.7853	9	0.41790	T	0.15	0.2163	15.7961	0.78412	1.0:0.0:0.0:0.0	.	131;178	Q9Y221-2;Q9Y221	.;NIP7_HUMAN	A	178;131	.	ENSP00000254940:T178A	T	+	1	0	NIP7	67933045	1.000000	0.71417	0.993000	0.49108	0.568000	0.35870	6.962000	0.76048	2.188000	0.69820	0.459000	0.35465	ACG	.	.		0.468	NIP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268947.2	NM_016101	
GLG1	2734	hgsc.bcm.edu	37	16	74528672	74528672	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:74528672A>G	ENST00000422840.2	-	6	1035	c.1036T>C	c.(1036-1038)Tcc>Ccc	p.S346P	GLG1_ENST00000447066.2_Missense_Mutation_p.S335P|GLG1_ENST00000205061.5_Missense_Mutation_p.S346P	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	346					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						TCACTCATGGATTCTTCAAAT	0.343																																					p.S346P		Atlas-SNP	.											.	GLG1	106	.	0			c.T1036C						.						88.0	87.0	88.0					16																	74528672		2198	4300	6498	SO:0001583	missense	2734	exon6			TCATGGATTCTTC		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"""golgi apparatus protein 1"""			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.1036T>C	chr16.hg19:g.74528672A>G	ENSP00000405984:p.Ser346Pro	94.0	0.0		88.0	4.0	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	hg19	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.502617	0.44455	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.94	5.94	0.96194	.	0.063063	0.64402	D	0.000004	T	0.44265	0.1285	L	0.32530	0.975	0.58432	D	0.999999	B;B;P	0.42584	0.003;0.005;0.784	B;B;B	0.38880	0.009;0.005;0.284	T	0.38650	-0.9651	9	0.38643	T	0.18	-7.8662	16.4075	0.83691	1.0:0.0:0.0:0.0	.	346;346;335	Q92896;Q92896-2;B7Z8Y4	GSLG1_HUMAN;.;.	P	346;335;346	.	ENSP00000205061:S346P	S	-	1	0	GLG1	73086173	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.122000	0.57910	2.275000	0.75901	0.528000	0.53228	TCC	.	.		0.343	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201	
ZFP1	162239	hgsc.bcm.edu	37	16	75203861	75203861	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:75203861A>G	ENST00000393430.2	+	4	977	c.853A>G	c.(853-855)Aca>Gca	p.T285A	ZFP1_ENST00000570010.1_Missense_Mutation_p.T285A|ZFP1_ENST00000464850.1_3'UTR|ZFP1_ENST00000568079.1_3'UTR|ZFP1_ENST00000332307.4_Missense_Mutation_p.T252A			Q6P2D0	ZFP1_HUMAN	ZFP1 zinc finger protein	285					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(2)|large_intestine(4)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	12						TGAACTCACCACACACCAGAG	0.418																																					p.T285A	NSCLC(187;1429 2122 10143 20357 42217)	Atlas-SNP	.											.	ZFP1	28	.	0			c.A853G						.						72.0	72.0	72.0					16																	75203861		2198	4300	6498	SO:0001583	missense	162239	exon4			CTCACCACACACC	AK094761	CCDS10914.2	16q22.3	2013-01-08	2012-11-27		ENSG00000184517	ENSG00000184517		"""Zinc fingers, C2H2-type"", ""-"""	23328	protein-coding gene	gene with protein product			"""zinc finger protein 1 homolog (mouse)"", ""zinc finger protein 1"""			2574853	Standard	NM_153688		Approved	FLJ34243, ZNF475	uc002fdo.3	Q6P2D0	OTTHUMG00000137602	ENST00000393430.2:c.853A>G	chr16.hg19:g.75203861A>G	ENSP00000377080:p.Thr285Ala	118.0	0.0		81.0	4.0	NM_153688	A8K5Q7|B4DKG9|Q8N188|Q8N9F9	Missense_Mutation	SNP	ENST00000393430.2	hg19	CCDS10914.2	.	.	.	.	.	.	.	.	.	.	A	3.669	-0.067883	0.07228	.	.	ENSG00000184517	ENST00000332307;ENST00000393430	T	0.07216	3.21	4.64	4.64	0.57946	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000134	T	0.03477	0.0100	N	0.05351	-0.065	0.21105	N	0.999788	P	0.41450	0.75	B	0.33960	0.173	T	0.41680	-0.9495	10	0.08381	T	0.77	-23.7449	12.6831	0.56932	1.0:0.0:0.0:0.0	.	285	Q6P2D0	ZFP1_HUMAN	A	285	ENSP00000377080:T285A	ENSP00000333192:T285A	T	+	1	0	ZFP1	73761362	0.000000	0.05858	0.992000	0.48379	0.992000	0.81027	-0.121000	0.10643	2.308000	0.77769	0.533000	0.62120	ACA	.	.		0.418	ZFP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269013.2	NM_153688	
WWOX	51741	hgsc.bcm.edu	37	16	78466543	78466543	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:78466543C>T	ENST00000566780.1	+	8	1316	c.950C>T	c.(949-951)aCg>aTg	p.T317M	WWOX_ENST00000539474.2_Intron|WWOX_ENST00000408984.3_Missense_Mutation_p.T317M|WWOX_ENST00000402655.2_Intron|WWOX_ENST00000406884.2_Intron	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase	317	Interaction with MAPT. {ECO:0000250}.				cellular response to transforming growth factor beta stimulus (GO:0071560)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of Wnt signaling pathway (GO:0030178)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system morphogenesis (GO:0048705)|steroid metabolic process (GO:0008202)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|cofactor binding (GO:0048037)|enzyme binding (GO:0019899)|oxidoreductase activity (GO:0016491)|protein dimerization activity (GO:0046983)			large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	7		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		CGCGGGGTCACGTCGAACGCA	0.537																																					p.T317M		Atlas-SNP	.											.	WWOX	98	.	0			c.C950T						.						141.0	144.0	143.0					16																	78466543		2082	4213	6295	SO:0001583	missense	51741	exon8			GGGTCACGTCGAA	AF187015	CCDS42196.1, CCDS42197.1	16q23.3-q24.1	2012-08-15	2002-01-14		ENSG00000186153	ENSG00000186153	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	12799	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 41C, member 1"""	605131	"""WW domain-containing oxidoreductase"""			10786676, 10861292, 19027726	Standard	XR_243411		Approved	FOR, WOX1, SDR41C1	uc002ffk.3	Q9NZC7	OTTHUMG00000176851	ENST00000566780.1:c.950C>T	chr16.hg19:g.78466543C>T	ENSP00000457230:p.Thr317Met	179.0	0.0		129.0	6.0	NM_016373	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	Missense_Mutation	SNP	ENST00000566780.1	hg19	CCDS42196.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.152312	0.57259	.	.	ENSG00000186153	ENST00000408984	T	0.24350	1.86	5.93	5.93	0.95920	NAD(P)-binding domain (1);	0.237347	0.41938	D	0.000798	T	0.55000	0.1893	M	0.89287	3.02	0.47737	D	0.999506	D	0.76494	0.999	P	0.56216	0.794	T	0.62676	-0.6804	10	0.87932	D	0	.	20.3261	0.98701	0.0:1.0:0.0:0.0	.	317	Q9NZC7	WWOX_HUMAN	M	317	ENSP00000386161:T317M	ENSP00000386161:T317M	T	+	2	0	WWOX	77024044	0.998000	0.40836	0.965000	0.40720	0.130000	0.20726	3.738000	0.55067	2.814000	0.96858	0.655000	0.94253	ACG	.	.		0.537	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434328.1		
DNAAF1	123872	hgsc.bcm.edu	37	16	84199541	84199541	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:84199541A>G	ENST00000378553.5	+	7	1140	c.1016A>G	c.(1015-1017)gAg>gGg	p.E339G	DNAAF1_ENST00000563818.1_3'UTR|DNAAF1_ENST00000334315.5_Missense_Mutation_p.E339G	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	339					axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						AGACAGAGAGAGAGTCAAGAG	0.522																																					p.E339G		Atlas-SNP	.											.	DNAAF1	81	.	0			c.A1016G						.						148.0	138.0	141.0					16																	84199541		2200	4300	6500	SO:0001583	missense	123872	exon7			AGAGAGAGAGTCA	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"""outer row dynein assembly 7 homolog (Chlamydomonas)"""	613190	"""leucine rich repeat containing 50"""	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1016A>G	chr16.hg19:g.84199541A>G	ENSP00000367815:p.Glu339Gly	116.0	0.0		94.0	4.0	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	hg19	CCDS10943.2	.	.	.	.	.	.	.	.	.	.	A	12.59	1.984904	0.35036	.	.	ENSG00000154099	ENST00000334315;ENST00000378553	T;T	0.38240	1.15;1.61	5.66	-3.15	0.05233	.	0.389186	0.24557	N	0.037519	T	0.23846	0.0577	L	0.46157	1.445	0.09310	N	1	B;B	0.24768	0.111;0.028	B;B	0.22753	0.041;0.027	T	0.15780	-1.0425	10	0.27785	T	0.31	-3.3565	7.9681	0.30111	0.3761:0.4341:0.1898:0.0	.	87;339	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	G	339	ENSP00000334593:E339G;ENSP00000367815:E339G	ENSP00000334593:E339G	E	+	2	0	DNAAF1	82757042	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.380000	0.20602	-0.642000	0.05480	-0.297000	0.09499	GAG	.	.		0.522	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
ZNF469	84627	hgsc.bcm.edu	37	16	88499778	88499778	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:88499778T>C	ENST00000437464.1	+	2	5816	c.5816T>C	c.(5815-5817)cTc>cCc	p.L1939P	ZNF469_ENST00000565624.1_Missense_Mutation_p.L1967P	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	1939					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						GTGACAACTCTCCCTGCAGTG	0.657																																					p.L1939P		Atlas-SNP	.											.	ZNF469	121	.	0			c.T5816C						.						17.0	24.0	22.0					16																	88499778		692	1585	2277	SO:0001583	missense	84627	exon2			CAACTCTCCCTGC	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.5816T>C	chr16.hg19:g.88499778T>C	ENSP00000402343:p.Leu1939Pro	52.0	0.0		54.0	4.0	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	hg19	CCDS45544.1	.	.	.	.	.	.	.	.	.	.	T	11.31	1.600101	0.28534	.	.	ENSG00000225614	ENST00000437464	T	0.08720	3.06	4.25	-4.85	0.03142	.	.	.	.	.	T	0.05227	0.0139	N	0.19112	0.55	0.09310	N	0.999999	P	0.50617	0.937	P	0.46110	0.504	T	0.14172	-1.0482	9	0.72032	D	0.01	.	2.2143	0.03955	0.1445:0.3991:0.1477:0.3087	.	1939	Q96JG9	ZN469_HUMAN	P	1939	ENSP00000402343:L1939P	ENSP00000402343:L1939P	L	+	2	0	ZNF469	87027279	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-1.992000	0.01476	-1.130000	0.02914	0.383000	0.25322	CTC	.	.		0.657	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
MVD	4597	hgsc.bcm.edu	37	16	88721665	88721665	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr16:88721665A>G	ENST00000301012.3	-	7	868	c.839T>C	c.(838-840)aTc>aCc	p.I280T	MVD_ENST00000568709.1_5'Flank	NM_002461.1	NP_002452.1	P53602	MVD1_HUMAN	mevalonate (diphospho) decarboxylase	280					cellular protein metabolic process (GO:0044267)|cholesterol biosynthetic process (GO:0006695)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|positive regulation of cell proliferation (GO:0008284)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|diphosphomevalonate decarboxylase activity (GO:0004163)|Hsp70 protein binding (GO:0030544)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(1)|lung(7)|ovary(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GCGCCAGGAGATGGCATTGAG	0.647																																					p.I280T		Atlas-SNP	.											.	MVD	27	.	0			c.T839C						.						251.0	192.0	212.0					16																	88721665		2189	4293	6482	SO:0001583	missense	4597	exon7			CAGGAGATGGCAT	U49260	CCDS10968.1	16q24.3	2010-04-29			ENSG00000167508	ENSG00000167508	4.1.1.33		7529	protein-coding gene	gene with protein product	"""mevalonate pyrophosphate decarboxylase"""	603236				8626466	Standard	NM_002461		Approved	MPD	uc002flg.1	P53602	OTTHUMG00000137865	ENST00000301012.3:c.839T>C	chr16.hg19:g.88721665A>G	ENSP00000301012:p.Ile280Thr	98.0	0.0		119.0	5.0	NM_002461	Q53Y65	Missense_Mutation	SNP	ENST00000301012.3	hg19	CCDS10968.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.003|0.003	-2.450778|-2.450778	0.00175|0.00175	.|.	.|.	ENSG00000167508|ENSG00000167508	ENST00000301012|ENST00000378400	T|.	0.28454|.	1.61|.	4.26|4.26	1.12|1.12	0.20585|0.20585	.|.	0.417901|.	0.26723|.	N|.	0.022833|.	T|T	0.08403|0.08403	0.0209|0.0209	N|N	0.00413|0.00413	-1.525|-1.525	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.26608|0.26608	-1.0098|-1.0098	10|6	0.08179|0.87932	T|D	0.78|0	-20.7405|-20.7405	7.6388|7.6388	0.28282|0.28282	0.5585:0.0:0.4415:0.0|0.5585:0.0:0.4415:0.0	.|.	280|.	P53602|.	MVD1_HUMAN|.	T|P	280|108	ENSP00000301012:I280T|.	ENSP00000301012:I280T|ENSP00000367653:S108P	I|S	-|-	2|1	0|0	MVD|MVD	87249166|87249166	0.034000|0.034000	0.19679|0.19679	0.064000|0.064000	0.19789|0.19789	0.028000|0.028000	0.11728|0.11728	2.503000|2.503000	0.45407|0.45407	0.041000|0.041000	0.15688|0.15688	-0.415000|-0.415000	0.06103|0.06103	ATC|TCT	.	.		0.647	MVD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269547.2	NM_002461	
FAM57A	79850	hgsc.bcm.edu	37	17	644578	644578	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:644578G>A	ENST00000308278.8	+	5	778	c.542G>A	c.(541-543)gGa>gAa	p.G181E	FAM57A_ENST00000301324.8_Missense_Mutation_p.G149E|FAM57A_ENST00000572018.1_3'UTR	NM_024792.1	NP_079068.1	Q8TBR7	FA57A_HUMAN	family with sequence similarity 57, member A	181	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G181E(1)		cervix(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(2)|urinary_tract(2)	10				UCEC - Uterine corpus endometrioid carcinoma (25;0.0217)		AAGGTGAATGGAATCCTCACG	0.542																																					p.G181E		Atlas-SNP	.											FAM57A,NS,carcinoma,0,1	FAM57A	17	.	1	Substitution - Missense(1)	prostate(1)	c.G542A						.						150.0	131.0	137.0					17																	644578		2203	4300	6503	SO:0001583	missense	79850	exon5			TGAATGGAATCCT	AK025935	CCDS10996.1	17p13.3	2014-08-14				ENSG00000167695			29646	protein-coding gene	gene with protein product		611627				12270127	Standard	NM_024792		Approved	FLJ22282, CT120	uc002frp.3	Q8TBR7		ENST00000308278.8:c.542G>A	chr17.hg19:g.644578G>A	ENSP00000312017:p.Gly181Glu	213.0	2.0		115.0	5.0	NM_024792	A8K7Q0|Q7Z464|Q96D97|Q9H6H3	Missense_Mutation	SNP	ENST00000308278.8	hg19	CCDS10996.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.472963	0.84640	.	.	ENSG00000167695	ENST00000308278;ENST00000301324;ENST00000451373	D;D	0.87256	-2.23;-2.23	6.17	5.15	0.70609	TRAM/LAG1/CLN8 homology domain (3);	0.047993	0.85682	D	0.000000	D	0.94331	0.8178	M	0.88979	2.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.94720	0.7900	10	0.87932	D	0	-12.009	16.1997	0.82060	0.0:0.1327:0.8673:0.0	.	149;181	Q8TBR7-1;Q8TBR7	.;FA57A_HUMAN	E	181;149;254	ENSP00000312017:G181E;ENSP00000301324:G149E	ENSP00000301324:G149E	G	+	2	0	FAM57A	591328	1.000000	0.71417	0.999000	0.59377	0.662000	0.39071	7.845000	0.86875	2.941000	0.99782	0.655000	0.94253	GGA	.	.		0.542	FAM57A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437155.2	NM_024792	
SMG6	23293	hgsc.bcm.edu	37	17	2202373	2202373	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:2202373A>G	ENST00000263073.6	-	2	1724	c.1674T>C	c.(1672-1674)ccT>ccC	p.P558P	SMG6_ENST00000544865.1_Silent_p.P527P	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	558					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						TGGTAGGTAGAGGGCTACACA	0.582																																					p.P558P	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.T1674C						.						199.0	186.0	191.0					17																	2202373		2203	4300	6503	SO:0001819	synonymous_variant	23293	exon2			AGGTAGAGGGCTA	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.1674T>C	chr17.hg19:g.2202373A>G		170.0	0.0		84.0	5.0	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Silent	SNP	ENST00000263073.6	hg19	CCDS11016.1																																																																																			.	.		0.582	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
OR1E2	8388	hgsc.bcm.edu	37	17	3336727	3336727	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:3336727A>G	ENST00000248384.1	-	1	408	c.409T>C	c.(409-411)Ttc>Ctc	p.F137L		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	137					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			endometrium(3)|large_intestine(3)|lung(3)	9						TGCAGGAGGAAGCAGATGGCG	0.552																																					p.F137L		Atlas-SNP	.											.	OR1E2	25	.	0			c.T409C						.						92.0	76.0	82.0					17																	3336727		2203	4300	6503	SO:0001583	missense	8388	exon1			GGAGGAAGCAGAT	U04686	CCDS11026.1	17p13.3	2012-08-09			ENSG00000127780	ENSG00000127780		"""GPCR / Class A : Olfactory receptors"""	8190	protein-coding gene	gene with protein product				OR1E4		8004088, 9500546	Standard	NM_003554		Approved	OR17-93, OR17-135	uc010vre.2	P47887	OTTHUMG00000090651	ENST00000248384.1:c.409T>C	chr17.hg19:g.3336727A>G	ENSP00000248384:p.Phe137Leu	260.0	0.0		116.0	6.0	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Missense_Mutation	SNP	ENST00000248384.1	hg19	CCDS11026.1	.	.	.	.	.	.	.	.	.	.	A	7.739	0.700830	0.15172	.	.	ENSG00000127780	ENST00000248384	T	0.01821	4.62	.	.	.	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.49466	-0.8937	5	0.87932	D	0	.	.	.	.	.	137	P47887	OR1E2_HUMAN	L	137	ENSP00000248384:F137L	ENSP00000248384:F137L	F	-	1	0	OR1E2	3283477	.	.	0.958000	0.39756	0.305000	0.27757	.	.	0.000000	0.14550	0.000000	0.15137	TTC	.	.		0.552	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1		
SPATA22	84690	hgsc.bcm.edu	37	17	3365782	3365782	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:3365782A>G	ENST00000573128.1	-	5	807	c.324T>C	c.(322-324)ggT>ggC	p.G108G	SPATA22_ENST00000355380.4_Silent_p.G65G|SPATA22_ENST00000572969.1_Silent_p.G108G|SPATA22_ENST00000397168.3_Silent_p.G108G|SPATA22_ENST00000268981.5_Silent_p.G108G|SPATA22_ENST00000541913.1_Silent_p.G92G|SPATA22_ENST00000575375.1_Silent_p.G108G			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	108					fertilization (GO:0009566)|gamete generation (GO:0007276)|meiotic DNA repair synthesis (GO:0000711)|regulation of meiotic cell cycle (GO:0051445)|reproductive system development (GO:0061458)|synapsis (GO:0007129)	chromosome (GO:0005694)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)	19						CTCACCTCCAACCACCCTGGC	0.403																																					p.G108G		Atlas-SNP	.											.	SPATA22	49	.	0			c.T324C						.						104.0	105.0	105.0					17																	3365782		2203	4300	6503	SO:0001819	synonymous_variant	84690	exon5			CCTCCAACCACCC	AY035868	CCDS11027.1, CCDS54066.1, CCDS54067.1	17p13.3	2005-12-19							30705	protein-coding gene	gene with protein product						12477932	Standard	NM_001170696		Approved	NYD-SP20	uc002fvn.3	Q8NHS9		ENST00000573128.1:c.324T>C	chr17.hg19:g.3365782A>G		122.0	0.0		64.0	4.0	NM_032598	B4DXB1|D3DTI9|J3KN63|Q969H3|Q96JT4	Silent	SNP	ENST00000573128.1	hg19	CCDS11027.1																																																																																			.	.		0.403	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598	
ZZEF1	23140	hgsc.bcm.edu	37	17	3917468	3917468	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:3917468A>G	ENST00000381638.2	-	51	8453	c.8329T>C	c.(8329-8331)Tac>Cac	p.Y2777H		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2777							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						GTGAAGCGGTAATACAGAGTG	0.562																																					p.Y2777H		Atlas-SNP	.											.	ZZEF1	195	.	0			c.T8329C						.						93.0	76.0	82.0					17																	3917468		2203	4300	6503	SO:0001583	missense	23140	exon51			AGCGGTAATACAG	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.8329T>C	chr17.hg19:g.3917468A>G	ENSP00000371051:p.Tyr2777His	156.0	0.0		85.0	5.0	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	hg19	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.894978	0.91962	.	.	ENSG00000074755	ENST00000381638	T	0.26223	1.75	5.69	5.69	0.88448	.	0.063428	0.64402	D	0.000003	T	0.41858	0.1177	L	0.32530	0.975	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.33675	-0.9859	10	0.87932	D	0	-15.9479	15.945	0.79787	1.0:0.0:0.0:0.0	.	2777	O43149	ZZEF1_HUMAN	H	2777	ENSP00000371051:Y2777H	ENSP00000371051:Y2777H	Y	-	1	0	ZZEF1	3864217	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.957000	0.93082	2.159000	0.67721	0.533000	0.62120	TAC	.	.		0.562	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
CAMTA2	23125	hgsc.bcm.edu	37	17	4883056	4883056	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:4883056T>C	ENST00000348066.3	-	9	1684	c.1561A>G	c.(1561-1563)Atc>Gtc	p.I521V	CAMTA2_ENST00000361571.5_Missense_Mutation_p.I520V|CAMTA2_ENST00000572543.1_Missense_Mutation_p.I526V|CAMTA2_ENST00000414043.3_Missense_Mutation_p.I544V|CAMTA2_ENST00000358183.4_Missense_Mutation_p.I521V|CAMTA2_ENST00000381311.5_Missense_Mutation_p.I523V|CAMTA2_ENST00000571831.1_5'Flank	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	521					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						GGAGCAGGGATGCTTGGAGCT	0.557																																					p.I544V		Atlas-SNP	.											.	CAMTA2	93	.	0			c.A1630G						.						132.0	131.0	131.0					17																	4883056		2203	4300	6503	SO:0001583	missense	23125	exon9			CAGGGATGCTTGG	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.1561A>G	chr17.hg19:g.4883056T>C	ENSP00000321813:p.Ile521Val	91.0	0.0		42.0	4.0	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	hg19	CCDS11063.1	.	.	.	.	.	.	.	.	.	.	T	3.368	-0.129134	0.06753	.	.	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.31247	2.71;1.73;1.5;1.73;1.51	4.79	-3.37	0.04898	.	0.844005	0.10161	N	0.708334	T	0.09862	0.0242	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001	T	0.34179	-0.9839	10	0.15499	T	0.54	-1.43	4.7504	0.13057	0.1368:0.5329:0.1394:0.1909	.	497;544;523;521;520	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	V	544;523;520;521;521	ENSP00000412886:I544V;ENSP00000370712:I523V;ENSP00000354828:I520V;ENSP00000350910:I521V;ENSP00000321813:I521V	ENSP00000321813:I521V	I	-	1	0	CAMTA2	4823780	0.000000	0.05858	0.162000	0.22713	0.726000	0.41606	-0.646000	0.05403	-0.476000	0.06842	0.533000	0.62120	ATC	.	.		0.557	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099	
FAM64A	54478	hgsc.bcm.edu	37	17	6352638	6352638	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:6352638T>C	ENST00000250056.8	+	4	680	c.597T>C	c.(595-597)tcT>tcC	p.S199S	FAM64A_ENST00000572595.2_Silent_p.S230S|FAM64A_ENST00000576056.1_Silent_p.S199S|FAM64A_ENST00000572447.1_Silent_p.S199S|FAM64A_ENST00000570337.2_Silent_p.S199S|FAM64A_ENST00000571373.1_Silent_p.S199S	NM_001195228.1	NP_001182157.1	Q9BSJ6	FA64A_HUMAN	family with sequence similarity 64, member A	199			S -> C (in dbSNP:rs16955870).		mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				COAD - Colon adenocarcinoma(228;0.141)		GCAGCGAGTCTGACAGTGACC	0.567																																					p.S199S		Atlas-SNP	.											.	FAM64A	20	.	0			c.T597C						.						100.0	98.0	99.0					17																	6352638		2203	4300	6503	SO:0001819	synonymous_variant	54478	exon4			CGAGTCTGACAGT		CCDS32541.1, CCDS56016.1	17p13.2	2013-10-11			ENSG00000129195	ENSG00000129195			25483	protein-coding gene	gene with protein product	"""CALM interacting protein expressed in thymus and spleen"""					19383357, 16491119	Standard	NM_019013		Approved	FLJ10156, FLJ10491, CATS	uc002gcw.2	Q9BSJ6	OTTHUMG00000177832	ENST00000250056.8:c.597T>C	chr17.hg19:g.6352638T>C		134.0	0.0		85.0	4.0	NM_019013	Q96CT4|Q9NVV1|Q9NWB5	Silent	SNP	ENST00000250056.8	hg19	CCDS56016.1																																																																																			.	.		0.567	FAM64A-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439156.1	NM_019013	
PITPNM3	83394	hgsc.bcm.edu	37	17	6367544	6367544	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:6367544A>G	ENST00000262483.8	-	16	2189	c.2102T>C	c.(2101-2103)gTg>gCg	p.V701A	PITPNM3_ENST00000576664.1_5'UTR|PITPNM3_ENST00000421306.3_Missense_Mutation_p.V665A	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	701					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		GGGCCGCGGCACATTGTATGT	0.577																																					p.V701A		Atlas-SNP	.											.	PITPNM3	91	.	0			c.T2102C						.						81.0	80.0	80.0					17																	6367544		2203	4300	6503	SO:0001583	missense	83394	exon16			CGCGGCACATTGT	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"""GPCR / Class A : Chemokine receptors : Atypical"""	21043	protein-coding gene	gene with protein product	"""atypical chemokine receptor 6"""	608921	"""cone rod dystrophy 5"""	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.2102T>C	chr17.hg19:g.6367544A>G	ENSP00000262483:p.Val701Ala	100.0	0.0		63.0	4.0	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Missense_Mutation	SNP	ENST00000262483.8	hg19	CCDS11076.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.021258	0.54576	.	.	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.50548	0.74;0.75	4.65	4.65	0.58169	.	0.192544	0.44285	D	0.000463	T	0.45216	0.1331	L	0.55990	1.75	0.40089	D	0.976238	P;B	0.44521	0.837;0.293	B;B	0.41412	0.356;0.108	T	0.54063	-0.8349	10	0.87932	D	0	.	12.3053	0.54898	1.0:0.0:0.0:0.0	.	665;701	F8WEW5;Q9BZ71	.;PITM3_HUMAN	A	701;665	ENSP00000262483:V701A;ENSP00000407882:V665A	ENSP00000262483:V701A	V	-	2	0	PITPNM3	6308268	1.000000	0.71417	0.931000	0.37212	0.506000	0.33950	9.235000	0.95353	1.855000	0.53841	0.418000	0.28097	GTG	.	.		0.577	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220	
PITPNM3	83394	hgsc.bcm.edu	37	17	6386875	6386875	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:6386875A>G	ENST00000262483.8	-	6	636	c.549T>C	c.(547-549)tgT>tgC	p.C183C	PITPNM3_ENST00000421306.3_Silent_p.C147C	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	183					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		AGATGGCAGGACAGGGGACGA	0.572																																					p.C183C		Atlas-SNP	.											.	PITPNM3	91	.	0			c.T549C						.						142.0	97.0	112.0					17																	6386875		2203	4300	6503	SO:0001819	synonymous_variant	83394	exon6			GGCAGGACAGGGG	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"""GPCR / Class A : Chemokine receptors : Atypical"""	21043	protein-coding gene	gene with protein product	"""atypical chemokine receptor 6"""	608921	"""cone rod dystrophy 5"""	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.549T>C	chr17.hg19:g.6386875A>G		200.0	0.0		83.0	4.0	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Silent	SNP	ENST00000262483.8	hg19	CCDS11076.1																																																																																			.	.		0.572	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220	
TMEM95	339168	hgsc.bcm.edu	37	17	7259191	7259191	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:7259191T>C	ENST00000576060.1	+	3	288	c.261T>C	c.(259-261)taT>taC	p.Y87Y	TMEM95_ENST00000330767.4_Silent_p.Y87Y|TMEM95_ENST00000389982.4_Silent_p.Y87Y|RP11-542C16.1_ENST00000572417.1_RNA			Q3KNT9	TMM95_HUMAN	transmembrane protein 95	87						integral component of membrane (GO:0016021)				large_intestine(1)|lung(2)	3		Prostate(122;0.173)				TCCCTTCATATTGGAGTTGGC	0.577											OREG0024137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y87Y		Atlas-SNP	.											.	TMEM95	11	.	0			c.T261C						.						98.0	83.0	88.0					17																	7259191		2203	4300	6503	SO:0001819	synonymous_variant	339168	exon3			TTCATATTGGAGT		CCDS32546.1	17p13.1	2005-12-15			ENSG00000182896	ENSG00000182896			27898	protein-coding gene	gene with protein product						12975309	Standard	NM_198154		Approved	MGC129793, UNQ9390	uc002ggf.1	Q3KNT9	OTTHUMG00000132899	ENST00000576060.1:c.261T>C	chr17.hg19:g.7259191T>C		130.0	0.0	640	72.0	4.0	NM_198154	B7WPI7|Q6UXT3|Q8IW68	Silent	SNP	ENST00000576060.1	hg19																																																																																				.	.		0.577	TMEM95-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440555.2	NM_198154	
TMEM102	284114	hgsc.bcm.edu	37	17	7340050	7340050	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:7340050C>T	ENST00000323206.1	+	3	1025	c.752C>T	c.(751-753)cCg>cTg	p.P251L	RP11-104H15.8_ENST00000576615.1_RNA|FGF11_ENST00000293829.4_5'Flank|RP11-104H15.7_ENST00000575310.1_RNA|RP11-104H15.10_ENST00000575331.1_RNA|RP11-104H15.9_ENST00000570444.1_RNA|FGF11_ENST00000575235.1_5'Flank|TMEM102_ENST00000396568.1_Missense_Mutation_p.P251L	NM_178518.2	NP_848613.1	Q8N9M5	TM102_HUMAN	transmembrane protein 102	251					apoptotic process (GO:0006915)|positive regulation of cell adhesion (GO:0045785)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell migration (GO:2000406)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				kidney(1)|lung(3)|skin(1)	5		Prostate(122;0.173)				GTCCCAAAGCCGTCGGAGGCT	0.607																																					p.P251L		Atlas-SNP	.											.	TMEM102	11	.	0			c.C752T						.						77.0	80.0	79.0					17																	7340050		2203	4300	6503	SO:0001583	missense	284114	exon3			CAAAGCCGTCGGA	AK094197	CCDS11104.1	17p13.1	2008-04-21			ENSG00000181284	ENSG00000181284			26722	protein-coding gene	gene with protein product		613936				12477932	Standard	NM_178518		Approved	FLJ36878	uc002ggx.1	Q8N9M5	OTTHUMG00000132901	ENST00000323206.1:c.752C>T	chr17.hg19:g.7340050C>T	ENSP00000315387:p.Pro251Leu	105.0	0.0		72.0	4.0	NM_178518	D3DTP8	Missense_Mutation	SNP	ENST00000323206.1	hg19	CCDS11104.1	.	.	.	.	.	.	.	.	.	.	C	6.007	0.369720	0.11352	.	.	ENSG00000181284	ENST00000323206;ENST00000396568	T;T	0.41400	1.0;1.0	4.7	1.57	0.23409	.	0.814572	0.10946	N	0.616737	T	0.28034	0.0691	L	0.29908	0.895	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.26360	-1.0105	10	0.72032	D	0.01	-13.1651	4.4547	0.11637	0.1759:0.6361:0.0:0.188	.	251	Q8N9M5	TM102_HUMAN	L	251	ENSP00000315387:P251L;ENSP00000379815:P251L	ENSP00000315387:P251L	P	+	2	0	TMEM102	7280774	0.000000	0.05858	0.000000	0.03702	0.090000	0.18270	0.013000	0.13310	0.290000	0.22444	0.561000	0.74099	CCG	.	.		0.607	TMEM102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256405.1	NM_178518	
ALOXE3	59344	hgsc.bcm.edu	37	17	8011902	8011902	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:8011902A>G	ENST00000448843.2	-	13	1908	c.1568T>C	c.(1567-1569)gTc>gCc	p.V523A	ALOXE3_ENST00000318227.3_Missense_Mutation_p.V655A|ALOXE3_ENST00000380149.1_Missense_Mutation_p.V679A	NM_021628.2	NP_067641.2	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3	523	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|fat cell differentiation (GO:0045444)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|sensory perception of pain (GO:0019233)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)	hepoxilin A3 synthase activity (GO:0051120)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	31						GATTTCTGAGACAAAGCTGCA	0.572																																					p.V655A		Atlas-SNP	.											.	ALOXE3	145	.	0			c.T1964C						.						75.0	73.0	74.0					17																	8011902		2203	4300	6503	SO:0001583	missense	59344	exon13			TCTGAGACAAAGC	AJ269499	CCDS11130.1, CCDS54084.1	17p13.1	2009-07-10			ENSG00000179148	ENSG00000179148	1.13.11.-	"""Arachidonate lipoxygenases"""	13743	protein-coding gene	gene with protein product		607206					Standard	NM_021628		Approved	eLOX3, E-LOX	uc010vuo.2	Q9BYJ1	OTTHUMG00000108179	ENST00000448843.2:c.1568T>C	chr17.hg19:g.8011902A>G	ENSP00000400581:p.Val523Ala	82.0	0.0		58.0	4.0	NM_001165960	B2R981|B7Z3W0|Q3ZB74|Q9H4F2|Q9HC22	Missense_Mutation	SNP	ENST00000448843.2	hg19	CCDS11130.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.400843	0.83120	.	.	ENSG00000179148	ENST00000380149;ENST00000318227;ENST00000448843	D;D;D	0.82803	-1.65;-1.65;-1.65	4.85	4.85	0.62838	Lipoxygenase, C-terminal (3);	0.058203	0.64402	D	0.000002	D	0.88980	0.6585	M	0.68952	2.095	0.58432	D	0.999999	D;D;D	0.63880	0.99;0.993;0.993	D;D;D	0.67382	0.91;0.951;0.951	D	0.89834	0.3998	10	0.62326	D	0.03	-35.6089	13.5611	0.61790	1.0:0.0:0.0:0.0	.	655;523;523	B7Z3W0;Q9BYJ1;B3KVD2	.;LOXE3_HUMAN;.	A	679;655;523	ENSP00000369494:V679A;ENSP00000314879:V655A;ENSP00000400581:V523A	ENSP00000314879:V655A	V	-	2	0	ALOXE3	7952627	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.725000	0.61979	2.051000	0.60960	0.460000	0.39030	GTC	.	.		0.572	ALOXE3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441475.1		
MYO15A	51168	hgsc.bcm.edu	37	17	18063265	18063265	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:18063265A>G	ENST00000205890.5	+	56	9658	c.9320A>G	c.(9319-9321)gAg>gGg	p.E3107G	MYO15A_ENST00000451725.2_5'UTR|MYO15A_ENST00000418233.3_Missense_Mutation_p.E371G	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3107	MyTH4 2. {ECO:0000255|PROSITE- ProRule:PRU00359}.|Tail.				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)					GGGGACCATGAGGTCATGCGG	0.532																																					p.E3107G		Atlas-SNP	.											.	MYO15A	268	.	0			c.A9320G						.						104.0	106.0	105.0					17																	18063265		2105	4225	6330	SO:0001583	missense	51168	exon55			ACCATGAGGTCAT	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.9320A>G	chr17.hg19:g.18063265A>G	ENSP00000205890:p.Glu3107Gly	95.0	0.0		66.0	4.0	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	A	13.24	2.179418	0.38511	.	.	ENSG00000091536	ENST00000205890;ENST00000418233;ENST00000556535	D;D	0.92446	-3.04;-3.04	5.6	5.6	0.85130	MyTH4 domain (3);	.	.	.	.	D	0.89739	0.6802	L	0.38733	1.17	0.80722	D	1	B;B;B;B	0.28783	0.018;0.222;0.217;0.037	B;B;B;B	0.37943	0.039;0.261;0.121;0.055	D	0.86719	0.1941	9	0.25751	T	0.34	.	15.7766	0.78224	1.0:0.0:0.0:0.0	.	96;371;3107;114	B4DLV9;B4DFC7;Q9UKN7;Q8TCK0	.;.;MYO15_HUMAN;.	G	3107;96;61	ENSP00000205890:E3107G;ENSP00000451782:E61G	ENSP00000205890:E3107G	E	+	2	0	MYO15A	18003990	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.985000	0.70556	2.143000	0.66587	0.459000	0.35465	GAG	.	.		0.532	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
SPECC1	92521	hgsc.bcm.edu	37	17	20108053	20108053	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:20108053G>A	ENST00000261503.5	+	4	742	c.691G>A	c.(691-693)Gag>Aag	p.E231K	SPECC1_ENST00000584527.1_5'Flank|SPECC1_ENST00000395530.2_Missense_Mutation_p.E150K|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000395527.4_Missense_Mutation_p.E231K|SPECC1_ENST00000395525.3_Missense_Mutation_p.E150K|SPECC1_ENST00000395522.2_Missense_Mutation_p.E150K|AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000395529.3_Missense_Mutation_p.E231K|SPECC1_ENST00000472876.1_Intron	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	231					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		AGCTCTTGAGGAGAAGAACAA	0.478																																					p.E231K		Atlas-SNP	.											.	SPECC1	100	.	0			c.G691A						.						131.0	145.0	140.0					17																	20108053		2203	4300	6503	SO:0001583	missense	92521	exon4			CTTGAGGAGAAGA	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"""sperm antigen HCMOGT 1"", ""cytokinesis and spindle organization B"", ""cytospin B"""	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.691G>A	chr17.hg19:g.20108053G>A	ENSP00000261503:p.Glu231Lys	87.0	0.0		87.0	7.0	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	hg19	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	G	32	5.184086	0.94885	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T	0.75050	-0.9;2.1;2.15;2.14	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.85509	0.5713	M	0.71036	2.16	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.999;0.999;1.0	D;D;D;D;D	0.85130	0.994;0.997;0.997;0.997;0.979	D	0.86658	0.1902	10	0.72032	D	0.01	-31.671	16.7847	0.85571	0.0:0.0:1.0:0.0	.	231;150;150;231;231	A8MV89;Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;.;CYTSB_HUMAN	K	231;231;231;150;150;150	ENSP00000261503:E231K;ENSP00000378900:E231K;ENSP00000378893:E150K;ENSP00000378896:E150K	ENSP00000261503:E231K	E	+	1	0	SPECC1	20048645	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.167000	0.94773	2.642000	0.89623	0.655000	0.94253	GAG	.	.		0.478	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
SUPT6H	6830	hgsc.bcm.edu	37	17	27025001	27025001	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:27025001A>G	ENST00000314616.6	+	32	4684	c.4401A>G	c.(4399-4401)gaA>gaG	p.E1467E	SUPT6H_ENST00000347486.4_Silent_p.E1467E	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1467					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)					CCTGCAAGGAACTGCCCGGCA	0.537																																					p.E1467E		Atlas-SNP	.											.	SUPT6H	165	.	0			c.A4401G						.						75.0	73.0	73.0					17																	27025001		2203	4300	6503	SO:0001819	synonymous_variant	6830	exon32			CAAGGAACTGCCC	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.4401A>G	chr17.hg19:g.27025001A>G		47.0	0.0		58.0	4.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.		0.537	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
RAB34	83871	hgsc.bcm.edu	37	17	27042082	27042082	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:27042082T>C	ENST00000395245.3	-	8	1198	c.572A>G	c.(571-573)aAg>aGg	p.K191R	RAB34_ENST00000395242.2_Missense_Mutation_p.K192R|RAB34_ENST00000301043.6_Missense_Mutation_p.K191R|RAB34_ENST00000450529.1_Missense_Mutation_p.K183R|RAB34_ENST00000436730.3_Missense_Mutation_p.K191R|RAB34_ENST00000453384.3_Splice_Site_p.K249R|RAB34_ENST00000447716.1_Missense_Mutation_p.K248R|RAB34_ENST00000415040.2_Missense_Mutation_p.K169R|RAB34_ENST00000395243.3_Missense_Mutation_p.K183R	NM_001256281.1|NM_031934.5	NP_001243210.1|NP_114140.4	Q9BZG1	RAB34_HUMAN	RAB34, member RAS oncogene family	191					antigen processing and presentation (GO:0019882)|Golgi to plasma membrane protein transport (GO:0043001)|lysosome localization (GO:0032418)|phagosome maturation (GO:0090382)|phagosome-lysosome fusion (GO:0090385)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|vesicle (GO:0031982)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|skin(2)	14	Lung NSC(42;0.00431)					GTACTCAGCCTTCATCTCCTG	0.587																																					p.K249R	Pancreas(175;216 2049 29940 32498 41589)	Atlas-SNP	.											.	RAB34	44	.	0			c.A746G						.						86.0	74.0	78.0					17																	27042082		2203	4300	6503	SO:0001583	missense	83871	exon9			TCAGCCTTCATCT	AF322067	CCDS11240.1, CCDS45636.1, CCDS54101.1, CCDS58536.1	17q11.2	2008-07-18			ENSG00000109113	ENSG00000109113		"""RAB, member RAS oncogene"""	16519	protein-coding gene	gene with protein product		610917				12446704	Standard	NM_031934		Approved	RAB39, RAH	uc010was.1	P0DI83	OTTHUMG00000132680	ENST00000395245.3:c.572A>G	chr17.hg19:g.27042082T>C	ENSP00000378666:p.Lys191Arg	86.0	0.0		70.0	4.0	NM_001142625	B4E3A0|E9PEJ9|Q5BJE6|Q8NCJ8|Q96AR4	Missense_Mutation	SNP	ENST00000395245.3	hg19	CCDS11240.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.65|12.65	2.001371|2.001371	0.35320|0.35320	.|.	.|.	ENSG00000109113|ENSG00000109113	ENST00000453384;ENST00000447716;ENST00000301043;ENST00000395243;ENST00000415040;ENST00000450529;ENST00000395242;ENST00000395245;ENST00000436730;ENST00000430132;ENST00000412625;ENST00000353676|ENST00000419712	T;T;T;T;T;T;T;T;T|.	0.80304|.	-1.1;-1.36;-1.36;-1.36;-1.36;-1.36;-1.36;-1.36;-1.36|.	5.01|5.01	5.01|5.01	0.66863|0.66863	Small GTP-binding protein domain (1);|.	0.268600|.	0.38778|.	N|.	0.001569|.	T|T	0.47377|0.47377	0.1442|0.1442	N|N	0.25789|0.25789	0.76|0.76	.|.	.|.	.|.	B;B;B;B;B;B;B|.	0.18610|.	0.029;0.001;0.002;0.002;0.004;0.005;0.001|.	B;B;B;B;B;B;B|.	0.15484|.	0.012;0.005;0.005;0.007;0.012;0.013;0.005|.	T|T	0.56649|0.56649	-0.7944|-0.7944	9|4	0.18710|.	T|.	0.47|.	-22.8504|-22.8504	13.7031|13.7031	0.62622|0.62622	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	249;169;183;214;206;192;191|.	E7ES60;E9PEJ9;Q9BZG1-2;C9JI96;B4DNC0;A8MYQ9;Q9BZG1|.	.;.;.;.;.;.;RAB34_HUMAN|.	R|G	249;248;191;183;169;206;192;191;214;192;191;191|212	ENSP00000413156:K249R;ENSP00000410403:K248R;ENSP00000301043:K191R;ENSP00000378664:K183R;ENSP00000410279:K169R;ENSP00000378663:K192R;ENSP00000378666:K191R;ENSP00000398706:K191R;ENSP00000226259:K191R|.	ENSP00000301043:K191R|.	K|R	-|-	2|1	0|2	RAB34|RAB34	24066209|24066209	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	3.085000|3.085000	0.50151|0.50151	2.107000|2.107000	0.64212|0.64212	0.379000|0.379000	0.24179|0.24179	AAG|AGA	.	.		0.587	RAB34-018	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345906.1	NM_031934	
PIPOX	51268	hgsc.bcm.edu	37	17	27371932	27371932	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:27371932A>G	ENST00000323372.4	+	2	496	c.170A>G	c.(169-171)aAg>aGg	p.K57R	PIPOX_ENST00000583215.1_3'UTR	NM_016518.2	NP_057602.2	Q9P0Z9	SOX_HUMAN	pipecolic acid oxidase	57					L-lysine catabolic process to acetyl-CoA via L-pipecolate (GO:0033514)|oxidation-reduction process (GO:0055114)|tetrahydrofolate metabolic process (GO:0046653)	peroxisome (GO:0005777)	L-pipecolate oxidase activity (GO:0050031)|receptor binding (GO:0005102)|sarcosine oxidase activity (GO:0008115)			endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10	Lung NSC(42;0.015)		Epithelial(11;9.87e-06)|BRCA - Breast invasive adenocarcinoma(11;3.92e-05)|all cancers(11;5.59e-05)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)		Glycine(DB00145)	ATAATCCGAAAGGCGTACCTG	0.522																																					p.K57R		Atlas-SNP	.											.	PIPOX	42	.	0			c.A170G						.						127.0	112.0	117.0					17																	27371932		2203	4300	6503	SO:0001583	missense	51268	exon2			TCCGAAAGGCGTA	AF134593	CCDS11248.1	17p13.2	2008-07-18			ENSG00000179761	ENSG00000179761			17804	protein-coding gene	gene with protein product	"""L-pipecolic acid oxidase"""					10772957, 10642506	Standard	NM_016518		Approved	LPIPOX	uc002hdr.1	Q9P0Z9	OTTHUMG00000132679	ENST00000323372.4:c.170A>G	chr17.hg19:g.27371932A>G	ENSP00000317721:p.Lys57Arg	147.0	0.0		114.0	5.0	NM_016518	B3KNH0|Q96H28|Q9C070	Missense_Mutation	SNP	ENST00000323372.4	hg19	CCDS11248.1	.	.	.	.	.	.	.	.	.	.	A	11.34	1.611071	0.28712	.	.	ENSG00000179761	ENST00000323372	T	0.80994	-1.44	5.8	1.45	0.22620	FAD dependent oxidoreductase (1);	0.236909	0.49305	N	0.000156	T	0.56247	0.1972	N	0.05351	-0.065	0.38045	D	0.935605	B	0.10296	0.003	B	0.16289	0.015	T	0.41052	-0.9530	10	0.14656	T	0.56	-6.9605	7.1044	0.25356	0.5947:0.0:0.4053:0.0	.	57	Q9P0Z9	SOX_HUMAN	R	57	ENSP00000317721:K57R	ENSP00000317721:K57R	K	+	2	0	PIPOX	24396058	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	2.181000	0.42547	0.637000	0.30526	0.528000	0.53228	AAG	.	.		0.522	PIPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255954.1	NM_016518	
MYO18A	399687	hgsc.bcm.edu	37	17	27414105	27414105	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:27414105T>A	ENST00000527372.1	-	38	5741	c.5561A>T	c.(5560-5562)aAg>aTg	p.K1854M	MYO18A_ENST00000533112.1_Missense_Mutation_p.K1817M|MYO18A_ENST00000354329.4_Missense_Mutation_p.K1854M|MYO18A_ENST00000531253.1_Missense_Mutation_p.K1854M|MYO18A_ENST00000529578.1_5'UTR|TIAF1_ENST00000408971.2_De_novo_Start_InFrame	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1854					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)			CTCAGTCAGCTTCTCCATGTT	0.592																																					p.K1854M	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.A5561T						.						97.0	101.0	100.0					17																	27414105		2042	4191	6233	SO:0001583	missense	399687	exon38			GTCAGCTTCTCCA	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.5561A>T	chr17.hg19:g.27414105T>A	ENSP00000437073:p.Lys1854Met	174.0	0.0		144.0	52.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.4|28.4	4.917267|4.917267	0.92249|0.92249	.|.	.|.	ENSG00000196535|ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000529799;ENST00000540575;ENST00000458428;ENST00000546105|ENST00000527859	D;D;D;D|.	0.90197|.	-2.4;-2.63;-2.38;-2.4|.	5.18|5.18	5.18|5.18	0.71444|0.71444	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75903|0.75903	0.3913|0.3913	M|M	0.78456|0.78456	2.415|2.415	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.91635|.	0.998;0.999;0.999;0.998|.	T|T	0.77083|0.77083	-0.2719|-0.2719	10|5	0.87932|.	D|.	0|.	.|.	15.5158|15.5158	0.75822|0.75822	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1457;1817;1854;1854|.	F8W6Y3;Q92614-3;Q92614-4;Q92614|.	.;.;.;MY18A_HUMAN|.	M|C	1854;1817;1817;1854;1854;750;750;1457;135|117	ENSP00000346291:K1854M;ENSP00000435932:K1817M;ENSP00000434228:K1854M;ENSP00000437073:K1854M|.	ENSP00000346291:K1854M|.	K|S	-|-	2|1	0|0	MYO18A|MYO18A	24438231|24438231	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	7.217000|7.217000	0.77982|0.77982	2.317000|2.317000	0.78254|0.78254	0.459000|0.459000	0.35465|0.35465	AAG|AGC	.	.		0.592	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
AP2B1	163	hgsc.bcm.edu	37	17	33925250	33925250	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:33925250A>G	ENST00000262325.7	+	3	592	c.39A>G	c.(37-39)ggA>ggG	p.G13G	AP2B1_ENST00000312678.8_Splice_Site_p.G13G|AP2B1_ENST00000592545.1_Splice_Site_p.G13G|AP2B1_ENST00000537622.2_Splice_Site_p.G13G|AP2B1_ENST00000538556.1_5'UTR|AP2B1_ENST00000589344.1_Splice_Site_p.G13G	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	13					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		CTCTTGCAGGAGAAATATTTG	0.418																																					p.G13G		Atlas-SNP	.											.	AP2B1	70	.	0			c.A39G						.						77.0	74.0	75.0					17																	33925250		2203	4300	6503	SO:0001630	splice_region_variant	163	exon3			TGCAGGAGAAATA	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.38-1A>G	chr17.hg19:g.33925250A>G		110.0	0.0		85.0	4.0	NM_001282	A6NJP3|P21851|Q7Z451|Q96J19	Silent	SNP	ENST00000262325.7	hg19	CCDS32622.1																																																																																			.	.		0.418	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1		Silent
CCL5	6352	hgsc.bcm.edu	37	17	34205643	34205643	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:34205643T>C	ENST00000293272.3	-	2	279	c.77A>G	c.(76-78)tAt>tGt	p.Y26C	AC015849.2_ENST00000413928.1_RNA|CCL5_ENST00000366113.3_Splice_Site_p.Y26C	NM_002985.2	NP_002976.2	P13501	CCL5_HUMAN	chemokine (C-C motif) ligand 5	26		Cleavage; by DPP4.			activation of phospholipase D activity (GO:0031584)|calcium ion transport (GO:0006816)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|cellular protein complex assembly (GO:0043623)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|eosinophil chemotaxis (GO:0048245)|exocytosis (GO:0006887)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage chemotaxis (GO:0048246)|MAPK cascade (GO:0000165)|monocyte chemotaxis (GO:0002548)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of T cell apoptotic process (GO:0070233)|negative regulation of viral genome replication (GO:0045071)|neutrophil activation (GO:0042119)|positive chemotaxis (GO:0050918)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of cellular biosynthetic process (GO:0031328)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of innate immune response (GO:0045089)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of natural killer cell chemotaxis (GO:2000503)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell apoptotic process (GO:0070234)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell migration (GO:2000406)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of translational initiation (GO:0045948)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|positive regulation of viral genome replication (GO:0045070)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein tetramerization (GO:0051262)|regulation of chronic inflammatory response (GO:0002676)|regulation of insulin secretion (GO:0050796)|regulation of neuron death (GO:1901214)|regulation of T cell activation (GO:0050863)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|CCR4 chemokine receptor binding (GO:0031729)|CCR5 chemokine receptor binding (GO:0031730)|chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)|chemokine receptor antagonist activity (GO:0046817)|chemokine receptor binding (GO:0042379)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase activator activity (GO:0016004)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|receptor signaling protein tyrosine kinase activator activity (GO:0030298)			breast(1)|kidney(1)|lung(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0183)		GTCCGAGGAATCTGGAAGAGG	0.483																																					p.Y26C		Atlas-SNP	.											.	CCL5	6	.	0			c.A77G						.						95.0	93.0	94.0					17																	34205643		2203	4300	6503	SO:0001630	splice_region_variant	6352	exon2			GAGGAATCTGGAA	AF043341	CCDS11300.1	17q11.2-q12	2014-04-17	2002-08-22	2002-08-23	ENSG00000161570	ENSG00000271503		"""Chemokine ligands"", ""Endogenous ligands"""	10632	protein-coding gene	gene with protein product	"""T-cell specific protein p288"", ""T-cell specific RANTES protein"", ""SIS-delta"", ""regulated upon activation, normally T-expressed, and presumably secreted"", ""beta-chemokine RANTES"", ""small inducible cytokine subfamily A (Cys-Cys), member 5"""	187011	"""small inducible cytokine A5 (RANTES)"""	D17S136E, SCYA5		1691736	Standard	NM_002985		Approved	RANTES, SISd, TCP228, MGC17164	uc002hkf.3	P13501	OTTHUMG00000188396	ENST00000293272.3:c.77-1A>G	chr17.hg19:g.34205643T>C		112.0	0.0		75.0	4.0	NM_002985	O43646|Q0QVW8|Q4ZGJ1|Q9NYA2|Q9UBG2|Q9UC99	Missense_Mutation	SNP	ENST00000293272.3	hg19	CCDS11300.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.963544	0.53507	.	.	ENSG00000161570	ENST00000293272;ENST00000366113	T;T	0.02369	4.32;4.32	5.39	5.39	0.77823	Chemokine interleukin-8-like domain (1);	0.488660	0.21839	N	0.068354	T	0.05135	0.0137	.	.	.	0.49483	D	0.999794	P	0.51537	0.946	P	0.46543	0.52	T	0.46898	-0.9158	9	0.42905	T	0.14	.	11.7182	0.51666	0.0:0.0:0.0:1.0	.	26	P13501	CCL5_HUMAN	C	26	ENSP00000293272:Y26C;ENSP00000375216:Y26C	ENSP00000293272:Y26C	Y	-	2	0	CCL5	31229756	1.000000	0.71417	1.000000	0.80357	0.598000	0.36846	1.134000	0.31442	2.266000	0.75297	0.533000	0.62120	TAT	.	.		0.483	CCL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256486.3	NM_002985	Missense_Mutation
GRB7	2886	hgsc.bcm.edu	37	17	37901211	37901211	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:37901211T>C	ENST00000309156.4	+	9	1242	c.985T>C	c.(985-987)Tgg>Cgg	p.W329R	GRB7_ENST00000309185.3_Missense_Mutation_p.W329R|GRB7_ENST00000394211.3_Missense_Mutation_p.W329R|GRB7_ENST00000394209.2_Missense_Mutation_p.W329R|GRB7_ENST00000445327.2_Missense_Mutation_p.W352R|GRB7_ENST00000394204.1_Missense_Mutation_p.W329R	NM_005310.3	NP_005301.2	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7	329	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|leukocyte migration (GO:0050900)|negative regulation of translation (GO:0017148)|positive regulation of cell migration (GO:0030335)|positive regulation of signal transduction (GO:0009967)|stress granule assembly (GO:0034063)	cell projection (GO:0042995)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CCGCACCTGCTGGCTGGCTGC	0.612																																					p.W352R		Atlas-SNP	.											.	GRB7	48	.	0			c.T1054C						.						37.0	40.0	39.0					17																	37901211		2202	4300	6502	SO:0001583	missense	2886	exon9			ACCTGCTGGCTGG	D43772	CCDS11345.1, CCDS56028.1	17q12	2013-02-14			ENSG00000141738	ENSG00000141738		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4567	protein-coding gene	gene with protein product		601522					Standard	NM_005310		Approved		uc021twu.1	Q14451	OTTHUMG00000133253	ENST00000309156.4:c.985T>C	chr17.hg19:g.37901211T>C	ENSP00000310771:p.Trp329Arg	84.0	0.0		83.0	4.0	NM_001242442	B2RAV1|B3KNL0|B3KWP9|B7WP75|J3KQM4|Q53YD3|Q92568|Q96DF9|Q9Y220	Missense_Mutation	SNP	ENST00000309156.4	hg19	CCDS11345.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.320788	0.81469	.	.	ENSG00000141738	ENST00000309185;ENST00000309156;ENST00000394211;ENST00000394209;ENST00000445327;ENST00000394204	D;D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37;-2.37	5.17	5.17	0.71159	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.108901	0.64402	D	0.000002	D	0.94105	0.8110	M	0.78916	2.43	0.80722	D	1	D;D	0.89917	0.973;1.0	P;D	0.87578	0.661;0.998	D	0.94802	0.7971	10	0.87932	D	0	-16.4513	14.836	0.70183	0.0:0.0:0.0:1.0	.	329;329	Q14451-2;Q14451	.;GRB7_HUMAN	R	329;329;329;329;352;329	ENSP00000311752:W329R;ENSP00000310771:W329R;ENSP00000377761:W329R;ENSP00000377759:W329R;ENSP00000403459:W352R;ENSP00000377754:W329R	ENSP00000310771:W329R	W	+	1	0	GRB7	35154737	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.760000	0.85248	2.165000	0.68154	0.459000	0.35465	TGG	.	.		0.612	GRB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257024.2	NM_005310	
MED24	9862	hgsc.bcm.edu	37	17	38179530	38179530	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:38179530G>A	ENST00000394128.2	-	20	2185	c.2104C>T	c.(2104-2106)Ccc>Tcc	p.P702S	MED24_ENST00000394126.1_Missense_Mutation_p.P727S|MED24_ENST00000394127.2_Missense_Mutation_p.P689S|MED24_ENST00000356271.3_Missense_Mutation_p.P689S|MED24_ENST00000501516.3_Missense_Mutation_p.P721S	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	702					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CGCTTGGGGGGCAGCAGGTTC	0.602																																					p.P702S		Atlas-SNP	.											.	MED24	89	.	0			c.C2104T						.						57.0	51.0	53.0					17																	38179530		2203	4300	6503	SO:0001583	missense	9862	exon20			TGGGGGGCAGCAG	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.2104C>T	chr17.hg19:g.38179530G>A	ENSP00000377686:p.Pro702Ser	128.0	0.0		94.0	20.0	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	hg19	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.908418	0.52333	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000535508;ENST00000501516;ENST00000431269	T;T;T	0.44482	0.92;0.92;0.92	4.43	4.43	0.53597	Mediator complex, subunit Med24, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.59459	0.2195	L	0.51422	1.61	0.80722	D	1	D;D;P;D;D;D	0.89917	1.0;1.0;0.81;1.0;1.0;1.0	D;D;P;D;D;D	0.91635	0.998;0.998;0.498;0.998;0.999;0.998	T	0.61302	-0.7090	10	0.51188	T	0.08	-25.0801	17.2528	0.87047	0.0:0.0:1.0:0.0	.	652;612;612;689;702;644	F5H5K2;F8W9R9;B4E1A5;O75448-2;O75448;F5H0K1	.;.;.;.;MED24_HUMAN;.	S	702;702;702;652;689;644;263;173;612	ENSP00000377686:P702S;ENSP00000443344:P652S;ENSP00000377685:P689S	ENSP00000348610:P702S	P	-	1	0	MED24	35433056	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.653000	0.83643	2.280000	0.76307	0.561000	0.74099	CCC	.	.		0.602	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
KRT19	3880	hgsc.bcm.edu	37	17	39680207	39680207	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:39680207A>G	ENST00000361566.3	-	6	1051	c.991T>C	c.(991-993)Ttt>Ctt	p.F331L	KRT15_ENST00000393974.3_5'Flank|KRT15_ENST00000393976.2_5'Flank|KRT15_ENST00000254043.3_5'Flank	NM_002276.4	NP_002267.2	P08727	K1C19_HUMAN	keratin 19	331	Coil 2.|Necessary for interaction with PNN.|Rod.				cell differentiation involved in embryonic placenta development (GO:0060706)|response to estrogen (GO:0043627)|sarcomere organization (GO:0045214)|viral process (GO:0016032)	cell periphery (GO:0071944)|costamere (GO:0043034)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12		Breast(137;0.00038)				TGGGCTCCAAAGCGCGCCTCC	0.597																																					p.F331L		Atlas-SNP	.											.	KRT19	41	.	0			c.T991C						.						40.0	41.0	41.0					17																	39680207		2203	4299	6502	SO:0001583	missense	3880	exon6			CTCCAAAGCGCGC		CCDS11399.1	17q21.2	2013-06-20			ENSG00000171345	ENSG00000171345		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6436	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 19"", ""keratin, type I, 40-kd"", ""cytokeratin 19"", ""40-kDa keratin intermediate filament"""	148020				16831889	Standard	NM_002276		Approved	K19, CK19, K1CS, MGC15366		P08727	OTTHUMG00000133422	ENST00000361566.3:c.991T>C	chr17.hg19:g.39680207A>G	ENSP00000355124:p.Phe331Leu	96.0	0.0		121.0	5.0	NM_002276	B2R874|Q5XG83|Q6NW33|Q7L5M9|Q96A53|Q96FV1|Q9BYF9|Q9P1Y4	Missense_Mutation	SNP	ENST00000361566.3	hg19	CCDS11399.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.239879	0.58995	.	.	ENSG00000171345	ENST00000361566	D	0.87571	-2.27	5.17	5.17	0.71159	Filament (1);	0.300651	0.23975	N	0.042732	D	0.87795	0.6267	L	0.56280	1.765	0.37628	D	0.921553	B;B	0.29341	0.027;0.242	B;B	0.39935	0.082;0.314	D	0.89297	0.3623	10	0.87932	D	0	.	15.0761	0.72077	1.0:0.0:0.0:0.0	.	494;331	B4DE59;P08727	.;K1C19_HUMAN	L	331	ENSP00000355124:F331L	ENSP00000355124:F331L	F	-	1	0	KRT19	36933733	0.947000	0.32204	0.104000	0.21259	0.222000	0.24845	7.406000	0.80017	1.963000	0.57068	0.454000	0.30748	TTT	.	.		0.597	KRT19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257285.1	NM_002276	
CCR10	2826	hgsc.bcm.edu	37	17	40831707	40831707	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:40831707C>T	ENST00000332438.4	-	2	972	c.953G>A	c.(952-954)cGc>cAc	p.R318H	CNTNAP1_ENST00000264638.4_5'Flank|PLEKHH3_ENST00000591022.1_5'Flank|PLEKHH3_ENST00000293349.6_5'Flank|CTD-3193K9.4_ENST00000593139.1_RNA|PLEKHH3_ENST00000412503.1_5'Flank|CCR10_ENST00000591765.1_Missense_Mutation_p.R96H	NM_016602.2	NP_057686.2	P46092	CCR10_HUMAN	chemokine (C-C motif) receptor 10	318					chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|G-protein coupled receptor activity (GO:0004930)			lung(1)|ovary(1)|skin(1)	3		Breast(137;0.000153)		BRCA - Breast invasive adenocarcinoma(366;0.14)		CAGGTCCTGGCGGAAGCGCAG	0.701																																					p.R318H		Atlas-SNP	.											.	CCR10	7	.	0			c.G953A						.						13.0	13.0	13.0					17																	40831707		2174	4252	6426	SO:0001583	missense	2826	exon2			TCCTGGCGGAAGC	AF215981	CCDS11435.1	17q21.1-q21.3	2012-08-08	2004-11-12	2004-11-12	ENSG00000184451	ENSG00000184451		"""GPCR / Class A : Chemokine receptors : C-C motif"""	4474	protein-coding gene	gene with protein product		600240	"""G protein-coupled receptor 2"""	GPR2		7851889	Standard	NM_016602		Approved		uc002iax.4	P46092	OTTHUMG00000132301	ENST00000332438.4:c.953G>A	chr17.hg19:g.40831707C>T	ENSP00000332504:p.Arg318His	59.0	0.0		63.0	20.0	NM_016602	Q4V749|Q6T7X2|Q9NZG2	Missense_Mutation	SNP	ENST00000332438.4	hg19	CCDS11435.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.790650	0.90367	.	.	ENSG00000184451	ENST00000332438	T	0.58358	0.34	4.22	4.22	0.49857	.	0.000000	0.40064	N	0.001189	T	0.53578	0.1805	N	0.08118	0	0.50039	D	0.999841	D	0.89917	1.0	D	0.85130	0.997	T	0.65500	-0.6153	10	0.87932	D	0	.	15.5224	0.75875	0.0:1.0:0.0:0.0	.	318	P46092	CCR10_HUMAN	H	318	ENSP00000332504:R318H	ENSP00000332504:R318H	R	-	2	0	CCR10	38085233	1.000000	0.71417	1.000000	0.80357	0.690000	0.40134	5.516000	0.67055	2.185000	0.69588	0.313000	0.20887	CGC	.	.		0.701	CCR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255406.1	NM_016602	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43516846	43516846	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:43516846A>G	ENST00000430334.3	-	11	3189	c.3056T>C	c.(3055-3057)gTc>gCc	p.V1019A	PLEKHM1_ENST00000421073.2_Missense_Mutation_p.V930A|PLEKHM1_ENST00000580404.1_5'UTR	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	1019					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					CGCATACCTGACTGTGGTGTC	0.632																																					p.V1019A		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.T3056C						.						90.0	75.0	80.0					17																	43516846		2203	4300	6503	SO:0001583	missense	9842	exon11			TACCTGACTGTGG	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.3056T>C	chr17.hg19:g.43516846A>G	ENSP00000389913:p.Val1019Ala	145.0	0.0		101.0	5.0	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Missense_Mutation	SNP	ENST00000430334.3	hg19	CCDS32671.1	.	.	.	.	.	.	.	.	.	.	A	11.22	1.575360	0.28092	.	.	ENSG00000225190	ENST00000430334;ENST00000421073	T;T	0.63255	-0.03;-0.03	5.08	1.6	0.23607	Protein kinase C-like, phorbol ester/diacylglycerol binding (2);	0.786081	0.11452	N	0.562701	T	0.36166	0.0957	N	0.10945	0.07	0.25339	N	0.988968	B;B	0.19445	0.029;0.036	B;B	0.20577	0.029;0.03	T	0.24261	-1.0165	10	0.11485	T	0.65	.	6.2057	0.20602	0.5906:0.0:0.4094:0.0	.	930;1019	F8W648;Q9Y4G2	.;PKHM1_HUMAN	A	1019;930	ENSP00000389913:V1019A;ENSP00000414352:V930A	ENSP00000414352:V930A	V	-	2	0	PLEKHM1	40872629	0.994000	0.37717	0.995000	0.50966	0.791000	0.44710	2.031000	0.41117	0.434000	0.26340	-0.475000	0.04921	GTC	.	.		0.632	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
NPEPPS	9520	hgsc.bcm.edu	37	17	45679095	45679095	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:45679095A>G	ENST00000322157.4	+	15	1959	c.1722A>G	c.(1720-1722)aaA>aaG	p.K574K	RP11-580I16.2_ENST00000582066.1_RNA|RP11-580I16.2_ENST00000582389.1_RNA|NPEPPS_ENST00000544660.1_Silent_p.K494K|NPEPPS_ENST00000530173.1_Silent_p.K570K	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	574					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						AAAATGTCAAACCAGACCAAT	0.388																																					p.K574K		Atlas-SNP	.											.	NPEPPS	59	.	0			c.A1722G						.						100.0	96.0	97.0					17																	45679095		1846	4085	5931	SO:0001819	synonymous_variant	9520	exon15			TGTCAAACCAGAC	Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"""puromycin-sensitive aminopeptidase"", ""metalloproteinase MP100"""	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.1722A>G	chr17.hg19:g.45679095A>G		147.0	0.0		118.0	5.0	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Silent	SNP	ENST00000322157.4	hg19	CCDS45721.1																																																																																			.	.		0.388	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310	
TBX21	30009	hgsc.bcm.edu	37	17	45822240	45822240	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:45822240C>T	ENST00000177694.1	+	6	1327	c.1116C>T	c.(1114-1116)gaC>gaT	p.D372D		NM_013351.1	NP_037483.1	Q9UL17	TBX21_HUMAN	T-box 21	372					cellular response to organic substance (GO:0071310)|lymphocyte migration (GO:0072676)|multicellular organismal development (GO:0007275)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(1)|large_intestine(3)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	22						TCTACCCCGACCTTCCTGGCC	0.612																																					p.D372D		Atlas-SNP	.											.	TBX21	50	.	0			c.C1116T						.						85.0	83.0	84.0					17																	45822240		2203	4300	6503	SO:0001819	synonymous_variant	30009	exon6			CCCCGACCTTCCT	AF093098	CCDS11514.1	17q21.2	2008-06-23				ENSG00000073861		"""T-boxes"""	11599	protein-coding gene	gene with protein product		604895					Standard	NM_013351		Approved	TBLYM, T-bet	uc002ilv.1	Q9UL17		ENST00000177694.1:c.1116C>T	chr17.hg19:g.45822240C>T		75.0	0.0		66.0	4.0	NM_013351		Silent	SNP	ENST00000177694.1	hg19	CCDS11514.1																																																																																			.	.		0.612	TBX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441365.1	NM_013351	
NFE2L1	4779	hgsc.bcm.edu	37	17	46128683	46128683	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:46128683A>G	ENST00000362042.3	+	2	819	c.203A>G	c.(202-204)cAc>cGc	p.H68R	NFE2L1_ENST00000585291.1_Missense_Mutation_p.H68R|NFE2L1_ENST00000357480.5_Missense_Mutation_p.H68R|NFE2L1_ENST00000361665.3_Missense_Mutation_p.H68R	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	68					anatomical structure morphogenesis (GO:0009653)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|inflammatory response (GO:0006954)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TATGGTATCCACCCCAAGAGC	0.567																																					p.H68R		Atlas-SNP	.											.	NFE2L1	60	.	0			c.A203G						.						107.0	103.0	104.0					17																	46128683		2203	4300	6503	SO:0001583	missense	4779	exon2			GTATCCACCCCAA	AK090459	CCDS11524.1	17q21.3	2013-08-23	2013-08-23			ENSG00000082641		"""basic leucine zipper proteins"""	7781	protein-coding gene	gene with protein product		163260	"""nuclear factor (erythroid-derived 2)-like 1"""	TCF11		8248256, 9501099	Standard	NM_003204		Approved	NRF1, LCR-F1, FLJ00380	uc002imz.4	Q14494		ENST00000362042.3:c.203A>G	chr17.hg19:g.46128683A>G	ENSP00000354855:p.His68Arg	99.0	0.0		81.0	4.0	NM_003204	D3DTU3|D3DTU5|Q12877|Q96FN6	Missense_Mutation	SNP	ENST00000362042.3	hg19	CCDS11524.1	.	.	.	.	.	.	.	.	.	.	A	11.74	1.727972	0.30593	.	.	ENSG00000082641	ENST00000362042;ENST00000361665;ENST00000357480	T;T	0.26373	2.16;1.74	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.52058	0.1711	M	0.79258	2.445	0.80722	D	1	D;D;D	0.89917	0.984;0.999;1.0	D;D;D	0.85130	0.964;0.994;0.997	T	0.57825	-0.7744	10	0.87932	D	0	-21.2442	13.8987	0.63790	1.0:0.0:0.0:0.0	.	68;68;68	A3KMG6;Q14494-2;Q14494	.;.;NF2L1_HUMAN	R	87;68;68	ENSP00000355190:H68R;ENSP00000350072:H68R	ENSP00000350072:H68R	H	+	2	0	NFE2L1	43483682	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.236000	0.95360	1.938000	0.56188	0.460000	0.39030	CAC	.	.		0.567	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204	
NFE2L1	4779	hgsc.bcm.edu	37	17	46136184	46136184	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:46136184T>C	ENST00000362042.3	+	6	2116	c.1500T>C	c.(1498-1500)tcT>tcC	p.S500S	RP5-890E16.4_ENST00000583349.1_RNA|NFE2L1_ENST00000585291.1_Silent_p.S470S|NFE2L1_ENST00000357480.5_Silent_p.S470S|NFE2L1_ENST00000583378.1_Silent_p.S301S|NFE2L1_ENST00000536222.1_Silent_p.S344S|NFE2L1_ENST00000361665.3_Silent_p.S489S|NFE2L1_ENST00000582155.1_Silent_p.S312S	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	500	Poly-Ser.				anatomical structure morphogenesis (GO:0009653)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|inflammatory response (GO:0006954)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						cttcctcttcttcctcctcct	0.537																																					p.S500S		Atlas-SNP	.											.	NFE2L1	60	.	0			c.T1500C						.						81.0	80.0	80.0					17																	46136184		2203	4300	6503	SO:0001819	synonymous_variant	4779	exon6			CTCTTCTTCCTCC	AK090459	CCDS11524.1	17q21.3	2013-08-23	2013-08-23			ENSG00000082641		"""basic leucine zipper proteins"""	7781	protein-coding gene	gene with protein product		163260	"""nuclear factor (erythroid-derived 2)-like 1"""	TCF11		8248256, 9501099	Standard	NM_003204		Approved	NRF1, LCR-F1, FLJ00380	uc002imz.4	Q14494		ENST00000362042.3:c.1500T>C	chr17.hg19:g.46136184T>C		71.0	0.0		87.0	4.0	NM_003204	D3DTU3|D3DTU5|Q12877|Q96FN6	Silent	SNP	ENST00000362042.3	hg19	CCDS11524.1																																																																																			.	.		0.537	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204	
SPOP	8405	hgsc.bcm.edu	37	17	47677854	47677854	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:47677854C>T	ENST00000393328.2	-	11	1376	c.1011G>A	c.(1009-1011)ggG>ggA	p.G337G	SPOP_ENST00000503676.1_Silent_p.G337G|SPOP_ENST00000393331.3_Silent_p.G337G|SPOP_ENST00000347630.2_Silent_p.G337G|SPOP_ENST00000504102.1_Silent_p.G337G	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	337	Important for homodimerization.				glucose homeostasis (GO:0042593)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						TTGACTTCCACCCAGAGGTCT	0.537										Prostate(2;0.17)																											p.G337G		Atlas-SNP	.											.	SPOP	91	.	0			c.G1011A						.						106.0	100.0	102.0					17																	47677854		2203	4300	6503	SO:0001819	synonymous_variant	8405	exon10			CTTCCACCCAGAG	AJ000644	CCDS11551.1	17q21.33	2013-01-09			ENSG00000121067	ENSG00000121067		"""BTB/POZ domain containing"""	11254	protein-coding gene	gene with protein product		602650				9414087	Standard	NM_001007227		Approved	TEF2, BTBD32	uc002ipg.3	O43791	OTTHUMG00000161496	ENST00000393328.2:c.1011G>A	chr17.hg19:g.47677854C>T		89.0	0.0		82.0	4.0	NM_001007228	B2R6S3|D3DTW7|Q53HJ1	Silent	SNP	ENST00000393328.2	hg19	CCDS11551.1																																																																																			.	.		0.537	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563	
SPAG9	9043	hgsc.bcm.edu	37	17	49072445	49072445	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:49072445A>G	ENST00000262013.7	-	18	2407	c.2199T>C	c.(2197-2199)agT>agC	p.S733S	SPAG9_ENST00000357122.4_Silent_p.S719S|SPAG9_ENST00000510283.1_Silent_p.S576S|SPAG9_ENST00000505279.1_Silent_p.S723S	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	733					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			ACTTATCTAAACTACTCTGAG	0.398																																					p.S733S		Atlas-SNP	.											.	SPAG9	151	.	0			c.T2199C						.						167.0	145.0	152.0					17																	49072445		2203	4300	6503	SO:0001819	synonymous_variant	9043	exon18			ATCTAAACTACTC	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"""sperm surface protein"", ""JNK/SAPK-associated protein"", ""JNK interacting protein"", ""sperm specific protein"", ""c-Jun NH2-terminal kinase-associated leucine zipper protein"", ""Max-binding protein"", ""JNK-associated leucine-zipper protein"", ""HLC-4 protein"", ""lung cancer oncogene 4"", ""proliferation-inducing gene 6"", ""cancer/testis antigen 89"""	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2199T>C	chr17.hg19:g.49072445A>G		97.0	0.0		79.0	4.0	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Silent	SNP	ENST00000262013.7	hg19	CCDS45740.1																																																																																			.	.		0.398	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971	
KIF2B	84643	hgsc.bcm.edu	37	17	51901222	51901222	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:51901222C>T	ENST00000268919.4	+	1	984	c.828C>T	c.(826-828)aaC>aaT	p.N276N		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	276	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)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AAGCCTCCAACGAGTTGGTGT	0.562																																					p.N276N		Atlas-SNP	.											.	KIF2B	254	.	0			c.C828T						.						114.0	95.0	101.0					17																	51901222		2203	4300	6503	SO:0001819	synonymous_variant	84643	exon1			CTCCAACGAGTTG	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.828C>T	chr17.hg19:g.51901222C>T		102.0	0.0		112.0	36.0	NM_032559	Q96MA2|Q9BXG6	Silent	SNP	ENST00000268919.4	hg19	CCDS32685.1																																																																																			.	.		0.562	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
TRIM25	7706	hgsc.bcm.edu	37	17	54969476	54969476	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:54969476T>C	ENST00000316881.4	-	9	1527	c.1478A>G	c.(1477-1479)cAg>cGg	p.Q493R	MIR3614_ENST00000581261.1_RNA|RP11-670E13.5_ENST00000574826.1_RNA|TRIM25_ENST00000537230.1_Missense_Mutation_p.Q493R|TRIM25_ENST00000573108.1_5'Flank	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25	493	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)|response to estrogen (GO:0043627)|response to vitamin D (GO:0033280)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Breast(9;6.15e-08)					TGTGAACCTCTGGGGATGCGG	0.547																																					p.Q493R		Atlas-SNP	.											.	TRIM25	52	.	0			c.A1478G						.						82.0	78.0	80.0					17																	54969476		2203	4300	6503	SO:0001583	missense	7706	exon9			AACCTCTGGGGAT	D21205	CCDS11591.1	17q23.1	2013-01-09	2011-01-25	2004-03-30				"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12932	protein-coding gene	gene with protein product		600453	"""zinc finger protein 147 (estrogen-responsive finger protein)"", ""tripartite motif-containing 25"""	ZNF147		7789997	Standard	NM_005082		Approved	EFP, RNF147	uc002iut.3	Q14258		ENST00000316881.4:c.1478A>G	chr17.hg19:g.54969476T>C	ENSP00000323889:p.Gln493Arg	79.0	0.0		72.0	4.0	NM_005082		Missense_Mutation	SNP	ENST00000316881.4	hg19	CCDS11591.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.253404	0.59212	.	.	ENSG00000121060	ENST00000316881;ENST00000537230	T;T	0.10668	2.85;2.85	4.84	3.76	0.43208	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	0.238747	0.29684	N	0.011479	T	0.12987	0.0315	L	0.50919	1.6	0.35027	D	0.758394	P	0.35468	0.503	B	0.40228	0.323	T	0.14924	-1.0455	10	0.46703	T	0.11	.	9.8174	0.40860	0.0:0.0818:0.0:0.9182	.	493	Q14258	TRI25_HUMAN	R	493	ENSP00000323889:Q493R;ENSP00000445961:Q493R	ENSP00000323889:Q493R	Q	-	2	0	TRIM25	52324475	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	1.549000	0.36212	1.807000	0.52817	0.418000	0.28097	CAG	.	.		0.547	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	NM_005082	
MKS1	54903	hgsc.bcm.edu	37	17	56290446	56290446	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:56290446T>C	ENST00000393119.2	-	8	829	c.755A>G	c.(754-756)gAg>gGg	p.E252G	MKS1_ENST00000337050.7_Missense_Mutation_p.E252G|MKS1_ENST00000546108.1_Missense_Mutation_p.E49G|MKS1_ENST00000537529.2_Missense_Mutation_p.E242G|MKS1_ENST00000313863.6_Missense_Mutation_p.E252G	NM_017777.3	NP_060247.2	Q9NXB0	MKS1_HUMAN	Meckel syndrome, type 1	252					branching morphogenesis of an epithelial tube (GO:0048754)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)				endometrium(5)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						CCCCTCCGTCTCAATCCTGTA	0.557																																					p.E252G		Atlas-SNP	.											.	MKS1	100	.	0			c.A755G						.						64.0	65.0	64.0					17																	56290446		1924	4133	6057	SO:0001583	missense	54903	exon8			TCCGTCTCAATCC	DQ185029	CCDS11603.2, CCDS54148.1	17q21-q24	2014-09-17			ENSG00000011143	ENSG00000011143			7121	protein-coding gene	gene with protein product	"""POC12 centriolar protein homolog (Chlamydomonas)"""	609883		MKS		7550354, 16415886, 18327255	Standard	NM_017777		Approved	FLJ20345, POC12, BBS13	uc002ivr.2	Q9NXB0	OTTHUMG00000133714	ENST00000393119.2:c.755A>G	chr17.hg19:g.56290446T>C	ENSP00000376827:p.Glu252Gly	74.0	0.0		53.0	4.0	NM_017777	B7WNX4|F5H885|Q284T0|Q96G13	Missense_Mutation	SNP	ENST00000393119.2	hg19	CCDS11603.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.12|16.12	3.033549|3.033549	0.54896|0.54896	.|.	.|.	ENSG00000011143|ENSG00000011143	ENST00000537529;ENST00000393120;ENST00000393119;ENST00000337050;ENST00000546108|ENST00000313863	T;T;T;T|.	0.76709|.	-0.61;-0.59;-0.35;-1.04|.	5.8|5.8	4.68|4.68	0.58851|0.58851	.|.	1.812070|.	0.02289|.	N|.	0.070158|.	T|T	0.70456|0.70456	0.3226|0.3226	M|M	0.69823|0.69823	2.125|2.125	0.54753|0.54753	D|D	0.999988|0.999988	D;P|.	0.60160|.	0.987;0.856|.	P;B|.	0.54856|.	0.762;0.345|.	T|T	0.70813|0.70813	-0.4770|-0.4770	9|5	.|.	.|.	.|.	-34.3665|-34.3665	11.3497|11.3497	0.49581|0.49581	0.1354:0.0:0.0:0.8646|0.1354:0.0:0.0:0.8646	.|.	252;252|.	A8MPP8;Q9NXB0|.	.;MKS1_HUMAN|.	G|G	242;252;252;252;49|253	ENSP00000442096:E242G;ENSP00000376827:E252G;ENSP00000338407:E252G;ENSP00000443012:E49G|.	.|.	E|R	-|-	2|1	0|2	MKS1|MKS1	53645445|53645445	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.270000|0.270000	0.26580|0.26580	3.900000|3.900000	0.56295|0.56295	2.203000|2.203000	0.70933|0.70933	0.523000|0.523000	0.50628|0.50628	GAG|AGA	.	.		0.557	MKS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258015.2	NM_017777	
LPO	4025	hgsc.bcm.edu	37	17	56345321	56345321	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:56345321T>C	ENST00000262290.4	+	13	2421	c.2105T>C	c.(2104-2106)cTg>cCg	p.L702P	LPO_ENST00000543544.1_Missense_Mutation_p.L643P|LPO_ENST00000582328.1_Missense_Mutation_p.L619P|LPO_ENST00000421678.2_Missense_Mutation_p.L619P	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	702					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						ATCGACAAGCTGGACCTGTCA	0.562																																					p.L702P		Atlas-SNP	.											.	LPO	73	.	0			c.T2105C						.						81.0	69.0	73.0					17																	56345321		2203	4300	6503	SO:0001583	missense	4025	exon13			ACAAGCTGGACCT	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.2105T>C	chr17.hg19:g.56345321T>C	ENSP00000262290:p.Leu702Pro	105.0	0.0		77.0	4.0	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Missense_Mutation	SNP	ENST00000262290.4	hg19	CCDS32689.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.013160	0.75161	.	.	ENSG00000167419	ENST00000262290;ENST00000421678;ENST00000543544;ENST00000389576	T;T;T	0.74737	-0.87;-0.87;-0.87	5.34	5.34	0.76211	.	0.070276	0.64402	D	0.000016	D	0.88709	0.6510	M	0.92604	3.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.90182	0.4243	10	0.45353	T	0.12	.	14.145	0.65344	0.0:0.0:0.0:1.0	.	619;702	E7EMJ3;P22079	.;PERL_HUMAN	P	702;619;643;447	ENSP00000262290:L702P;ENSP00000400245:L619P;ENSP00000445344:L643P	ENSP00000262290:L702P	L	+	2	0	LPO	53700320	0.945000	0.32115	1.000000	0.80357	0.819000	0.46315	6.718000	0.74713	2.029000	0.59856	0.533000	0.62120	CTG	.	.		0.562	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1		
MTMR4	9110	hgsc.bcm.edu	37	17	56586080	56586080	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:56586080A>G	ENST00000323456.5	-	6	540	c.416T>C	c.(415-417)cTg>cCg	p.L139P	MTMR4_ENST00000579925.1_Missense_Mutation_p.L139P	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	139					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTCCTCGGTCAGCCCCAGGCA	0.577																																					p.L139P		Atlas-SNP	.											.	MTMR4	91	.	0			c.T416C						.						75.0	59.0	64.0					17																	56586080		2203	4300	6503	SO:0001583	missense	9110	exon6			TCGGTCAGCCCCA	AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.416T>C	chr17.hg19:g.56586080A>G	ENSP00000325285:p.Leu139Pro	118.0	0.0		86.0	26.0	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Missense_Mutation	SNP	ENST00000323456.5	hg19	CCDS11608.1	.	.	.	.	.	.	.	.	.	.	A	11.91	1.778475	0.31502	.	.	ENSG00000108389	ENST00000323456	D	0.93712	-3.27	5.91	5.91	0.95273	.	0.316163	0.29995	N	0.010672	D	0.92446	0.7602	L	0.40543	1.245	0.80722	D	1	D	0.54397	0.966	P	0.49421	0.61	D	0.93097	0.6505	10	0.66056	D	0.02	.	15.5248	0.75894	1.0:0.0:0.0:0.0	.	139	Q9NYA4	MTMR4_HUMAN	P	139	ENSP00000325285:L139P	ENSP00000325285:L139P	L	-	2	0	MTMR4	53941079	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	2.881000	0.48538	2.269000	0.75478	0.533000	0.62120	CTG	.	.		0.577	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687	
C17orf64	124773	hgsc.bcm.edu	37	17	58508620	58508620	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:58508620A>G	ENST00000269127.4	+	6	788	c.704A>G	c.(703-705)gAa>gGa	p.E235G	RPL12P38_ENST00000588627.1_RNA	NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	235										breast(2)|large_intestine(1)|lung(3)	6	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)			CCAGAGACTGAACCGTAAGAA	0.453																																					p.E235G		Atlas-SNP	.											.	C17orf64	19	.	0			c.A704G						.						42.0	54.0	50.0					17																	58508620		2203	4300	6503	SO:0001583	missense	124773	exon6			AGACTGAACCGTA	BC048806	CCDS32698.2	17q23.2	2005-12-16			ENSG00000141371	ENSG00000141371			26990	protein-coding gene	gene with protein product						12477932	Standard	NM_181707		Approved		uc002iyq.3	Q86WR6	OTTHUMG00000157171	ENST00000269127.4:c.704A>G	chr17.hg19:g.58508620A>G	ENSP00000269127:p.Glu235Gly	109.0	0.0		84.0	5.0	NM_181707	Q8IY87	Missense_Mutation	SNP	ENST00000269127.4	hg19	CCDS32698.2	.	.	.	.	.	.	.	.	.	.	A	4.088	0.014223	0.07959	.	.	ENSG00000141371	ENST00000269127	.	.	.	4.42	-4.73	0.03259	.	1.446720	0.04997	U	0.468448	T	0.14570	0.0352	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16837	-1.0389	9	0.15066	T	0.55	1.8762	3.916	0.09224	0.4688:0.0:0.2506:0.2806	.	235	Q86WR6	CQ064_HUMAN	G	235	.	ENSP00000269127:E235G	E	+	2	0	C17orf64	55863402	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.020000	0.12525	-0.698000	0.05085	-0.242000	0.12053	GAA	.	.		0.453	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707	
BCAS3	54828	hgsc.bcm.edu	37	17	58756812	58756812	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:58756812A>G	ENST00000390652.5	+	2	26		c.e2-1		BCAS3_ENST00000588462.1_5'Flank|BCAS3_ENST00000407086.3_Splice_Site|BCAS3_ENST00000589222.1_Splice_Site|BCAS3_ENST00000408905.3_5'Flank	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)			ttCTGGAAACAGGTTTTATGA	0.438																																					.		Atlas-SNP	.											.	BCAS3	90	.	0			.						.						136.0	132.0	133.0					17																	58756812		1847	4100	5947	SO:0001630	splice_region_variant	54828	.			GGAAACAGGTTTT	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.-5-1A>G	chr17.hg19:g.58756812A>G		79.0	0.0		73.0	4.0	.		Splice_Site	SNP	ENST00000390652.5	hg19	CCDS45749.1																																																																																			.	.		0.438	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679	Intron
INTS2	57508	hgsc.bcm.edu	37	17	59981858	59981858	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:59981858A>G	ENST00000444766.3	-	9	1369	c.1294T>C	c.(1294-1296)Tcc>Ccc	p.S432P	INTS2_ENST00000251334.6_Missense_Mutation_p.S424P	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	432					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						ATACAAAAGGAAAGTGAAACA	0.403																																					p.S432P		Atlas-SNP	.											.	INTS2	89	.	0			c.T1294C						.						81.0	82.0	82.0					17																	59981858		1932	4111	6043	SO:0001583	missense	57508	exon9			AAAAGGAAAGTGA	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"""KIAA1287"""	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.1294T>C	chr17.hg19:g.59981858A>G	ENSP00000414237:p.Ser432Pro	129.0	0.0		94.0	4.0	NM_020748	Q9ULD3	Missense_Mutation	SNP	ENST00000444766.3	hg19	CCDS45750.1	.	.	.	.	.	.	.	.	.	.	A	29.3	4.994479	0.93167	.	.	ENSG00000108506	ENST00000444766;ENST00000251334	T	0.46451	0.87	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.54967	0.1891	L	0.47716	1.5	0.80722	D	1	D	0.69078	0.997	D	0.63793	0.918	T	0.52555	-0.8560	9	.	.	.	-5.8668	15.3009	0.73949	1.0:0.0:0.0:0.0	.	432	Q9H0H0	INT2_HUMAN	P	432;431	ENSP00000414237:S432P	.	S	-	1	0	INTS2	57336640	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	8.618000	0.90932	2.020000	0.59435	0.383000	0.25322	TCC	.	.		0.403	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748	
ACE	1636	hgsc.bcm.edu	37	17	61560881	61560881	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:61560881A>G	ENST00000290866.4	+	10	1572	c.1548A>G	c.(1546-1548)ggA>ggG	p.G516G	ACE_ENST00000490216.2_5'Flank|ACE_ENST00000538928.1_Missense_Mutation_p.E468G|ACE_ENST00000428043.1_Silent_p.G516G|ACE_ENST00000584529.1_3'UTR|ACE_ENST00000413513.3_5'Flank|ACE_ENST00000290863.6_5'Flank|ACE_ENST00000421982.2_5'Flank|ACE_ENST00000577647.1_5'Flank	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	516	Peptidase M2 1.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	TTGATGCTGGAGCTAAGTTTC	0.498																																					p.G516G		Atlas-SNP	.											.	ACE	187	.	0			c.A1548G						.						145.0	134.0	138.0					17																	61560881		2203	4300	6503	SO:0001819	synonymous_variant	1636	exon10			TGCTGGAGCTAAG	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"""CD molecules"""	2707	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	106180	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"""	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.1548A>G	chr17.hg19:g.61560881A>G		156.0	0.0		106.0	5.0	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Silent	SNP	ENST00000290866.4	hg19	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	A	14.00	2.405739	0.42715	.	.	ENSG00000159640	ENST00000538928	T	0.34275	1.37	4.9	0.00178	0.14048	.	.	.	.	.	T	0.19725	0.0474	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.08680	-1.0710	7	.	.	.	-13.7745	5.723	0.17998	0.4736:0.0:0.3945:0.1319	.	468	F5H1K1	.	G	468	ENSP00000439591:E468G	.	E	+	2	0	ACE	58914613	0.346000	0.24844	0.997000	0.53966	0.986000	0.74619	-0.463000	0.06696	0.046000	0.15833	0.374000	0.22700	GAG	.	.		0.498	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2		
PSMC5	5705	hgsc.bcm.edu	37	17	61902423	61902423	+	5'Flank	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:61902423A>G	ENST00000310144.6	+	0	0				PSMC5_ENST00000580864.1_5'Flank|PSMC5_ENST00000581882.1_5'Flank|FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000375812.4_5'Flank|FTSJ3_ENST00000427159.2_Silent_p.T232T	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein 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)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						GCTTCTTCTTAGTAACCAATT	0.488																																					p.T232T		Atlas-SNP	.											.	FTSJ3	63	.	0			c.T696C						.						95.0	102.0	100.0					17																	61902423		2203	4300	6503	SO:0001631	upstream_gene_variant	117246	exon8			CTTCTTAGTAACC	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195			chr17.hg19:g.61902423A>G	Exception_encountered	98.0	0.0		86.0	5.0	NM_017647	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Silent	SNP	ENST00000310144.6	hg19	CCDS11645.1																																																																																			.	.		0.488	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805	
SMARCD2	6603	hgsc.bcm.edu	37	17	61914400	61914400	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:61914400C>T	ENST00000448276.2	-	4	714	c.449G>A	c.(448-450)cGg>cAg	p.R150Q	SMARCD2_ENST00000323347.10_Missense_Mutation_p.R102Q|SMARCD2_ENST00000225742.9_Missense_Mutation_p.R75Q|RN7SL805P_ENST00000581353.1_RNA	NM_001098426.1	NP_001091896.1	Q92925	SMRD2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	150					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						AACAAGCTCCCGGATCTGAAG	0.557																																					p.R150Q		Atlas-SNP	.											.	SMARCD2	29	.	0			c.G449A						.						55.0	56.0	56.0					17																	61914400		2001	4194	6195	SO:0001583	missense	6603	exon4			AGCTCCCGGATCT	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.449G>A	chr17.hg19:g.61914400C>T	ENSP00000392617:p.Arg150Gln	77.0	0.0		71.0	4.0	NM_001098426	A5PLL5|A6NNQ7|B4DV56|B4E1R6|Q7L2I6|Q9UHZ1	Missense_Mutation	SNP	ENST00000448276.2	hg19	CCDS45756.1	.	.	.	.	.	.	.	.	.	.	.	22.4	4.290308	0.80914	.	.	ENSG00000108604	ENST00000448276;ENST00000225742;ENST00000450364;ENST00000323347	T;T;T	0.57595	0.39;0.81;0.39	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.73536	0.3599	M	0.76938	2.355	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	P;D;D	0.79108	0.863;0.992;0.992	T	0.75622	-0.3254	10	0.72032	D	0.01	-1.2528	16.9239	0.86170	0.0:1.0:0.0:0.0	.	102;113;150	Q92925-3;B9EGA3;Q92925	.;.;SMRD2_HUMAN	Q	150;92;113;102	ENSP00000392617:R150Q;ENSP00000225742:R92Q;ENSP00000318451:R102Q	ENSP00000225742:R92Q	R	-	2	0	SMARCD2	59268132	1.000000	0.71417	1.000000	0.80357	0.059000	0.15707	7.651000	0.83577	2.865000	0.98341	0.655000	0.94253	CGG	.	.		0.557	SMARCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444544.1	NM_001098426	
SCN4A	6329	hgsc.bcm.edu	37	17	62022142	62022142	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:62022142T>C	ENST00000435607.1	-	21	3879	c.3803A>G	c.(3802-3804)aAc>aGc	p.N1268S	SCN4A_ENST00000578147.1_Missense_Mutation_p.N1268S	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1268					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.N1268S(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CATGTAGAGGTTCACCTCGTA	0.562																																					p.N1268S		Atlas-SNP	.											SCN4A,colon,carcinoma,0,1	SCN4A	205	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3803G						.						128.0	130.0	129.0					17																	62022142		2178	4292	6470	SO:0001583	missense	6329	exon21			TAGAGGTTCACCT	U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.3803A>G	chr17.hg19:g.62022142T>C	ENSP00000396320:p.Asn1268Ser	108.0	1.0		90.0	5.0	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	hg19	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	T	19.62	3.862049	0.71949	.	.	ENSG00000007314	ENST00000435607	D	0.98296	-4.85	3.49	3.49	0.39957	Ion transport (1);	0.114478	0.64402	D	0.000014	D	0.97207	0.9087	L	0.31207	0.915	0.51012	D	0.999909	D	0.63880	0.993	P	0.61874	0.895	D	0.96063	0.9040	10	0.36615	T	0.2	.	11.6187	0.51104	0.0:0.0:0.0:1.0	.	1268	P35499	SCN4A_HUMAN	S	1268	ENSP00000396320:N1268S	ENSP00000396320:N1268S	N	-	2	0	SCN4A	59375874	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	7.825000	0.86693	1.596000	0.50062	0.379000	0.24179	AAC	.	.		0.562	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
ABCA8	10351	hgsc.bcm.edu	37	17	66873815	66873815	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:66873815T>C	ENST00000269080.2	-	31	4061	c.3924A>G	c.(3922-3924)ctA>ctG	p.L1308L	ABCA8_ENST00000430352.2_Silent_p.L1348L|ABCA8_ENST00000586539.1_Silent_p.L1348L	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1308	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					TCCCTTTCAGTAGCACCTGCA	0.537																																					p.L1308L		Atlas-SNP	.											.	ABCA8	213	.	0			c.A3924G						.						81.0	74.0	76.0					17																	66873815		2203	4300	6503	SO:0001819	synonymous_variant	10351	exon31			TTTCAGTAGCACC	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3924A>G	chr17.hg19:g.66873815T>C		95.0	0.0		62.0	4.0	NM_007168	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	hg19	CCDS11680.1																																																																																			.	.		0.537	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
ABCA8	10351	hgsc.bcm.edu	37	17	66890418	66890418	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:66890418T>C	ENST00000269080.2	-	21	2949	c.2812A>G	c.(2812-2814)Aga>Gga	p.R938G	ABCA8_ENST00000430352.2_Missense_Mutation_p.R978G|ABCA8_ENST00000586539.1_Missense_Mutation_p.R978G	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	938					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					CAATTCAATCTTTTGGCATTG	0.313																																					p.R938G		Atlas-SNP	.											.	ABCA8	213	.	0			c.A2812G						.						68.0	62.0	64.0					17																	66890418		2203	4300	6503	SO:0001583	missense	10351	exon21			TCAATCTTTTGGC	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.2812A>G	chr17.hg19:g.66890418T>C	ENSP00000269080:p.Arg938Gly	71.0	0.0		80.0	4.0	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	hg19	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.812218	0.50527	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225	D;D	0.85702	-2.02;-2.02	5.08	5.08	0.68730	.	0.000000	0.64402	D	0.000013	D	0.86994	0.6067	M	0.83384	2.64	0.35528	D	0.802039	B;B;B;B;B	0.30664	0.154;0.289;0.021;0.039;0.097	B;B;B;B;B	0.40477	0.132;0.33;0.029;0.099;0.16	D	0.86141	0.1581	10	0.17832	T	0.49	.	11.4185	0.49967	0.0:0.0:0.0:1.0	.	917;978;978;978;938	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	G	938;978;917	ENSP00000269080:R938G;ENSP00000402814:R978G	ENSP00000269080:R938G	R	-	1	2	ABCA8	64402013	0.006000	0.16342	1.000000	0.80357	0.962000	0.63368	1.194000	0.32174	2.260000	0.74910	0.533000	0.62120	AGA	.	.		0.313	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
ARMC7	79637	hgsc.bcm.edu	37	17	73124841	73124841	+	Missense_Mutation	SNP	T	T	C	rs374083928	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:73124841T>C	ENST00000245543.1	+	3	607	c.305T>C	c.(304-306)cTc>cCc	p.L102P	ARMC7_ENST00000579096.1_3'UTR|NT5C_ENST00000579082.1_5'Flank|ARMC7_ENST00000581078.1_Missense_Mutation_p.S81P	NM_024585.2	NP_078861.1	Q9H6L4	ARMC7_HUMAN	armadillo repeat containing 7	102						cytoplasm (GO:0005737)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|pancreas(3)	9	all_lung(278;0.14)|Lung NSC(278;0.168)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)			GGTGTCCCACTCATCATCAAC	0.612																																					p.L102P		Atlas-SNP	.											.,1	ARMC7	14	.	0			c.T305C						.						69.0	53.0	58.0					17																	73124841		2203	4300	6503	SO:0001583	missense	79637	exon3			TCCCACTCATCAT	AK025813	CCDS11714.1	17q25	2013-02-14				ENSG00000125449		"""Armadillo repeat containing"""	26168	protein-coding gene	gene with protein product						12477932	Standard	NM_024585		Approved	FLJ22160	uc002jmw.1	Q9H6L4		ENST00000245543.1:c.305T>C	chr17.hg19:g.73124841T>C	ENSP00000245543:p.Leu102Pro	122.0	1.0		119.0	6.0	NM_024585	B4DVA4	Missense_Mutation	SNP	ENST00000245543.1	hg19	CCDS11714.1	.	.	.	.	.	.	.	.	.	.	T	11.56	1.675109	0.29783	.	.	ENSG00000125449	ENST00000245543	T	0.65732	-0.17	4.97	2.63	0.31362	Armadillo-like helical (1);Armadillo-type fold (1);	0.263954	0.32258	N	0.006355	T	0.49355	0.1552	L	0.53249	1.67	0.58432	D	0.999993	B	0.15719	0.014	B	0.22152	0.038	T	0.48603	-0.9021	10	0.30078	T	0.28	.	3.1657	0.06535	0.2061:0.1592:0.0:0.6346	.	102	Q9H6L4	ARMC7_HUMAN	P	102	ENSP00000245543:L102P	ENSP00000245543:L102P	L	+	2	0	ARMC7	70636436	1.000000	0.71417	0.996000	0.52242	0.840000	0.47671	3.182000	0.50910	2.007000	0.58848	0.533000	0.62120	CTC	.	.		0.612	ARMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445846.1	NM_024585	
ENGASE	64772	hgsc.bcm.edu	37	17	77075681	77075681	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:77075681G>C	ENST00000579016.1	+	4	527	c.527G>C	c.(526-528)tGg>tCg	p.W176S	ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	176						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						CCAGTGGGCTGGACCAACACT	0.607																																					p.W176S		Atlas-SNP	.											.	ENGASE	55	.	0			c.G527C						.						90.0	112.0	105.0					17																	77075681		2118	4220	6338	SO:0001583	missense	64772	exon4			TGGGCTGGACCAA	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.527G>C	chr17.hg19:g.77075681G>C	ENSP00000462333:p.Trp176Ser	123.0	0.0		124.0	52.0	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	hg19	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	G	17.52	3.409801	0.62399	.	.	ENSG00000167280	ENST00000311595;ENST00000545583	.	.	.	5.22	5.22	0.72569	Glycoside hydrolase, family 85 (1);	0.057777	0.85682	D	0.000000	D	0.86368	0.5916	M	0.94142	3.5	0.80722	D	1	D;D	0.61080	0.972;0.989	D;D	0.66847	0.929;0.947	D	0.89986	0.4104	9	0.72032	D	0.01	-0.1925	17.3151	0.87221	0.0:0.0:1.0:0.0	.	176;176	Q8NFI3;Q8NFI3-3	ENASE_HUMAN;.	S	176	.	ENSP00000308158:W176S	W	+	2	0	ENGASE	74587276	1.000000	0.71417	1.000000	0.80357	0.431000	0.31685	9.007000	0.93597	2.587000	0.87381	0.655000	0.94253	TGG	.	.		0.607	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
SLC38A10	124565	hgsc.bcm.edu	37	17	79234066	79234066	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:79234066C>T	ENST00000374759.3	-	11	1643	c.1260G>A	c.(1258-1260)ttG>ttA	p.L420L	SLC38A10_ENST00000288439.5_Silent_p.L420L|SLC38A10_ENST00000546352.1_5'Flank	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	420					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCACCTTCATCAAACCCTCGG	0.647																																					p.L420L		Atlas-SNP	.											.	SLC38A10	133	.	0			c.G1260A						.						24.0	25.0	25.0					17																	79234066		2199	4291	6490	SO:0001819	synonymous_variant	124565	exon11			CTTCATCAAACCC	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.1260G>A	chr17.hg19:g.79234066C>T		63.0	0.0		50.0	17.0	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	hg19	CCDS42397.1																																																																																			.	.		0.647	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
TBCD	6904	hgsc.bcm.edu	37	17	80828170	80828170	+	Silent	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr17:80828170C>A	ENST00000355528.4	+	14	1519	c.1389C>A	c.(1387-1389)gtC>gtA	p.V463V	TBCD_ENST00000397466.2_Silent_p.V77V|TBCD_ENST00000539345.2_Silent_p.V463V	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	463					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			GCACCAACGTCAGGGACGCCG	0.617																																					p.V463V		Atlas-SNP	.											.	TBCD	94	.	0			c.C1389A						.						48.0	56.0	53.0					17																	80828170		2148	4244	6392	SO:0001819	synonymous_variant	6904	exon14			CAACGTCAGGGAC	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.1389C>A	chr17.hg19:g.80828170C>A		90.0	0.0		97.0	6.0	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Silent	SNP	ENST00000355528.4	hg19	CCDS45818.1																																																																																			.	.		0.617	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
MTCL1	23255	hgsc.bcm.edu	37	18	8718463	8718463	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:8718463A>G	ENST00000306329.11	+	2	1095	c.1095A>G	c.(1093-1095)agA>agG	p.R365R	SOGA2_ENST00000400050.3_Silent_p.R5R|SOGA2_ENST00000359865.3_Silent_p.R5R|SOGA2_ENST00000306285.7_5'UTR|Y_RNA_ENST00000516510.1_RNA|SOGA2_ENST00000517570.1_Silent_p.R5R																							AAGAGATGAGAGACAGTTATT	0.448																																					p.R5R		Atlas-SNP	.											.	.	.	.	0			c.A15G						.						97.0	92.0	94.0					18																	8718463		2203	4300	6503	SO:0001819	synonymous_variant	23255	exon3			GATGAGAGACAGT																												ENST00000306329.11:c.1095A>G	chr18.hg19:g.8718463A>G		125.0	0.0		93.0	4.0	NM_015210		Silent	SNP	ENST00000306329.11	hg19																																																																																				.	.		0.448	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
PPP4R1	9989	hgsc.bcm.edu	37	18	9593834	9593834	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:9593834T>C	ENST00000400556.3	-	4	300	c.227A>G	c.(226-228)gAa>gGa	p.E76G	PPP4R1_ENST00000580583.1_5'UTR|PPP4R1_ENST00000400555.3_Missense_Mutation_p.E59G	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	76					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						ATCGCAGACTTCCCTCAAGGT	0.368																																					p.E76G	Melanoma(188;1232 2082 5061 11948 35994)	Atlas-SNP	.											.	PPP4R1	63	.	0			c.A227G						.						102.0	95.0	97.0					18																	9593834		1911	4137	6048	SO:0001583	missense	9989	exon4			CAGACTTCCCTCA	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.227A>G	chr18.hg19:g.9593834T>C	ENSP00000383402:p.Glu76Gly	89.0	0.0		91.0	4.0	NM_001042388	Q99774|Q9UNQ7	Missense_Mutation	SNP	ENST00000400556.3	hg19	CCDS42412.1	.	.	.	.	.	.	.	.	.	.	T	13.34	2.207615	0.39003	.	.	ENSG00000154845	ENST00000400556;ENST00000400555	T;T	0.18502	2.21;2.21	5.3	5.3	0.74995	Armadillo-like helical (1);Armadillo-type fold (1);	0.252844	0.36002	N	0.002853	T	0.17789	0.0427	L	0.48642	1.525	0.48236	D	0.99961	B;B;B	0.21606	0.058;0.026;0.044	B;B;B	0.23852	0.033;0.022;0.049	T	0.03807	-1.1002	9	.	.	.	-19.2209	15.0953	0.72229	0.0:0.0:0.0:1.0	.	59;76;59	A8K923;Q8TF05;Q8TF05-2	.;PP4R1_HUMAN;.	G	76;59	ENSP00000383402:E76G;ENSP00000383401:E59G	.	E	-	2	0	PPP4R1	9583834	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.162000	0.58177	2.240000	0.73641	0.477000	0.44152	GAA	.	.		0.368	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134	
GNAL	2774	hgsc.bcm.edu	37	18	11862404	11862404	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:11862404A>G	ENST00000423027.3	+	6	823	c.502A>G	c.(502-504)Aga>Gga	p.R168G	GNAL_ENST00000269162.5_Missense_Mutation_p.R168G|GNAL_ENST00000602628.1_5'UTR|GNAL_ENST00000535121.1_Missense_Mutation_p.R168G|GNAL_ENST00000334049.6_Missense_Mutation_p.R245G			P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type	168					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						CTTCCTGGAAAGAATCGACAG	0.507																																					p.R245G		Atlas-SNP	.											.	GNAL	59	.	0			c.A733G						.						94.0	79.0	84.0					18																	11862404		2203	4300	6503	SO:0001583	missense	2774	exon6			CTGGAAAGAATCG	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.502A>G	chr18.hg19:g.11862404A>G	ENSP00000408489:p.Arg168Gly	88.0	0.0		76.0	6.0	NM_182978	B7ZA26|Q86XU3	Missense_Mutation	SNP	ENST00000423027.3	hg19	CCDS11852.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.030689	0.54790	.	.	ENSG00000141404	ENST00000540217;ENST00000334049;ENST00000535121;ENST00000269162;ENST00000423027	D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51	5.1	2.68	0.31781	G protein alpha subunit, helical insertion (2);	0.084546	0.85682	D	0.000000	D	0.89777	0.6813	L	0.59967	1.855	0.80722	D	1	P;P	0.47604	0.776;0.898	P;P	0.55508	0.601;0.777	D	0.87055	0.2149	10	0.59425	D	0.04	.	7.4967	0.27494	0.768:0.1559:0.0761:0.0	.	168;245	P38405;Q86XU3	GNAL_HUMAN;.	G	107;245;168;168;168	ENSP00000334051:R245G;ENSP00000439023:R168G;ENSP00000269162:R168G;ENSP00000408489:R168G	ENSP00000269162:R168G	R	+	1	2	GNAL	11852404	1.000000	0.71417	0.629000	0.29254	0.987000	0.75469	6.928000	0.75846	0.275000	0.22094	0.459000	0.35465	AGA	.	.		0.507	GNAL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254561.2	NM_182978, NM_002071	
GREB1L	80000	hgsc.bcm.edu	37	18	19095396	19095396	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:19095396A>G	ENST00000580732.2	+	29	5301	c.4920A>G	c.(4918-4920)ggA>ggG	p.G1640G	GREB1L_ENST00000424526.1_Silent_p.G1640G|GREB1L_ENST00000400483.4_3'UTR|GREB1L_ENST00000269218.6_Silent_p.G1531G			Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast cancer-like	1640						integral component of membrane (GO:0016021)				breast(5)|endometrium(4)|kidney(6)|lung(1)|skin(1)	17						TGGAAGTAGGAGTTTCCAGTA	0.378																																					p.G1640G		Atlas-SNP	.											.	GREB1L	69	.	0			c.A4920G						.						56.0	44.0	48.0					18																	19095396		692	1591	2283	SO:0001819	synonymous_variant	80000	exon29			AGTAGGAGTTTCC	AK023749	CCDS45836.1	18q11.2	2009-09-08	2009-09-08	2009-09-08					31042	protein-coding gene	gene with protein product			"""KIAA1772"""	KIAA1772		11214970	Standard	NM_001142966		Approved	FLJ13687, C18orf6	uc010xam.2	Q9C091		ENST00000580732.2:c.4920A>G	chr18.hg19:g.19095396A>G		79.0	0.0		66.0	4.0	NM_001142966	A4QN17|Q9H8F1	Silent	SNP	ENST00000580732.2	hg19	CCDS45836.1																																																																																			.	.		0.378	GREB1L-003	KNOWN	not_organism_supported|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443782.2	NM_024935	
GREB1L	80000	hgsc.bcm.edu	37	18	19100757	19100757	+	Missense_Mutation	SNP	G	G	C	rs373460361		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:19100757G>C	ENST00000580732.2	+	32	5962	c.5581G>C	c.(5581-5583)Gat>Cat	p.D1861H	GREB1L_ENST00000424526.1_Missense_Mutation_p.D1861H|GREB1L_ENST00000400483.4_3'UTR|GREB1L_ENST00000269218.6_Missense_Mutation_p.D1752H			Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast cancer-like	1861						integral component of membrane (GO:0016021)				breast(5)|endometrium(4)|kidney(6)|lung(1)|skin(1)	17						TGTAGGTGCTGATCTTAAGAA	0.373																																					p.D1861H		Atlas-SNP	.											.	GREB1L	69	.	0			c.G5581C						.						115.0	94.0	100.0					18																	19100757		692	1591	2283	SO:0001583	missense	80000	exon32			GGTGCTGATCTTA	AK023749	CCDS45836.1	18q11.2	2009-09-08	2009-09-08	2009-09-08					31042	protein-coding gene	gene with protein product			"""KIAA1772"""	KIAA1772		11214970	Standard	NM_001142966		Approved	FLJ13687, C18orf6	uc010xam.2	Q9C091		ENST00000580732.2:c.5581G>C	chr18.hg19:g.19100757G>C	ENSP00000464162:p.Asp1861His	225.0	0.0		196.0	12.0	NM_001142966	A4QN17|Q9H8F1	Missense_Mutation	SNP	ENST00000580732.2	hg19	CCDS45836.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.032967	0.75504	.	.	ENSG00000141449	ENST00000424526;ENST00000269218	T;T	0.07444	3.19;3.19	5.56	5.56	0.83823	.	.	.	.	.	T	0.15478	0.0373	L	0.48642	1.525	0.80722	D	1	P	0.49559	0.925	P	0.48141	0.568	T	0.00320	-1.1820	9	0.45353	T	0.12	-13.6379	19.5359	0.95254	0.0:0.0:1.0:0.0	.	1861	Q9C091	GRB1L_HUMAN	H	1861;1752	ENSP00000412060:D1861H;ENSP00000269218:D1752H	ENSP00000269218:D1752H	D	+	1	0	GREB1L	17354755	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.611000	0.82962	2.615000	0.88500	0.650000	0.86243	GAT	.	.		0.373	GREB1L-003	KNOWN	not_organism_supported|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443782.2	NM_024935	
GREB1L	80000	hgsc.bcm.edu	37	18	19100763	19100763	+	Missense_Mutation	SNP	A	A	C	rs201565664		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:19100763A>C	ENST00000580732.2	+	32	5968	c.5587A>C	c.(5587-5589)Aag>Cag	p.K1863Q	GREB1L_ENST00000424526.1_Missense_Mutation_p.K1863Q|GREB1L_ENST00000400483.4_3'UTR|GREB1L_ENST00000269218.6_Missense_Mutation_p.K1754Q			Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast cancer-like	1863						integral component of membrane (GO:0016021)				breast(5)|endometrium(4)|kidney(6)|lung(1)|skin(1)	17						TGCTGATCTTAAGAAATTTAA	0.363																																					p.K1863Q		Atlas-SNP	.											.	GREB1L	69	.	0			c.A5587C						.						72.0	60.0	64.0					18																	19100763		692	1591	2283	SO:0001583	missense	80000	exon32			GATCTTAAGAAAT	AK023749	CCDS45836.1	18q11.2	2009-09-08	2009-09-08	2009-09-08					31042	protein-coding gene	gene with protein product			"""KIAA1772"""	KIAA1772		11214970	Standard	NM_001142966		Approved	FLJ13687, C18orf6	uc010xam.2	Q9C091		ENST00000580732.2:c.5587A>C	chr18.hg19:g.19100763A>C	ENSP00000464162:p.Lys1863Gln	198.0	0.0		174.0	12.0	NM_001142966	A4QN17|Q9H8F1	Missense_Mutation	SNP	ENST00000580732.2	hg19	CCDS45836.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.634565	0.87660	.	.	ENSG00000141449	ENST00000424526;ENST00000269218	T;T	0.09817	2.94;2.96	5.56	5.56	0.83823	.	.	.	.	.	T	0.34164	0.0888	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.04976	-1.0914	9	0.54805	T	0.06	-10.3868	15.7196	0.77697	1.0:0.0:0.0:0.0	.	1863	Q9C091	GRB1L_HUMAN	Q	1863;1754	ENSP00000412060:K1863Q;ENSP00000269218:K1754Q	ENSP00000269218:K1754Q	K	+	1	0	GREB1L	17354761	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.947000	0.93000	2.113000	0.64589	0.528000	0.53228	AAG	.	.		0.363	GREB1L-003	KNOWN	not_organism_supported|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443782.2	NM_024935	
TAF4B	6875	hgsc.bcm.edu	37	18	23915177	23915177	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:23915177A>G	ENST00000269142.5	+	13	3296	c.2298A>G	c.(2296-2298)ttA>ttG	p.L766L	TAF4B_ENST00000578121.1_Silent_p.L771L	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	766					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)			AGCTGAGATTAAAGCAGAAAG	0.388																																					p.L766L		Atlas-SNP	.											.	TAF4B	71	.	0			c.A2298G						.						110.0	103.0	105.0					18																	23915177		1865	4101	5966	SO:0001819	synonymous_variant	6875	exon13			GAGATTAAAGCAG	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.2298A>G	chr18.hg19:g.23915177A>G		119.0	0.0		96.0	4.0	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	hg19	CCDS42421.1																																																																																			.	.		0.388	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
MEP1B	4225	hgsc.bcm.edu	37	18	29790544	29790544	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:29790544C>A	ENST00000269202.6	+	10	1047	c.1000C>A	c.(1000-1002)Cct>Act	p.P334T	MEP1B_ENST00000581447.1_Missense_Mutation_p.P334T	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	334	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						AACGCTGTACCCTAAAAGAGG	0.413																																					p.P334T		Atlas-SNP	.											.	MEP1B	54	.	0			c.C1000A						.						90.0	85.0	87.0					18																	29790544		1887	4104	5991	SO:0001583	missense	4225	exon10			CTGTACCCTAAAA	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.1000C>A	chr18.hg19:g.29790544C>A	ENSP00000269202:p.Pro334Thr	82.0	0.0		58.0	25.0	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	hg19	CCDS45846.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.502801	0.85176	.	.	ENSG00000141434	ENST00000269202	T	0.02103	4.45	5.33	5.33	0.75918	Concanavalin A-like lectin/glucanase (1);MAM domain (4);	0.000000	0.85682	D	0.000000	T	0.13200	0.0320	M	0.87038	2.855	0.80722	D	1	D	0.54207	0.965	P	0.56163	0.793	T	0.00380	-1.1776	10	0.87932	D	0	-19.3465	19.0127	0.92881	0.0:1.0:0.0:0.0	.	334	Q16820	MEP1B_HUMAN	T	334	ENSP00000269202:P334T	ENSP00000269202:P334T	P	+	1	0	MEP1B	28044542	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.439000	0.80444	2.507000	0.84556	0.585000	0.79938	CCT	.	.		0.413	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
C18orf54	162681	hgsc.bcm.edu	37	18	51889221	51889221	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:51889221A>G	ENST00000300091.5	+	4	1002	c.670A>G	c.(670-672)Aag>Gag	p.K224E	C18orf54_ENST00000578138.1_Missense_Mutation_p.K3E|C18orf54_ENST00000382911.4_Missense_Mutation_p.K385E	NM_173529.4	NP_775800.3	Q8IYD9	LAS2_HUMAN	chromosome 18 open reading frame 54	224						extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)		GTCCATGAAAAAGGATGACAG	0.348																																					p.K224E		Atlas-SNP	.											.	C18orf54	40	.	0			c.A670G						.						87.0	86.0	86.0					18																	51889221		2203	4300	6503	SO:0001583	missense	162681	exon4			ATGAAAAAGGATG	AK126503	CCDS11956.1, CCDS74223.1	18q21	2012-10-24			ENSG00000166845	ENSG00000166845			13796	protein-coding gene	gene with protein product	"""lung adenoma susceptibility protein 2"""	613258					Standard	XM_005258201		Approved	MGC33382, LAS2	uc031rij.1	Q8IYD9	OTTHUMG00000132703	ENST00000300091.5:c.670A>G	chr18.hg19:g.51889221A>G	ENSP00000300091:p.Lys224Glu	101.0	0.0		81.0	4.0	NM_173529	I7HFJ6|Q6MZU3|Q6ZTL6	Missense_Mutation	SNP	ENST00000300091.5	hg19	CCDS11956.1	.	.	.	.	.	.	.	.	.	.	A	9.452	1.090743	0.20471	.	.	ENSG00000166845	ENST00000300091;ENST00000382911	T;T	0.17854	2.25;2.25	5.12	3.95	0.45737	.	0.480335	0.23358	N	0.049045	T	0.13628	0.0330	L	0.55481	1.735	0.27894	N	0.939224	B;B	0.32829	0.053;0.386	B;B	0.25291	0.015;0.059	T	0.15350	-1.0440	10	0.34782	T	0.22	-0.0055	6.552	0.22440	0.6711:0.181:0.0:0.1479	.	385;224	Q8IYD9-2;Q8IYD9	.;CR054_HUMAN	E	224;385	ENSP00000300091:K224E;ENSP00000372368:K385E	ENSP00000300091:K224E	K	+	1	0	C18orf54	50143219	0.972000	0.33761	0.925000	0.36789	0.882000	0.50991	1.215000	0.32431	0.778000	0.33520	0.402000	0.26972	AAG	.	.		0.348	C18orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256001.1	NM_173529	
RNF152	220441	hgsc.bcm.edu	37	18	59483299	59483299	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:59483299A>G	ENST00000312828.3	-	2	1497	c.398T>C	c.(397-399)gTg>gCg	p.V133A		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	133					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				AGGGATGGTCACCACGGTGAC	0.677																																					p.V133A		Atlas-SNP	.											.	RNF152	37	.	0			c.T398C						.						56.0	58.0	58.0					18																	59483299		2203	4300	6503	SO:0001583	missense	220441	exon2			ATGGTCACCACGG	AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"""RING-type (C3HC4) zinc fingers"""	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.398T>C	chr18.hg19:g.59483299A>G	ENSP00000316628:p.Val133Ala	107.0	0.0		68.0	4.0	NM_173557	B3KV99|Q52LA4	Missense_Mutation	SNP	ENST00000312828.3	hg19	CCDS11978.1	.	.	.	.	.	.	.	.	.	.	A	17.22	3.333643	0.60853	.	.	ENSG00000176641	ENST00000312828	D	0.84516	-1.86	4.82	4.82	0.62117	.	0.148937	0.42821	D	0.000646	T	0.76990	0.4065	N	0.24115	0.695	0.43050	D	0.99465	B	0.21147	0.052	B	0.19391	0.025	T	0.74147	-0.3759	10	0.45353	T	0.12	-10.2772	14.5495	0.68057	1.0:0.0:0.0:0.0	.	133	Q8N8N0	RN152_HUMAN	A	133	ENSP00000316628:V133A	ENSP00000316628:V133A	V	-	2	0	RNF152	57634279	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.965000	0.87945	2.046000	0.60703	0.533000	0.62120	GTG	.	.		0.677	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256180.1	NM_173557	
PHLPP1	23239	hgsc.bcm.edu	37	18	60642674	60642674	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:60642674T>C	ENST00000262719.5	+	16	4034	c.3800T>C	c.(3799-3801)cTt>cCt	p.L1267P	PHLPP1_ENST00000400316.4_Missense_Mutation_p.L755P			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	1267	PP2C-like.				apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(2)|kidney(2)|lung(13)	17						GCCGCTGTCCTTTGTCATATC	0.522																																					p.L1267P		Atlas-SNP	.											.	PHLPP1	164	.	0			c.T3800C						.						157.0	151.0	153.0					18																	60642674		2034	4182	6216	SO:0001583	missense	23239	exon16			CTGTCCTTTGTCA	AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"", ""Pleckstrin homology (PH) domain containing"""	20610	protein-coding gene	gene with protein product		609396	"""pleckstrin homology domain containing, family E (with leucine rich repeats) member 1"", ""PH domain and leucine rich repeat protein phosphatase"""	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.3800T>C	chr18.hg19:g.60642674T>C	ENSP00000262719:p.Leu1267Pro	145.0	0.0		141.0	6.0	NM_194449	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Missense_Mutation	SNP	ENST00000262719.5	hg19	CCDS45881.2	.	.	.	.	.	.	.	.	.	.	T	27.1	4.796057	0.90453	.	.	ENSG00000081913	ENST00000400316;ENST00000262719	T;T	0.19532	2.14;2.14	5.28	5.28	0.74379	Protein phosphatase 2C-like (4);	.	.	.	.	T	0.43634	0.1256	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.18871	-1.0323	9	0.38643	T	0.18	-12.2446	15.374	0.74590	0.0:0.0:0.0:1.0	.	1267	O60346	PHLP1_HUMAN	P	755;1267	ENSP00000383170:L755P;ENSP00000262719:L1267P	ENSP00000262719:L1267P	L	+	2	0	PHLPP1	58793654	1.000000	0.71417	0.995000	0.50966	0.979000	0.70002	7.841000	0.86834	2.220000	0.72140	0.454000	0.30748	CTT	.	.		0.522	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449	
TSHZ1	10194	hgsc.bcm.edu	37	18	72998514	72998514	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr18:72998514A>G	ENST00000580243.1	+	2	1500	c.1152A>G	c.(1150-1152)aaA>aaG	p.K384K	TSHZ1_ENST00000322038.5_Silent_p.K339K			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	384					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		AGGATCAGAAAGCAGCGAACC	0.622																																					p.K339K		Atlas-SNP	.											.	TSHZ1	104	.	0			c.A1017G						.						104.0	109.0	107.0					18																	72998514		2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			TCAGAAAGCAGCG	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1152A>G	chr18.hg19:g.72998514A>G		97.0	0.0		66.0	5.0	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	hg19																																																																																				.	.		0.622	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
MISP	126353	hgsc.bcm.edu	37	19	758323	758323	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:758323T>C	ENST00000215582.6	+	2	1480	c.1377T>C	c.(1375-1377)acT>acC	p.T459T		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	459					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											AGGCTGCGACTTCACCAAAGG	0.622																																					p.T459T		Atlas-SNP	.											.	C19orf21	56	.	0			c.T1377C						.						50.0	41.0	44.0					19																	758323		2203	4300	6503	SO:0001819	synonymous_variant	126353	exon2			TGCGACTTCACCA	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"""mitotic interactor and substrate of Plk1"""	615289	"""chromosome 19 open reading frame 21"""	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.1377T>C	chr19.hg19:g.758323T>C		75.0	0.0		81.0	4.0	NM_173481		Silent	SNP	ENST00000215582.6	hg19	CCDS12042.1																																																																																			.	.		0.622	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481	
ABCA7	10347	hgsc.bcm.edu	37	19	1043779	1043779	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:1043779A>G	ENST00000263094.6	+	10	1217	c.986A>G	c.(985-987)gAg>gGg	p.E329G	ABCA7_ENST00000435683.2_Missense_Mutation_p.E191G|ABCA7_ENST00000433129.1_Missense_Mutation_p.E329G	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	329					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		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)		GAGGTGTGGGAGATGCTGGGA	0.632																																					p.E329G		Atlas-SNP	.											.	ABCA7	174	.	0			c.A986G						.						169.0	165.0	167.0					19																	1043779		2203	4300	6503	SO:0001583	missense	10347	exon10			TGTGGGAGATGCT	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.986A>G	chr19.hg19:g.1043779A>G	ENSP00000263094:p.Glu329Gly	76.0	0.0		62.0	8.0	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	A	10.80	1.451769	0.26074	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.85702	-2.02;-2.02	4.33	-8.66	0.00866	.	.	.	.	.	T	0.63710	0.2534	N	0.05510	-0.035	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.15052	0.012;0.005	T	0.51903	-0.8646	9	0.37606	T	0.19	.	6.4939	0.22132	0.4551:0.321:0.2239:0.0	.	191;329	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	G	329	ENSP00000263094:E329G;ENSP00000414062:E329G	ENSP00000263094:E329G	E	+	2	0	ABCA7	994779	0.000000	0.05858	0.001000	0.08648	0.070000	0.16714	-0.637000	0.05459	-1.689000	0.01434	-0.640000	0.03970	GAG	.	.		0.632	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
KDM4B	23030	hgsc.bcm.edu	37	19	5041177	5041177	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:5041177A>G	ENST00000159111.4	+	5	565	c.347A>G	c.(346-348)gAt>gGt	p.D116G	KDM4B_ENST00000381759.4_Missense_Mutation_p.D116G|KDM4B_ENST00000536461.1_Missense_Mutation_p.D116G	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	116					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						CAGGACTTTGATGACCTTGAA	0.557																																					p.D116G		Atlas-SNP	.											.	KDM4B	120	.	0			c.A347G						.						133.0	119.0	123.0					19																	5041177		2203	4300	6503	SO:0001583	missense	23030	exon5			ACTTTGATGACCT	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	29136	protein-coding gene	gene with protein product	"""tudor domain containing 14B"""	609765	"""jumonji domain containing 2B"""	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.347A>G	chr19.hg19:g.5041177A>G	ENSP00000159111:p.Asp116Gly	126.0	0.0		92.0	4.0	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	SNP	ENST00000159111.4	hg19	CCDS12138.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.284955	0.59867	.	.	ENSG00000127663	ENST00000159111;ENST00000381759;ENST00000536461	T;T;T	0.50813	0.73;0.73;0.73	4.62	4.62	0.57501	.	0.117692	0.56097	D	0.000027	T	0.46580	0.1400	L	0.53729	1.69	0.80722	D	1	B;B;B	0.28378	0.021;0.209;0.012	B;B;B	0.31946	0.01;0.138;0.004	T	0.50338	-0.8840	10	0.56958	D	0.05	-36.0385	14.1735	0.65525	1.0:0.0:0.0:0.0	.	116;116;116	F5GX28;O94953-2;O94953	.;.;KDM4B_HUMAN	G	116	ENSP00000159111:D116G;ENSP00000371178:D116G;ENSP00000440495:D116G	ENSP00000159111:D116G	D	+	2	0	KDM4B	4992177	1.000000	0.71417	0.963000	0.40424	0.664000	0.39144	8.972000	0.93424	1.943000	0.56356	0.459000	0.35465	GAT	.	.		0.557	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015	
SAFB	6294	hgsc.bcm.edu	37	19	5654111	5654111	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:5654111A>G	ENST00000292123.5	+	12	1673	c.1566A>G	c.(1564-1566)aaA>aaG	p.K522K	SAFB_ENST00000588852.1_Silent_p.K522K|SAFB_ENST00000538656.1_Silent_p.K365K|SAFB_ENST00000592224.1_Silent_p.K522K|SAFB_ENST00000454510.1_Silent_p.K453K|SAFB_ENST00000433404.1_Silent_p.K352K	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	522					chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		GTGACAGAAAAGATGATGCTA	0.468																																					p.K522K	Colon(88;338 1345 6184 8214 20897)	Atlas-SNP	.											.	SAFB	74	.	0			c.A1566G						.						107.0	101.0	103.0					19																	5654111		2203	4300	6503	SO:0001819	synonymous_variant	6294	exon12			CAGAAAAGATGAT	L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"""RNA binding motif (RRM) containing"""	10520	protein-coding gene	gene with protein product	"""Hsp27 ERE-TATA binding protein"""	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.1566A>G	chr19.hg19:g.5654111A>G		91.0	0.0		66.0	4.0	NM_002967	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Silent	SNP	ENST00000292123.5	hg19	CCDS12142.1																																																																																			.	.		0.468	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2		
VAV1	7409	hgsc.bcm.edu	37	19	6853046	6853046	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:6853046T>C	ENST00000602142.1	+	25	2370	c.2288T>C	c.(2287-2289)tTc>tCc	p.F763S	VAV1_ENST00000596764.1_Missense_Mutation_p.F731S|VAV1_ENST00000539284.1_Missense_Mutation_p.F666S|VAV1_ENST00000304076.2_Missense_Mutation_p.F741S|VAV1_ENST00000599806.1_Missense_Mutation_p.F708S	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	763	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						ACCTTGCAGTTCCCCTTCAAG	0.542																																					p.F763S		Atlas-SNP	.											.	VAV1	140	.	0			c.T2288C						.						88.0	81.0	84.0					19																	6853046		2203	4300	6503	SO:0001583	missense	7409	exon25			TGCAGTTCCCCTT		CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12657	protein-coding gene	gene with protein product		164875	"""vav 1 oncogene"""	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.2288T>C	chr19.hg19:g.6853046T>C	ENSP00000472929:p.Phe763Ser	107.0	0.0		95.0	5.0	NM_005428	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	hg19	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.501424	0.26861	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	T	0.75477	-0.94	4.36	3.32	0.38043	SH2 motif (2);	0.321581	0.29185	N	0.012883	T	0.62901	0.2466	L	0.31371	0.925	0.33694	D	0.613715	B;B;B;B	0.31009	0.014;0.238;0.021;0.303	B;B;B;B	0.36808	0.044;0.058;0.032;0.233	T	0.67891	-0.5553	10	0.59425	D	0.04	.	6.9586	0.24585	0.3717:0.0:0.0:0.6283	.	666;763;708;763	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	S	763;666	ENSP00000443242:F666S	ENSP00000302269:F763S	F	+	2	0	VAV1	6804046	0.759000	0.28416	0.997000	0.53966	0.813000	0.45954	0.651000	0.24873	0.687000	0.31509	0.460000	0.39030	TTC	.	.		0.542	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1		
INSR	3643	hgsc.bcm.edu	37	19	7267868	7267868	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:7267868A>G	ENST00000302850.5	-	2	282	c.140T>C	c.(139-141)tTg>tCg	p.L47S	INSR_ENST00000341500.5_Missense_Mutation_p.L47S	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	47	Leu-rich.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	CAGCTCATGCAACCTAGTGAG	0.488																																					p.L47S		Atlas-SNP	.											.	INSR	265	.	0			c.T140C						.						59.0	54.0	55.0					19																	7267868		2203	4300	6503	SO:0001583	missense	3643	exon2			TCATGCAACCTAG	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.140T>C	chr19.hg19:g.7267868A>G	ENSP00000303830:p.Leu47Ser	69.0	0.0		68.0	4.0	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	hg19	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	A	15.25	2.777137	0.49786	.	.	ENSG00000171105	ENST00000302850;ENST00000341500	D;D	0.83914	-1.78;-1.78	5.06	5.06	0.68205	.	0.000000	0.35096	U	0.003442	D	0.88746	0.6520	L	0.58810	1.83	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.996	D	0.89728	0.3924	10	0.87932	D	0	.	12.802	0.57591	1.0:0.0:0.0:0.0	.	38;47;47	Q86WY9;P06213-2;P06213	.;.;INSR_HUMAN	S	47	ENSP00000303830:L47S;ENSP00000342838:L47S	ENSP00000303830:L47S	L	-	2	0	INSR	7218868	1.000000	0.71417	0.396000	0.26296	0.217000	0.24651	8.844000	0.92147	1.907000	0.55213	0.377000	0.23210	TTG	.	.		0.488	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
PCP2	126006	hgsc.bcm.edu	37	19	7696666	7696666	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:7696666A>G	ENST00000311069.5	-	4	610	c.320T>C	c.(319-321)cTc>cCc	p.L107P	XAB2_ENST00000358368.4_5'Flank|CTD-3214H19.4_ENST00000595866.1_Intron|PET100_ENST00000594797.1_3'UTR|PCP2_ENST00000598935.1_Missense_Mutation_p.L91P|CTD-3214H19.6_ENST00000601797.1_RNA|XAB2_ENST00000534844.1_5'Flank	NM_174895.1	NP_777555.1	Q8IVA1	PCP2_HUMAN	Purkinje cell protein 2	107					rhodopsin mediated signaling pathway (GO:0016056)	neuronal cell body (GO:0043025)	GTPase regulator activity (GO:0030695)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|urinary_tract(1)	2						TTGGGGACTGAGGGTCCCAGC	0.677																																					p.L107P		Atlas-SNP	.											.	PCP2	6	.	0			c.T320C						.						61.0	58.0	59.0					19																	7696666		2202	4290	6492	SO:0001583	missense	126006	exon4			GGACTGAGGGTCC	BC025387	CCDS32893.1, CCDS62521.1	19p13.3	2008-02-05				ENSG00000174788			30209	protein-coding gene	gene with protein product						12477932	Standard	NM_174895		Approved	MGC41903, GPSM4	uc031rjd.1	Q8IVA1		ENST00000311069.5:c.320T>C	chr19.hg19:g.7696666A>G	ENSP00000310585:p.Leu107Pro	78.0	0.0		99.0	7.0	NM_174895	M0R2R7|Q3KRG7	Missense_Mutation	SNP	ENST00000311069.5	hg19	CCDS32893.1	.	.	.	.	.	.	.	.	.	.	A	17.19	3.326551	0.60743	.	.	ENSG00000174788	ENST00000311069	.	.	.	4.63	2.41	0.29592	.	0.794590	0.10342	N	0.686157	T	0.37156	0.0993	N	0.19112	0.55	0.58432	D	0.999996	D	0.61697	0.99	P	0.51615	0.675	T	0.26258	-1.0108	9	0.29301	T	0.29	-28.547	4.2383	0.10637	0.5832:0.2276:0.0:0.1892	.	107	Q8IVA1	PCP2_HUMAN	P	107	.	ENSP00000310585:L107P	L	-	2	0	PCP2	7602666	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	0.601000	0.24119	1.730000	0.51580	0.459000	0.35465	CTC	.	.		0.677	PCP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461026.2	XM_058956	
HNRNPM	4670	hgsc.bcm.edu	37	19	8550522	8550522	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:8550522A>G	ENST00000325495.4	+	14	1251	c.1210A>G	c.(1210-1212)Atg>Gtg	p.M404V	HNRNPM_ENST00000348943.3_Missense_Mutation_p.M365V	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	404	27 X 6 AA repeats of [GEVSTPAN]-[ILMV]- [DE]-[RH]-[MLVI]-[GAV].				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)			endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						GATCGAGAGGATGGGTCCTGG	0.642																																					p.M404V		Atlas-SNP	.											.	HNRNPM	61	.	0			c.A1210G						.						122.0	128.0	126.0					19																	8550522		2203	4300	6503	SO:0001583	missense	4670	exon14			GAGAGGATGGGTC	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"""RNA binding motif (RRM) containing"""	5046	protein-coding gene	gene with protein product	"""CEA receptor"""	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.1210A>G	chr19.hg19:g.8550522A>G	ENSP00000325376:p.Met404Val	62.0	0.0		74.0	4.0	NM_005968	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Missense_Mutation	SNP	ENST00000325495.4	hg19	CCDS12203.1	.	.	.	.	.	.	.	.	.	.	A	15.55	2.865759	0.51588	.	.	ENSG00000099783	ENST00000325495;ENST00000348943;ENST00000544159	T;T	0.14022	2.54;2.84	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.24774	0.0601	L	0.48986	1.54	0.48087	D	0.99958	P;B;D;P	0.58970	0.817;0.323;0.984;0.665	B;B;P;B	0.55871	0.164;0.267;0.786;0.157	T	0.00645	-1.1629	10	0.36615	T	0.2	.	13.2541	0.60068	1.0:0.0:0.0:0.0	.	244;404;365;289	Q7KYM9;P52272;P52272-2;Q59ES8	.;HNRPM_HUMAN;.;.	V	404;365;289	ENSP00000325376:M404V;ENSP00000325732:M365V	ENSP00000325376:M404V	M	+	1	0	HNRNPM	8456522	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.231000	0.72307	2.155000	0.67459	0.402000	0.26972	ATG	.	.		0.642	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		
ZNF699	374879	hgsc.bcm.edu	37	19	9406618	9406618	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:9406618A>G	ENST00000591998.1	-	6	1690	c.1462T>C	c.(1462-1464)Tca>Cca	p.S488P	ZNF699_ENST00000308650.3_Missense_Mutation_p.S488P|CTC-325H20.4_ENST00000591336.1_RNA			Q32M78	ZN699_HUMAN	zinc finger protein 699	488					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)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GTGAGGGATGAGGAACGACTA	0.458																																					p.S488P		Atlas-SNP	.											.	ZNF699	67	.	0			c.T1462C						.						80.0	85.0	83.0					19																	9406618		2200	4297	6497	SO:0001583	missense	374879	exon5			GGGATGAGGAACG	BC109268	CCDS42495.1	19p13.2	2013-01-08				ENSG00000196110		"""Zinc fingers, C2H2-type"", ""-"""	24750	protein-coding gene	gene with protein product	hangover homolog (Drosophila)	609571				16940975	Standard	NM_198535		Approved	FLJ38144, hang	uc002mlc.1	Q32M78		ENST00000591998.1:c.1462T>C	chr19.hg19:g.9406618A>G	ENSP00000467723:p.Ser488Pro	136.0	0.0		94.0	4.0	NM_198535	Q8N9A1	Missense_Mutation	SNP	ENST00000591998.1	hg19	CCDS42495.1	.	.	.	.	.	.	.	.	.	.	A	14.57	2.574165	0.45902	.	.	ENSG00000196110	ENST00000308650	T	0.07908	3.15	3.3	3.3	0.37823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.31221	N	0.008024	T	0.23094	0.0558	M	0.71871	2.18	0.09310	N	1	D	0.76494	0.999	D	0.66716	0.946	T	0.01169	-1.1430	10	0.66056	D	0.02	.	10.254	0.43385	1.0:0.0:0.0:0.0	.	488	Q32M78	ZN699_HUMAN	P	488	ENSP00000311596:S488P	ENSP00000311596:S488P	S	-	1	0	ZNF699	9267618	0.008000	0.16893	0.043000	0.18650	0.957000	0.61999	2.114000	0.41911	1.751000	0.51876	0.454000	0.30748	TCA	.	.		0.458	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449010.1	NM_198535	
PRKCSH	5589	hgsc.bcm.edu	37	19	11560105	11560105	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:11560105A>G	ENST00000589838.1	+	16	1465	c.1465A>G	c.(1465-1467)Acc>Gcc	p.T489A	PRKCSH_ENST00000592741.1_Missense_Mutation_p.T496A|PRKCSH_ENST00000591462.1_Missense_Mutation_p.T486A|PRKCSH_ENST00000587327.1_Missense_Mutation_p.T486A|PRKCSH_ENST00000412601.1_Missense_Mutation_p.T486A|PRKCSH_ENST00000252455.2_Missense_Mutation_p.T489A			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	489					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						CGGGAAAGAGACCATGGTGAC	0.697																																					p.T489A		Atlas-SNP	.											.	PRKCSH	55	.	0			c.A1465G						.						60.0	55.0	56.0					19																	11560105		2203	4300	6503	SO:0001583	missense	5589	exon17			AAAGAGACCATGG		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"""EF-hand domain containing"""	9411	protein-coding gene	gene with protein product		177060	"""polycystic liver disease"""	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.1465A>G	chr19.hg19:g.11560105A>G	ENSP00000465461:p.Thr489Ala	72.0	0.0		89.0	5.0	NM_002743	A8K318|Q96BU9|Q96D06|Q9P0W9	Missense_Mutation	SNP	ENST00000589838.1	hg19	CCDS32911.1	.	.	.	.	.	.	.	.	.	.	A	12.84	2.060014	0.36373	.	.	ENSG00000130175	ENST00000252455;ENST00000412601	D;D	0.81996	-1.56;-1.56	3.72	3.72	0.42706	Mannose-6-phosphate receptor, binding (1);	0.060522	0.64402	D	0.000004	D	0.88066	0.6337	M	0.79123	2.44	0.47819	D	0.999526	D;D;P;D	0.64830	0.984;0.994;0.629;0.994	P;D;B;D	0.64237	0.78;0.923;0.439;0.923	D	0.87571	0.2478	10	0.56958	D	0.05	-10.354	7.3549	0.26713	0.8044:0.0:0.0:0.1956	.	496;496;486;489	E7EQZ9;B4DJQ5;A8K318;P14314	.;.;.;GLU2B_HUMAN	A	489;486	ENSP00000252455:T489A;ENSP00000395616:T486A	ENSP00000252455:T489A	T	+	1	0	PRKCSH	11421105	1.000000	0.71417	0.848000	0.33437	0.330000	0.28571	4.618000	0.61211	1.543000	0.49345	0.460000	0.39030	ACC	.	.		0.697	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1		
ZNF844	284391	hgsc.bcm.edu	37	19	12186579	12186579	+	Missense_Mutation	SNP	A	A	G	rs537864739		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:12186579A>G	ENST00000439326.3	+	4	819	c.644A>G	c.(643-645)cAt>cGt	p.H215R	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	215					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						TATCTTATACATGAACGAGTT	0.358													.|||	1	0.000199681	0.0008	0.0	5008	,	,		22325	0.0		0.0	False		,,,				2504	0.0				p.H215R		Atlas-SNP	.											.	ZNF844	69	.	0			c.A644G						.						39.0	34.0	35.0					19																	12186579		692	1591	2283	SO:0001583	missense	284391	exon4			TTATACATGAACG	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.644A>G	chr19.hg19:g.12186579A>G	ENSP00000392024:p.His215Arg	138.0	0.0		92.0	4.0	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	hg19	CCDS45985.1	.	.	.	.	.	.	.	.	.	.	A	16.52	3.145874	0.57044	.	.	ENSG00000223547	ENST00000439326;ENST00000541708;ENST00000535505;ENST00000550826	D;D	0.86865	-2.18;-2.18	2.29	2.29	0.28610	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94755	0.8307	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.94229	0.7474	9	0.87932	D	0	.	9.2449	0.37520	1.0:0.0:0.0:0.0	.	215	Q08AG5	ZN844_HUMAN	R	215;215;190;58	ENSP00000392024:H215R;ENSP00000448588:H58R	ENSP00000392024:H215R	H	+	2	0	ZNF844	12047579	0.992000	0.36948	0.003000	0.11579	0.200000	0.23975	5.061000	0.64319	1.043000	0.40175	0.172000	0.16884	CAT	.	.		0.358	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
CD97	976	hgsc.bcm.edu	37	19	14516617	14516617	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:14516617C>T	ENST00000242786.5	+	14	1767	c.1687C>T	c.(1687-1689)Ctg>Ttg	p.L563L	CTC-548K16.5_ENST00000590626.1_RNA|CD97_ENST00000357355.3_Silent_p.L514L|CD97_ENST00000358600.3_Silent_p.L470L	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	563					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CTTCTGCCTGCTGCTGTGCAT	0.622																																					p.L563L		Atlas-SNP	.											.	CD97	86	.	0			c.C1687T						.						180.0	139.0	153.0					19																	14516617		2203	4300	6503	SO:0001819	synonymous_variant	976	exon14			TGCCTGCTGCTGT		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	1711	protein-coding gene	gene with protein product	"""leukocyte antigen CD97"", ""seven-span transmembrane protein"", ""seven-transmembrane, heterodimeric receptor associated with inflammation"", ""seven transmembrane helix receptor"""	601211	"""CD97 antigen"""			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.1687C>T	chr19.hg19:g.14516617C>T		107.0	0.0		85.0	4.0	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Silent	SNP	ENST00000242786.5	hg19	CCDS32929.1																																																																																			.	.		0.622	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481	
SLC1A6	6511	hgsc.bcm.edu	37	19	15067448	15067448	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:15067448C>T	ENST00000221742.3	-	6	1016	c.1009G>A	c.(1009-1011)Ggt>Agt	p.G337S	SLC1A6_ENST00000600144.1_Intron|SLC1A6_ENST00000430939.2_Missense_Mutation_p.G273S	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	337					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						CCCAGCTGACCCCCCAGGACG	0.582																																					p.G337S		Atlas-SNP	.											.	SLC1A6	111	.	0			c.G1009A						.						143.0	124.0	130.0					19																	15067448		2203	4300	6503	SO:0001583	missense	6511	exon6			GCTGACCCCCCAG		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1009G>A	chr19.hg19:g.15067448C>T	ENSP00000221742:p.Gly337Ser	109.0	0.0		84.0	8.0	NM_005071	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	hg19	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	c	14.32	2.499178	0.44455	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.58940	0.36;0.3	3.97	3.97	0.46021	.	0.152513	0.64402	D	0.000018	T	0.52757	0.1754	L	0.27053	0.805	0.80722	D	1	B;B	0.24823	0.112;0.001	B;B	0.42062	0.374;0.009	T	0.49331	-0.8951	10	0.23891	T	0.37	-6.5217	13.9019	0.63809	0.0:1.0:0.0:0.0	.	273;337	E7EV13;P48664	.;EAA4_HUMAN	S	273;337	ENSP00000409386:G273S;ENSP00000221742:G337S	ENSP00000221742:G337S	G	-	1	0	SLC1A6	14928448	0.974000	0.33945	1.000000	0.80357	0.933000	0.57130	2.444000	0.44890	2.229000	0.72834	0.596000	0.82720	GGT	.	.		0.582	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
AKAP8	10270	hgsc.bcm.edu	37	19	15472941	15472941	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:15472941T>C	ENST00000269701.2	-	10	1342	c.1282A>G	c.(1282-1284)Aag>Gag	p.K428E		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	428					mitotic chromosome condensation (GO:0007076)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)	condensed chromosome (GO:0000793)|female pronucleus (GO:0001939)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)	26						TCCACGGTCTTGTCGGGCAGC	0.542																																					p.K428E	GBM(190;1671 2163 3274 27186 30476)	Atlas-SNP	.											.	AKAP8	68	.	0			c.A1282G						.						87.0	82.0	84.0					19																	15472941		2203	4300	6503	SO:0001583	missense	10270	exon10			CGGTCTTGTCGGG	Y11997	CCDS12329.1	19p13.12	2012-05-16			ENSG00000105127	ENSG00000105127		"""A-kinase anchor proteins"""	378	protein-coding gene	gene with protein product	"""A-kinase anchor protein, 95kDa"""	604692				9473338	Standard	NM_005858		Approved	AKAP95, DKFZp586B1222	uc002nav.3	O43823		ENST00000269701.2:c.1282A>G	chr19.hg19:g.15472941T>C	ENSP00000269701:p.Lys428Glu	77.0	0.0		74.0	4.0	NM_005858		Missense_Mutation	SNP	ENST00000269701.2	hg19	CCDS12329.1	.	.	.	.	.	.	.	.	.	.	T	17.49	3.402471	0.62288	.	.	ENSG00000105127	ENST00000269701;ENST00000537303	T	0.43688	0.94	5.52	5.52	0.82312	.	0.000000	0.64402	D	0.000009	T	0.41650	0.1168	L	0.29908	0.895	0.28242	N	0.925637	D;D	0.56746	0.977;0.977	P;P	0.52424	0.698;0.698	T	0.38520	-0.9657	10	0.56958	D	0.05	-34.2549	10.7411	0.46154	0.0:0.0:0.1594:0.8406	.	428;428	Q8NE02;O43823	.;AKAP8_HUMAN	E	428;177	ENSP00000269701:K428E	ENSP00000269701:K428E	K	-	1	0	AKAP8	15333941	1.000000	0.71417	1.000000	0.80357	0.438000	0.31896	2.842000	0.48230	2.096000	0.63516	0.379000	0.24179	AAG	.	.		0.542	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858	
RASAL3	64926	hgsc.bcm.edu	37	19	15565287	15565287	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:15565287A>G	ENST00000343625.7	-	13	2130	c.2045T>C	c.(2044-2046)gTa>gCa	p.V682A	RASAL3_ENST00000608577.1_5'Flank	NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	682					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)	Ras GTPase activator activity (GO:0005099)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|skin(1)	18						CACCATGGCTACCTGGTCCAG	0.557											OREG0025322	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V682A		Atlas-SNP	.											.	RASAL3	49	.	0			c.T2045C						.						87.0	97.0	94.0					19																	15565287		2106	4216	6322	SO:0001583	missense	64926	exon13			ATGGCTACCTGGT		CCDS46006.1	19p13.12	2008-12-18			ENSG00000105122	ENSG00000105122			26129	protein-coding gene	gene with protein product						12477932	Standard	NM_022904		Approved	FLJ21438	uc002nbe.2	Q86YV0		ENST00000343625.7:c.2045T>C	chr19.hg19:g.15565287A>G	ENSP00000341905:p.Val682Ala	130.0	0.0	703	128.0	6.0	NM_022904	Q8N2T9|Q9H735	Missense_Mutation	SNP	ENST00000343625.7	hg19	CCDS46006.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.991511	0.74703	.	.	ENSG00000105122	ENST00000343625	D	0.84589	-1.87	5.29	5.29	0.74685	Rho GTPase activation protein (1);Ras GTPase-activating protein (2);	0.000000	0.34507	U	0.003905	D	0.90665	0.7072	M	0.69823	2.125	0.43874	D	0.996482	D;D	0.76494	0.999;0.999	D;P	0.66084	0.941;0.874	D	0.91680	0.5357	10	0.87932	D	0	.	13.1841	0.59672	1.0:0.0:0.0:0.0	.	682;682	Q86YV0-2;Q86YV0	.;RASL3_HUMAN	A	682	ENSP00000341905:V682A	ENSP00000341905:V682A	V	-	2	0	RASAL3	15426287	0.651000	0.27340	1.000000	0.80357	0.980000	0.70556	3.598000	0.54038	2.008000	0.58898	0.459000	0.35465	GTA	.	.		0.557	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904	
RASAL3	64926	hgsc.bcm.edu	37	19	15569377	15569377	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:15569377A>G	ENST00000343625.7	-	7	837	c.752T>C	c.(751-753)cTg>cCg	p.L251P	RASAL3_ENST00000608577.1_5'Flank	NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	251	PH.		L -> V (in dbSNP:rs58123634).		negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)	Ras GTPase activator activity (GO:0005099)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|skin(1)	18						GCTGGGGTGCAGTGGCCAGAT	0.642																																					p.L251P		Atlas-SNP	.											.	RASAL3	49	.	0			c.T752C						.						40.0	45.0	43.0					19																	15569377		2095	4223	6318	SO:0001583	missense	64926	exon7			GGGTGCAGTGGCC		CCDS46006.1	19p13.12	2008-12-18			ENSG00000105122	ENSG00000105122			26129	protein-coding gene	gene with protein product						12477932	Standard	NM_022904		Approved	FLJ21438	uc002nbe.2	Q86YV0		ENST00000343625.7:c.752T>C	chr19.hg19:g.15569377A>G	ENSP00000341905:p.Leu251Pro	113.0	0.0		95.0	6.0	NM_022904	Q8N2T9|Q9H735	Missense_Mutation	SNP	ENST00000343625.7	hg19	CCDS46006.1	.	.	.	.	.	.	.	.	.	.	A	19.11	3.764256	0.69878	.	.	ENSG00000105122	ENST00000343625	D	0.92752	-3.1	4.47	4.47	0.54385	Pleckstrin homology domain (1);	0.000000	0.26948	U	0.021700	D	0.94042	0.8091	L	0.57536	1.79	0.80722	D	1	D	0.76494	0.999	D	0.69307	0.963	D	0.93341	0.6710	10	0.44086	T	0.13	.	11.6946	0.51536	1.0:0.0:0.0:0.0	.	251	Q86YV0	RASL3_HUMAN	P	251	ENSP00000341905:L251P	ENSP00000341905:L251P	L	-	2	0	RASAL3	15430377	0.709000	0.27886	0.994000	0.49952	0.560000	0.35617	4.484000	0.60271	1.662000	0.50781	0.402000	0.26972	CTG	.	.		0.642	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904	
SIN3B	23309	hgsc.bcm.edu	37	19	16952755	16952755	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:16952755C>A	ENST00000248054.5	+	4	579	c.558C>A	c.(556-558)ttC>ttA	p.F186L	SIN3B_ENST00000379803.1_Missense_Mutation_p.F186L|SIN3B_ENST00000596802.1_Missense_Mutation_p.F186L|CTD-2538G9.5_ENST00000600987.1_RNA					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						ACAGGTCATTCCTGGAGATCC	0.463																																					p.F186L		Atlas-SNP	.											.	SIN3B	90	.	0			c.C558A						.						72.0	68.0	69.0					19																	16952755		2203	4300	6503	SO:0001583	missense	23309	exon4			GTCATTCCTGGAG	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.558C>A	chr19.hg19:g.16952755C>A	ENSP00000248054:p.Phe186Leu	168.0	0.0		143.0	6.0	NM_015260		Missense_Mutation	SNP	ENST00000248054.5	hg19		.	.	.	.	.	.	.	.	.	.	C	19.73	3.882872	0.72410	.	.	ENSG00000127511	ENST00000379803;ENST00000248054	T;T	0.81247	-1.47;-1.29	5.22	4.19	0.49359	.	0.000000	0.85682	D	0.000000	D	0.91168	0.7218	H	0.95712	3.71	0.54753	D	0.999987	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.98;0.999	D	0.91355	0.5107	10	0.51188	T	0.08	-2.1933	8.8518	0.35203	0.0:0.8382:0.0:0.1618	.	186;186;186	O75182-2;O75182;O75182-3	.;SIN3B_HUMAN;.	L	186	ENSP00000369131:F186L;ENSP00000248054:F186L	ENSP00000248054:F186L	F	+	3	2	SIN3B	16813755	0.994000	0.37717	0.999000	0.59377	0.880000	0.50808	0.677000	0.25262	2.427000	0.82271	0.557000	0.71058	TTC	.	.		0.463	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260	
OCEL1	79629	hgsc.bcm.edu	37	19	17339715	17339715	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:17339715A>G	ENST00000215061.4	+	6	820	c.776A>G	c.(775-777)gAg>gGg	p.E259G	OCEL1_ENST00000597836.1_Missense_Mutation_p.E203G|OCEL1_ENST00000601529.1_3'UTR	NM_024578.1	NP_078854.1	Q9H607	OCEL1_HUMAN	occludin/ELL domain containing 1	259										central_nervous_system(2)|endometrium(2)|kidney(1)|lung(2)	7						GGAGACAGCGAGGGCTCCGTG	0.542																																					p.E259G		Atlas-SNP	.											.	OCEL1	20	.	0			c.A776G						.						103.0	92.0	96.0					19																	17339715		2203	4300	6503	SO:0001583	missense	79629	exon6			ACAGCGAGGGCTC	BC029361	CCDS12351.1	19p13.11	2008-02-05				ENSG00000099330			26221	protein-coding gene	gene with protein product						12477932	Standard	NM_024578		Approved	FLJ22709	uc002nfp.3	Q9H607		ENST00000215061.4:c.776A>G	chr19.hg19:g.17339715A>G	ENSP00000215061:p.Glu259Gly	22.0	0.0		19.0	4.0	NM_024578		Missense_Mutation	SNP	ENST00000215061.4	hg19	CCDS12351.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.369493	0.42003	.	.	ENSG00000099330	ENST00000215061	T	0.38077	1.16	4.45	4.45	0.53987	.	0.352018	0.25394	N	0.030993	T	0.47040	0.1424	L	0.47716	1.5	0.20764	N	0.99985	D	0.76494	0.999	D	0.66716	0.946	T	0.31833	-0.9929	10	0.72032	D	0.01	-17.9301	7.3058	0.26447	0.8041:0.0:0.0:0.1959	.	259	Q9H607	OCEL1_HUMAN	G	259	ENSP00000215061:E259G	ENSP00000215061:E259G	E	+	2	0	OCEL1	17200715	0.985000	0.35326	0.981000	0.43875	0.213000	0.24496	2.629000	0.46485	1.866000	0.54105	0.402000	0.26972	GAG	.	.		0.542	OCEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463307.1	NM_024578	
TM6SF2	53345	hgsc.bcm.edu	37	19	19381177	19381177	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:19381177A>G	ENST00000389363.4	-	3	346	c.274T>C	c.(274-276)Ttc>Ctc	p.F92L	AC138430.4_ENST00000586064.2_RNA|TM6SF2_ENST00000586107.1_Intron	NM_001001524.2	NP_001001524.2	Q9BZW4	TM6S2_HUMAN	transmembrane 6 superfamily member 2	92						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14			Epithelial(12;0.0151)			AACTCCATGAAGCCCACCACA	0.617																																					p.F92L		Atlas-SNP	.											.	TM6SF2	39	.	0			c.T274C						.						42.0	45.0	44.0					19																	19381177		2005	4170	6175	SO:0001583	missense	53345	exon3			CCATGAAGCCCAC	AF255923	CCDS42528.1	19p13.3-p12	2008-02-05							11861	protein-coding gene	gene with protein product		606563				11124529	Standard	NM_001001524		Approved	Lpr4	uc002nmd.1	Q9BZW4		ENST00000389363.4:c.274T>C	chr19.hg19:g.19381177A>G	ENSP00000374014:p.Phe92Leu	102.0	0.0		90.0	4.0	NM_001001524	Q0IJ64	Missense_Mutation	SNP	ENST00000389363.4	hg19	CCDS42528.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.502192	0.44455	.	.	ENSG00000213996	ENST00000389363;ENST00000431465;ENST00000269990	T	0.52754	0.65	5.31	3.16	0.36331	.	0.000000	0.39475	U	0.001360	T	0.39145	0.1067	L	0.49640	1.575	0.44587	D	0.997553	B	0.17465	0.022	B	0.12156	0.007	T	0.22452	-1.0216	10	0.42905	T	0.14	-13.1688	8.7867	0.34825	0.8339:0.0:0.1661:0.0	.	92	Q9BZW4	TM6S2_HUMAN	L	92	ENSP00000374014:F92L	ENSP00000269990:F92L	F	-	1	0	TM6SF2	19242177	1.000000	0.71417	0.999000	0.59377	0.228000	0.25075	4.465000	0.60141	0.818000	0.34468	0.413000	0.27773	TTC	.	.		0.617	TM6SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460122.2	NM_203510	
CILP2	148113	hgsc.bcm.edu	37	19	19650506	19650506	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:19650506A>G	ENST00000291495.5	+	2	168	c.83A>G	c.(82-84)gAg>gGg	p.E28G	CILP2_ENST00000586018.1_Missense_Mutation_p.E28G	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	28						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CCCACCGAGGAGCCAATGGCG	0.647																																					p.E28G		Atlas-SNP	.											.	CILP2	84	.	0			c.A83G						.						88.0	90.0	89.0					19																	19650506		2203	4300	6503	SO:0001583	missense	148113	exon2			CCGAGGAGCCAAT	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.83A>G	chr19.hg19:g.19650506A>G	ENSP00000291495:p.Glu28Gly	105.0	0.0		99.0	4.0	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	hg19	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	a	14.46	2.542691	0.45280	.	.	ENSG00000160161	ENST00000291495	T	0.54675	0.56	3.42	0.164	0.14990	.	0.147700	0.30028	N	0.010585	T	0.31888	0.0811	L	0.29908	0.895	0.29199	N	0.875351	P;B	0.47409	0.895;0.436	B;B	0.38056	0.264;0.049	T	0.32268	-0.9913	10	0.72032	D	0.01	-14.8919	5.7698	0.18247	0.6397:0.0:0.3603:0.0	.	28;28	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	G	28	ENSP00000291495:E28G	ENSP00000291495:E28G	E	+	2	0	CILP2	19511506	1.000000	0.71417	0.926000	0.36857	0.254000	0.26022	1.051000	0.30417	-0.034000	0.13713	0.364000	0.22116	GAG	.	.		0.647	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
ZNF506	440515	hgsc.bcm.edu	37	19	19917871	19917871	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:19917871A>G	ENST00000540806.2	-	2	98	c.10T>C	c.(10-12)Ttg>Ctg	p.L4L	ZNF506_ENST00000545006.1_Silent_p.L4L|CTC-559E9.6_ENST00000589657.1_RNA|ZNF506_ENST00000450683.2_Silent_p.L4L|ZNF506_ENST00000587461.1_Silent_p.L4L|ZNF506_ENST00000587452.1_Silent_p.L4L|CTC-559E9.6_ENST00000591884.1_RNA|CTC-559E9.4_ENST00000590274.1_lincRNA|ZNF506_ENST00000443905.2_Silent_p.L4L			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	4	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						CTAAATTGCAATGGTCCCTGA	0.418																																					p.L4L		Atlas-SNP	.											.	ZNF506	36	.	0			c.T10C						.						80.0	88.0	85.0					19																	19917871		2199	4299	6498	SO:0001819	synonymous_variant	440515	exon2			ATTGCAATGGTCC	AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665		"""Zinc fingers, C2H2-type"", ""-"""	23780	protein-coding gene	gene with protein product							Standard	NM_001099269		Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000540806.2:c.10T>C	chr19.hg19:g.19917871A>G		112.0	0.0		87.0	4.0	NM_001099269	B3KTH6	Silent	SNP	ENST00000540806.2	hg19	CCDS42531.1																																																																																			.	.		0.418	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218	
ZNF714	148206	hgsc.bcm.edu	37	19	21299777	21299777	+	Missense_Mutation	SNP	G	G	A	rs111443257		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:21299777G>A	ENST00000596143.1	+	5	632	c.307G>A	c.(307-309)Gaa>Aaa	p.E103K	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						AAAAGGTTATGAACTAAACCA	0.328																																					p.E103K		Atlas-SNP	.											.	ZNF714	121	.	0			c.G307A						.						39.0	38.0	38.0					19																	21299777		2190	4291	6481	SO:0001583	missense	148206	exon5			GGTTATGAACTAA	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"""Zinc fingers, C2H2-type"""	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.307G>A	chr19.hg19:g.21299777G>A	ENSP00000472368:p.Glu103Lys	291.0	0.0		256.0	14.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	0.388	-0.924824	0.02377	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.394	0.394	0.16299	.	.	.	.	.	T	0.22322	0.0538	L	0.27975	0.815	0.09310	N	1	B;P	0.37781	0.004;0.608	B;B	0.35413	0.004;0.202	T	0.14062	-1.0486	7	0.56958	D	0.05	.	.	.	.	.	104;103	Q96N38-2;A6NEM4	.;.	K	103	.	ENSP00000291770:E103K	E	+	1	0	ZNF714	21091617	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	-0.857000	0.04286	0.452000	0.26830	0.456000	0.33151	GAA	.	.		0.328	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515	
ZNF208	7757	hgsc.bcm.edu	37	19	22154522	22154522	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:22154522C>T	ENST00000397126.4	-	4	3462	c.3314G>A	c.(3313-3315)aGa>aAa	p.R1105K	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	1105					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R977I(2)|p.R1105I(1)		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)				AGTATGAATTCTCTTATGTTC	0.393																																					p.R1105K		Atlas-SNP	.											ZNF208_ENST00000428290,colon,carcinoma,0,3	ZNF208	817	.	3	Substitution - Missense(3)	large_intestine(3)	c.G3314A						.						65.0	68.0	67.0					19																	22154522		2086	4239	6325	SO:0001583	missense	7757	exon4			TGAATTCTCTTAT	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.3314G>A	chr19.hg19:g.22154522C>T	ENSP00000380315:p.Arg1105Lys	63.0	0.0		92.0	7.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	hg19	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	7.902	0.734632	0.15574	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.02197	4.4	2.59	1.06	0.20224	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02649	0.0080	.	.	.	0.09310	N	1	B	0.29627	0.252	B	0.34590	0.186	T	0.45411	-0.9263	8	0.45353	T	0.12	.	9.2481	0.37539	0.0:0.8399:0.0:0.16	.	977	O43345	ZN208_HUMAN	K	1105;977	ENSP00000380315:R1105K	ENSP00000380315:R1105K	R	-	2	0	ZNF208	21946362	0.000000	0.05858	0.003000	0.11579	0.124000	0.20399	-0.834000	0.04391	1.029000	0.39812	0.297000	0.19635	AGA	.	.		0.393	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
ZNF676	163223	hgsc.bcm.edu	37	19	22363103	22363103	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:22363103A>G	ENST00000397121.2	-	3	1733	c.1416T>C	c.(1414-1416)gcT>gcC	p.A472A		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	472					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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				GTTTCTCTGCAGCATGAATTC	0.393																																					p.A472A		Atlas-SNP	.											.	ZNF676	146	.	0			c.T1416C						.						116.0	120.0	119.0					19																	22363103		2146	4271	6417	SO:0001819	synonymous_variant	163223	exon3			CTCTGCAGCATGA	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.1416T>C	chr19.hg19:g.22363103A>G		93.0	0.0		73.0	4.0	NM_001001411	A8MVX5	Silent	SNP	ENST00000397121.2	hg19	CCDS42539.1																																																																																			.	.		0.393	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411	
CEBPA	1050	hgsc.bcm.edu	37	19	33793069	33793069	+	Silent	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:33793069G>A	ENST00000498907.2	-	1	401	c.252C>T	c.(250-252)caC>caT	p.H84H	CTD-2540B15.9_ENST00000593041.1_lincRNA|CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.7_ENST00000587312.1_RNA|CTD-2540B15.11_ENST00000589932.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	84					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Y7_G130del(1)|p.L78_A174del(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					GCTGCCGGCTGTGCTGGAACA	0.741			"""Mis, N, F"""		"""AML, MDS"""				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.H84H		Atlas-SNP	.		Dom	yes		19	19q13.1	1050	"""CCAAT/enhancer binding protein (C/EBP), alpha"""		L	.	CEBPA	986	.	2	Deletion - In frame(2)	haematopoietic_and_lymphoid_tissue(2)	c.C252T						.						3.0	4.0	4.0					19																	33793069		1098	2308	3406	SO:0001819	synonymous_variant	1050	exon1	Familial Cancer Database	Familial AML	CCGGCTGTGCTGG	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"""basic leucine zipper proteins"""	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.252C>T	chr19.hg19:g.33793069G>A		66.0	0.0		74.0	4.0	NM_004364	A7LNP2|P78319|Q05CA4	Silent	SNP	ENST00000498907.2	hg19	CCDS54243.1																																																																																			.	.		0.741	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364	
HAMP	57817	hgsc.bcm.edu	37	19	35775715	35775715	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:35775715A>G	ENST00000598398.1	+	3	410	c.114A>G	c.(112-114)caA>caG	p.Q38Q	HAMP_ENST00000222304.3_Silent_p.Q38Q	NM_021175.2	NP_066998.1	P81172	HEPC_HUMAN	hepcidin antimicrobial peptide	38					cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|immune response (GO:0006955)|killing of cells of other organism (GO:0031640)	apical cortex (GO:0045179)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CAGAGCTGCAACCCCAGGACA	0.637																																					p.Q38Q		Atlas-SNP	.											.	HAMP	14	.	0			c.A114G						.						86.0	84.0	85.0					19																	35775715		2203	4300	6503	SO:0001819	synonymous_variant	57817	exon2			GCTGCAACCCCAG	AF309489	CCDS12454.1	19q13.1	2014-09-17				ENSG00000105697			15598	protein-coding gene	gene with protein product		606464				11034317, 11113132	Standard	NM_021175		Approved	LEAP-1, HEPC, HFE2B, LEAP1	uc002nyw.3	P81172		ENST00000598398.1:c.114A>G	chr19.hg19:g.35775715A>G		98.0	0.0		81.0	4.0	NM_021175	Q1HE14|Q9BY68	Silent	SNP	ENST00000598398.1	hg19	CCDS12454.1																																																																																			.	.		0.637	HAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466067.1	NM_021175	
KMT2B	9757	hgsc.bcm.edu	37	19	36221615	36221615	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:36221615C>A	ENST00000222270.7	+	26	5284	c.5284C>A	c.(5284-5286)Cgt>Agt	p.R1762S	KMT2B_ENST00000420124.1_Missense_Mutation_p.R1762S|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1762	FYR N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00875}.				chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R1764C(1)									CAGGTGCTCCCGTCTGTACTG	0.612																																					p.R1762S		Atlas-SNP	.											MLL4,NS,carcinoma,0,2	MLL4	229	.	1	Substitution - Missense(1)	endometrium(1)	c.C5284A						.						65.0	68.0	67.0					19																	36221615		2004	4182	6186	SO:0001583	missense	8085	exon26			TGCTCCCGTCTGT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5284C>A	chr19.hg19:g.36221615C>A	ENSP00000222270:p.Arg1762Ser	83.0	0.0		58.0	4.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.946063	0.53079	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.89939	-2.59;-2.59	5.97	3.71	0.42584	FY-rich, N-terminal (1);FY-rich, N-terminal subgroup (1);	0.000000	0.45606	D	0.000345	D	0.95014	0.8386	M	0.90309	3.105	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	D	0.95879	0.8897	10	0.87932	D	0	.	13.8947	0.63764	0.2769:0.723:0.0:0.0	.	1762	Q9UMN6	MLL4_HUMAN	S	1762	ENSP00000222270:R1762S;ENSP00000398837:R1762S	ENSP00000222270:R1762S	R	+	1	0	AD000671.1	40913455	0.338000	0.24775	0.998000	0.56505	0.989000	0.77384	0.780000	0.26760	1.500000	0.48636	0.655000	0.94253	CGT	.	.		0.612	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
KMT2B	9757	hgsc.bcm.edu	37	19	36223465	36223465	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:36223465A>G	ENST00000222270.7	+	28	6015	c.6015A>G	c.(6013-6015)gaA>gaG	p.E2005E	KMT2B_ENST00000420124.1_Silent_p.E2005E|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2005					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CCTTCCAGGAAGAGATTGTAG	0.667																																					p.E2005E		Atlas-SNP	.											.	MLL4	229	.	0			c.A6015G						.						26.0	32.0	30.0					19																	36223465		1971	4144	6115	SO:0001819	synonymous_variant	8085	exon28			CCAGGAAGAGATT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.6015A>G	chr19.hg19:g.36223465A>G		91.0	0.0		77.0	7.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	hg19	CCDS46055.1																																																																																			.	.		0.667	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
SIRT2	22933	hgsc.bcm.edu	37	19	39389044	39389044	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:39389044T>C	ENST00000249396.7	-	2	339	c.38A>G	c.(37-39)cAg>cGg	p.Q13R	NFKBIB_ENST00000572515.1_5'Flank|SIRT2_ENST00000392081.2_Intron|SIRT2_ENST00000358931.5_Missense_Mutation_p.Q13R|SIRT2_ENST00000481381.1_5'UTR|NFKBIB_ENST00000392079.3_5'Flank|NFKBIB_ENST00000313582.5_5'Flank	NM_012237.3	NP_036369.2	Q8IXJ6	SIR2_HUMAN	sirtuin 2	13					autophagy (GO:0006914)|cellular lipid catabolic process (GO:0044242)|cellular response to caloric restriction (GO:0061433)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to hypoxia (GO:0071456)|cellular response to molecule of bacterial origin (GO:0071219)|cellular response to oxidative stress (GO:0034599)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|chromatin silencing at telomere (GO:0006348)|gene silencing (GO:0016458)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|innate immune response (GO:0045087)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|myelination in peripheral nervous system (GO:0022011)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)|negative regulation of defense response to bacterium (GO:1900425)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of oligodendrocyte progenitor proliferation (GO:0070446)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cell division (GO:0051781)|positive regulation of DNA binding (GO:0043388)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of meiosis (GO:0045836)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia (GO:2000777)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)|protein kinase B signaling (GO:0043491)|regulation of cell cycle (GO:0051726)|regulation of exit from mitosis (GO:0007096)|regulation of myelination (GO:0031641)|regulation of phosphorylation (GO:0042325)|response to redox state (GO:0051775)|ripoptosome assembly involved in necroptotic process (GO:1901026)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)	centriole (GO:0005814)|centrosome (GO:0005813)|chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|glial cell projection (GO:0097386)|juxtaparanode region of axon (GO:0044224)|lateral loop (GO:0043219)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|myelin sheath (GO:0043209)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|spindle (GO:0005819)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|NAD-dependent protein deacetylase activity (GO:0034979)|protein deacetylase activity (GO:0033558)|transcription factor binding (GO:0008134)|tubulin deacetylase activity (GO:0042903)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(5)|skin(1)	9	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00125)|LUSC - Lung squamous cell carcinoma(53;0.00191)			CTTCCCTGCCTGGGTCTCCAG	0.602																																					p.Q13R		Atlas-SNP	.											.	SIRT2	29	.	0			c.A38G						.						73.0	52.0	59.0					19																	39389044		2203	4300	6503	SO:0001583	missense	22933	exon2			CCTGCCTGGGTCT	AF083107	CCDS12523.1, CCDS46069.1, CCDS74361.1	19q13	2010-06-25	2010-06-25		ENSG00000068903	ENSG00000068903			10886	protein-coding gene	gene with protein product		604480	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 2"", ""sirtuin (silent mating type information regulation 2 homolog) 2 (S. cerevisiae)"""	SIR2L		10393250, 10381378	Standard	NM_012237		Approved		uc002ojt.2	Q8IXJ6	OTTHUMG00000150480	ENST00000249396.7:c.38A>G	chr19.hg19:g.39389044T>C	ENSP00000249396:p.Gln13Arg	73.0	0.0		89.0	4.0	NM_012237	A8K3V1|B2RB45|O95889|Q924Y7|Q9P0G8|Q9UNT0|Q9Y6E9|U5TP13	Missense_Mutation	SNP	ENST00000249396.7	hg19	CCDS12523.1	.	.	.	.	.	.	.	.	.	.	T	11.61	1.690352	0.29962	.	.	ENSG00000068903	ENST00000249396;ENST00000358931	T;T	0.42900	1.52;0.96	3.22	3.22	0.36961	.	.	.	.	.	T	0.33673	0.0871	N	0.08118	0	0.28455	N	0.916147	P	0.45126	0.851	P	0.55391	0.775	T	0.10683	-1.0619	9	0.23302	T	0.38	-4.1004	8.2043	0.31443	0.0:0.0:0.0:1.0	.	13	Q8IXJ6	SIRT2_HUMAN	R	13	ENSP00000249396:Q13R;ENSP00000351809:Q13R	ENSP00000249396:Q13R	Q	-	2	0	SIRT2	44080884	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.057000	0.49931	1.703000	0.51240	0.379000	0.24179	CAG	.	.		0.602	SIRT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318278.1		
MED29	55588	hgsc.bcm.edu	37	19	39880716	39880716	+	5'Flank	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:39880716G>T	ENST00000599213.2	+	0	0				PAF1_ENST00000595564.1_Missense_Mutation_p.Q45K|MED29_ENST00000315588.5_5'Flank|PAF1_ENST00000221266.7_Missense_Mutation_p.Q45K|MED29_ENST00000594368.1_5'Flank|PAF1_ENST00000221265.3_Missense_Mutation_p.Q55K			Q9NX70	MED29_HUMAN	mediator complex subunit 29						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mediator complex (GO:0016592)|nucleus (GO:0005634)				lung(2)|ovary(1)|pancreas(1)	4	all_cancers(60;7.82e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.88e-06)|Ovarian(47;0.0512)		Epithelial(26;1.04e-26)|all cancers(26;7.68e-24)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			CACCTGTTCTGGTCGAAGGGG	0.527																																					p.Q55K		Atlas-SNP	.											.	PAF1	43	.	0			c.C163A						.						155.0	151.0	153.0					19																	39880716		2203	4300	6503	SO:0001631	upstream_gene_variant	54623	exon3			TGTTCTGGTCGAA	AL137304, AY729650	CCDS33021.1	19q13.2	2007-07-30	2007-07-30	2007-07-30		ENSG00000063322			23074	protein-coding gene	gene with protein product		612914	"""intersex-like (Drosophila)"""	IXL		15555573	Standard	NM_017592		Approved	DKFZp434H247	uc010xux.3	Q9NX70			chr19.hg19:g.39880716G>T	Exception_encountered	90.0	0.0		79.0	4.0	NM_019088	B4DNQ6|M0R2E4|Q5XX09|Q9NTF4	Missense_Mutation	SNP	ENST00000599213.2	hg19		.	.	.	.	.	.	.	.	.	.	g	13.38	2.219967	0.39201	.	.	ENSG00000006712	ENST00000221265;ENST00000221266	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.29288	0.0729	N	0.10874	0.06	0.80722	D	1	B;B	0.28605	0.217;0.159	B;B	0.19946	0.016;0.027	T	0.18713	-1.0328	9	0.06099	T	0.92	-28.8987	15.0781	0.72093	0.0:0.0:1.0:0.0	.	45;55	F8W9Q2;Q8N7H5	.;PAF1_HUMAN	K	55;45	.	ENSP00000221265:Q55K	Q	-	1	0	PAF1	44572556	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.671000	0.74472	2.937000	0.99478	0.651000	0.88453	CAG	.	.		0.527	MED29-011	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470870.1	XM_290829	
MEGF8	1954	hgsc.bcm.edu	37	19	42874933	42874933	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:42874933A>G	ENST00000251268.6	+	40	7086	c.7086A>G	c.(7084-7086)aaA>aaG	p.K2362K	MEGF8_ENST00000334370.4_Silent_p.K2295K|MEGF8_ENST00000378073.4_Start_Codon_SNP_p.M1V	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2362					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				ATGGGGAGAAATGCGAGAGCT	0.632																																					p.K2362K		Atlas-SNP	.											.	MEGF8	358	.	0			c.A7086G						.						63.0	54.0	57.0					19																	42874933		2201	4295	6496	SO:0001819	synonymous_variant	1954	exon40			GGAGAAATGCGAG	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.7086A>G	chr19.hg19:g.42874933A>G		66.0	0.0		80.0	4.0	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	A	15.17	2.752735	0.49362	.	.	ENSG00000105429	ENST00000378073	.	.	.	4.96	-5.22	0.02806	.	.	.	.	.	T	0.59362	0.2188	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40942	-0.9536	7	0.87932	D	0	-3.8313	19.3059	0.94163	0.197:0.0:0.803:0.0	.	1	F5GZG7	.	V	1	.	ENSP00000367313:M1V	M	+	1	0	MEGF8	47566773	0.947000	0.32204	0.830000	0.32933	0.904000	0.53231	0.042000	0.13949	-1.128000	0.02922	-0.441000	0.05720	ATG	.	.		0.632	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410	
TEX101	83639	hgsc.bcm.edu	37	19	43920080	43920080	+	Silent	SNP	C	C	T	rs149972012		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:43920080C>T	ENST00000598265.1	+	2	175	c.9C>T	c.(7-9)acC>acT	p.T3T	TEX101_ENST00000601707.1_3'UTR|TEX101_ENST00000253435.7_Silent_p.T21T|TEX101_ENST00000602198.1_Silent_p.T21T	NM_001130011.1	NP_001123483.1	Q9BY14	TX101_HUMAN	testis expressed 101	3						acrosomal membrane (GO:0002080)|anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				large_intestine(1)|lung(12)|ovary(1)|skin(1)	15		Prostate(69;0.0199)				CCATGGGAACCCCTCGTATCC	0.542																																					p.T21T		Atlas-SNP	.											.	TEX101	28	.	0			c.C63T						.	C	,	5,4401	9.9+/-24.2	0,5,2198	194.0	185.0	188.0		9,63	-2.2	0.0	19	dbSNP_134	188	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TEX101	NM_001130011.1,NM_031451.4	,	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	,	3/250,21/268	43920080	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	83639	exon5			GGGAACCCCTCGT	AF241268	CCDS12619.1, CCDS59393.1	19q13.31	2013-06-06	2007-03-13			ENSG00000131126			30722	protein-coding gene	gene with protein product	"""cancer/testis antigen 131"", ""spermatogenesis associated 44"""	612665	"""testis expressed sequence 101"""			16388701, 16516155	Standard	NM_031451		Approved	MGC4766, SGRG, CT131, SPATA44	uc010xwo.2	Q9BY14		ENST00000598265.1:c.9C>T	chr19.hg19:g.43920080C>T		192.0	0.0		158.0	70.0	NM_031451	Q7L5R2|Q9BPY7	Silent	SNP	ENST00000598265.1	hg19	CCDS59393.1																																																																																			.	C|1.000;T|0.000		0.542	TEX101-004	KNOWN	non_canonical_other|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000463176.1	NM_031451	
ZNF223	7766	hgsc.bcm.edu	37	19	44571110	44571110	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:44571110T>C	ENST00000434772.3	+	5	1384	c.1129T>C	c.(1129-1131)Tgt>Cgt	p.C377R	ZNF223_ENST00000591793.1_Missense_Mutation_p.C487R	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				ATGTGACAAGTGTGGGAAGAG	0.443																																					p.C377R		Atlas-SNP	.											.	ZNF223	61	.	0			c.T1129C						.						92.0	87.0	88.0					19																	44571110		2203	4300	6503	SO:0001583	missense	7766	exon5			GACAAGTGTGGGA	AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"""Zinc fingers, C2H2-type"", ""-"""	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.1129T>C	chr19.hg19:g.44571110T>C	ENSP00000401947:p.Cys377Arg	142.0	0.0		86.0	4.0	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Missense_Mutation	SNP	ENST00000434772.3	hg19	CCDS12635.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.370067	0.82573	.	.	ENSG00000178386	ENST00000434772	D	0.85955	-2.05	2.46	2.46	0.29980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94155	0.8125	H	0.97540	4.025	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93926	0.7210	9	0.87932	D	0	.	9.5423	0.39260	0.0:0.0:0.0:1.0	.	377	Q9UK11	ZN223_HUMAN	R	377	ENSP00000401947:C377R	ENSP00000401947:C377R	C	+	1	0	ZNF223	49262950	1.000000	0.71417	0.269000	0.24586	0.939000	0.58152	5.547000	0.67249	1.118000	0.41863	0.260000	0.18958	TGT	.	.		0.443	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2		
ZNF180	7733	hgsc.bcm.edu	37	19	44983588	44983588	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:44983588T>C	ENST00000221327.4	-	4	527	c.246A>G	c.(244-246)acA>acG	p.T82T	ZNF180_ENST00000592529.1_Silent_p.T55T|ZNF180_ENST00000587047.1_Intron|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000586637.1_Missense_Mutation_p.T92A|ZNF180_ENST00000391956.4_Silent_p.T57T	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	82	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)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				GTTCCTCCCGTGTGAAGTCCA	0.493																																					p.T82T	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.A246G						.						118.0	110.0	113.0					19																	44983588		2203	4300	6503	SO:0001819	synonymous_variant	7733	exon4			CTCCCGTGTGAAG	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.246A>G	chr19.hg19:g.44983588T>C		133.0	0.0		92.0	4.0	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Silent	SNP	ENST00000221327.4	hg19	CCDS12639.1																																																																																			.	.		0.493	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
CEACAM20	125931	hgsc.bcm.edu	37	19	45015089	45015089	+	RNA	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:45015089T>C	ENST00000454753.1	-	0	2015							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				TAAACATACCTCATAGATTGA	0.458																																					p.E579G		Atlas-SNP	.											.	CEACAM20	31	.	0			c.A1736G						.						85.0	86.0	86.0					19																	45015089		1874	4110	5984			125931	exon12			CATACCTCATAGA	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		chr19.hg19:g.45015089T>C		137.0	0.0		124.0	5.0	NM_001102597		Missense_Mutation	SNP	ENST00000454753.1	hg19																																																																																				.	.		0.458	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
CLPTM1	1209	hgsc.bcm.edu	37	19	45493763	45493763	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:45493763A>G	ENST00000337392.5	+	10	1393	c.1243A>G	c.(1243-1245)Acc>Gcc	p.T415A	CLPTM1_ENST00000541297.2_Missense_Mutation_p.T401A|CLPTM1_ENST00000546079.1_Missense_Mutation_p.T313A	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	415					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		GGACAACGAGACCAACTTCGT	0.602																																					p.T415A		Atlas-SNP	.											.	CLPTM1	109	.	0			c.A1243G						.						127.0	117.0	120.0					19																	45493763		2203	4300	6503	SO:0001583	missense	1209	exon10			AACGAGACCAACT	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.1243A>G	chr19.hg19:g.45493763A>G	ENSP00000336994:p.Thr415Ala	131.0	0.0		123.0	5.0	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Missense_Mutation	SNP	ENST00000337392.5	hg19	CCDS12651.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.101075	0.76983	.	.	ENSG00000104853	ENST00000546079;ENST00000541297;ENST00000337392;ENST00000347493	.	.	.	5.22	5.22	0.72569	.	0.052052	0.85682	D	0.000000	T	0.67534	0.2903	M	0.81802	2.56	0.80722	D	1	P;P	0.37352	0.591;0.497	B;B	0.41135	0.158;0.348	T	0.70788	-0.4777	9	0.48119	T	0.1	-40.3779	13.0899	0.59162	1.0:0.0:0.0:0.0	.	401;415	F5H8J3;O96005	.;CLPT1_HUMAN	A	313;401;415;415	.	ENSP00000336994:T415A	T	+	1	0	CLPTM1	50185603	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.654000	0.91092	1.986000	0.57962	0.397000	0.26171	ACC	.	.		0.602	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294	
TPRX1	284355	hgsc.bcm.edu	37	19	48305720	48305720	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:48305720T>A	ENST00000322175.3	-	2	703	c.548A>T	c.(547-549)aAc>aTc	p.N183I	TPRX1_ENST00000543508.1_Missense_Mutation_p.N173I|TPRX1_ENST00000535759.1_Missense_Mutation_p.N280I	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	183	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.N183I(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		cgggcctgggtttgggcctgg	0.657																																					p.N183I	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											TPRX1,NS,carcinoma,0,1	TPRX1	46	.	1	Substitution - Missense(1)	endometrium(1)	c.A548T						.						14.0	12.0	13.0					19																	48305720		1705	3156	4861	SO:0001583	missense	284355	exon2			CCTGGGTTTGGGC		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.548A>T	chr19.hg19:g.48305720T>A	ENSP00000323455:p.Asn183Ile	89.0	2.0		67.0	7.0	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	hg19	CCDS33066.1	.	.	.	.	.	.	.	.	.	.	a	1.744	-0.491054	0.04322	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.42900	0.96;0.96;0.96	0.303	-0.607	0.11615	.	.	.	.	.	T	0.19248	0.0462	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16217	-1.0410	8	0.30854	T	0.27	.	.	.	.	.	183	Q8N7U7	TPRX1_HUMAN	I	183;280;173	ENSP00000323455:N183I;ENSP00000438832:N280I;ENSP00000438712:N173I	ENSP00000323455:N183I	N	-	2	0	TPRX1	52997532	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.060000	0.01392	-2.335000	0.00629	-2.486000	0.00196	AAC	.	.		0.657	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
LMTK3	114783	hgsc.bcm.edu	37	19	49001397	49001397	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:49001397C>T	ENST00000600059.1	-	11	3156	c.2929G>A	c.(2929-2931)Ggg>Agg	p.G977R	LMTK3_ENST00000270238.3_Missense_Mutation_p.G1006R			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	977	Pro-rich.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		CTCAGCTCCCCATTCTCCAGC	0.637																																					p.G1006R		Atlas-SNP	.											.	LMTK3	125	.	0			c.G3016A						.						105.0	111.0	109.0					19																	49001397		1907	4119	6026	SO:0001583	missense	114783	exon12			GCTCCCCATTCTC	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 101"""						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.2929G>A	chr19.hg19:g.49001397C>T	ENSP00000472020:p.Gly977Arg	160.0	0.0		122.0	5.0	NM_001080434	Q4G0U1	Missense_Mutation	SNP	ENST00000600059.1	hg19		.	.	.	.	.	.	.	.	.	.	C	5.475	0.272724	0.10349	.	.	ENSG00000142235	ENST00000270238	D	0.88896	-2.44	4.23	3.17	0.36434	.	0.089661	0.39985	N	0.001217	T	0.79064	0.4383	N	0.24115	0.695	0.26218	N	0.979191	B	0.30584	0.286	B	0.21546	0.035	T	0.71794	-0.4485	10	0.66056	D	0.02	.	9.6468	0.39872	0.2092:0.7907:0.0:0.0	.	977	Q96Q04	LMTK3_HUMAN	R	1006	ENSP00000270238:G1006R	ENSP00000270238:G1006R	G	-	1	0	LMTK3	53693209	0.994000	0.37717	0.996000	0.52242	0.034000	0.12701	2.662000	0.46766	0.904000	0.36572	-0.556000	0.04195	GGG	.	.		0.637	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895	
VSTM1	284415	hgsc.bcm.edu	37	19	54545427	54545427	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:54545427T>C	ENST00000338372.2	-	6	686	c.511A>G	c.(511-513)Aag>Gag	p.K171E	VSTM1_ENST00000376626.1_Missense_Mutation_p.K140E|VSTM1_ENST00000366170.2_Missense_Mutation_p.K83E|VSTM1_ENST00000425006.2_3'UTR	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	171					immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		ATCTACCTCTTGGTGGATTCC	0.507																																					p.K171E		Atlas-SNP	.											.	VSTM1	30	.	0			c.A511G						.						148.0	152.0	151.0					19																	54545427		2203	4300	6503	SO:0001583	missense	284415	exon6			ACCTCTTGGTGGA	AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.511A>G	chr19.hg19:g.54545427T>C	ENSP00000343366:p.Lys171Glu	123.0	0.0		92.0	4.0	NM_198481	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Missense_Mutation	SNP	ENST00000338372.2	hg19	CCDS12872.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.057261	0.36277	.	.	ENSG00000189068	ENST00000419106;ENST00000338372;ENST00000376626;ENST00000366170	T;T;T;T	0.44482	2.58;6.81;6.49;0.92	3.24	0.898	0.19264	.	0.497894	0.14973	N	0.287670	T	0.22205	0.0535	L	0.29908	0.895	0.09310	N	0.999995	B;B	0.30584	0.286;0.286	B;B	0.20384	0.029;0.029	T	0.10382	-1.0632	10	0.31617	T	0.26	-4.4272	3.0861	0.06278	0.0:0.1536:0.2457:0.6007	.	140;171	D2DJS4;Q6UX27	.;VSTM1_HUMAN	E	61;171;140;83	ENSP00000409412:K61E;ENSP00000343366:K171E;ENSP00000365813:K140E;ENSP00000444153:K83E	ENSP00000343366:K171E	K	-	1	0	VSTM1	59237239	0.004000	0.15560	0.127000	0.21898	0.003000	0.03518	-0.405000	0.07196	0.130000	0.18549	-0.394000	0.06481	AAG	.	.		0.507	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481	
EPS8L1	54869	hgsc.bcm.edu	37	19	55597306	55597306	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:55597306A>G	ENST00000201647.6	+	15	1539	c.1483A>G	c.(1483-1485)Agt>Ggt	p.S495G	EPS8L1_ENST00000245618.5_Missense_Mutation_p.S368G|EPS8L1_ENST00000588359.1_Missense_Mutation_p.S181G|EPS8L1_ENST00000586329.1_Missense_Mutation_p.S509G|EPS8L1_ENST00000540810.1_Missense_Mutation_p.S431G	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	495	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CCGCAACAGCAGTGAGCTGTC	0.577																																					p.S495G	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.A1483G						.						69.0	66.0	67.0					19																	55597306		2203	4300	6503	SO:0001583	missense	54869	exon15			AACAGCAGTGAGC	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.1483A>G	chr19.hg19:g.55597306A>G	ENSP00000201647:p.Ser495Gly	68.0	0.0		100.0	4.0	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	hg19	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	A	19.09	3.759217	0.69763	.	.	ENSG00000131037	ENST00000310075;ENST00000201647;ENST00000540810;ENST00000245618;ENST00000539118	T;T;T	0.27720	1.65;1.65;1.65	4.43	4.43	0.53597	Src homology-3 domain (4);	0.153050	0.53938	D	0.000041	T	0.31167	0.0788	N	0.05414	-0.055	0.47123	D	0.999324	P;D;B;D	0.69078	0.928;0.995;0.34;0.997	P;D;B;P	0.64410	0.632;0.925;0.153;0.908	T	0.25847	-1.0120	10	0.49607	T	0.09	-19.6723	11.9022	0.52690	1.0:0.0:0.0:0.0	.	509;274;368;495	Q8TE68-3;Q8TE68-4;Q8TE68-2;Q8TE68	.;.;.;ES8L1_HUMAN	G	509;495;431;368;181	ENSP00000201647:S495G;ENSP00000437541:S431G;ENSP00000245618:S368G	ENSP00000201647:S495G	S	+	1	0	EPS8L1	60289118	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	7.850000	0.86915	1.775000	0.52247	0.397000	0.26171	AGT	.	.		0.577	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729	
PTPRH	5794	hgsc.bcm.edu	37	19	55697237	55697237	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:55697237A>G	ENST00000376350.3	-	17	2916	c.2894T>C	c.(2893-2895)cTc>cCc	p.L965P	PTPRH_ENST00000263434.5_Missense_Mutation_p.L787P	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	965	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CACCTGGAGGAGCAGCAGTTC	0.627																																					p.L965P		Atlas-SNP	.											.	PTPRH	139	.	0			c.T2894C						.						88.0	74.0	79.0					19																	55697237		2203	4300	6503	SO:0001583	missense	5794	exon17			TGGAGGAGCAGCA		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.2894T>C	chr19.hg19:g.55697237A>G	ENSP00000365528:p.Leu965Pro	100.0	0.0		88.0	5.0	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	hg19	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.247235	0.59103	.	.	ENSG00000080031	ENST00000376350;ENST00000263434	D;D	0.85955	-2.05;-2.05	4.68	4.68	0.58851	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.499063	0.15092	N	0.281037	D	0.94456	0.8216	H	0.96080	3.765	0.24885	N	0.992207	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.987	D	0.88001	0.2756	10	0.87932	D	0	.	12.0896	0.53717	1.0:0.0:0.0:0.0	.	787;965	C9JCH2;Q9HD43	.;PTPRH_HUMAN	P	965;787	ENSP00000365528:L965P;ENSP00000263434:L787P	ENSP00000263434:L787P	L	-	2	0	PTPRH	60389049	0.997000	0.39634	0.005000	0.12908	0.122000	0.20287	5.461000	0.66699	2.121000	0.65114	0.529000	0.55759	CTC	.	.		0.627	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
ZNF470	388566	hgsc.bcm.edu	37	19	57088312	57088312	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:57088312A>G	ENST00000330619.8	+	6	1201	c.515A>G	c.(514-516)gAt>gGt	p.D172G	ZNF470_ENST00000391709.3_Missense_Mutation_p.D172G|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	172					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)		GAAAAAAGAGATCACTCTAAC	0.323																																					p.D172G		Atlas-SNP	.											.	ZNF470	103	.	0			c.A515G						.						50.0	52.0	51.0					19																	57088312		2203	4300	6503	SO:0001583	missense	388566	exon6			AAAGAGATCACTC	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.515A>G	chr19.hg19:g.57088312A>G	ENSP00000333223:p.Asp172Gly	156.0	0.0		132.0	6.0	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Missense_Mutation	SNP	ENST00000330619.8	hg19	CCDS33122.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.171175	0.00315	.	.	ENSG00000197016	ENST00000391709;ENST00000330619	T;T	0.06294	3.32;3.32	3.2	2.18	0.27775	.	.	.	.	.	T	0.03178	0.0093	N	0.08118	0	0.09310	N	1	B	0.24186	0.099	B	0.14578	0.011	T	0.44892	-0.9298	9	0.32370	T	0.25	.	6.7702	0.23589	0.8826:0.0:0.1174:0.0	.	172	Q6ECI4	ZN470_HUMAN	G	172	ENSP00000375590:D172G;ENSP00000333223:D172G	ENSP00000333223:D172G	D	+	2	0	ZNF470	61780124	0.001000	0.12720	0.001000	0.08648	0.032000	0.12392	1.101000	0.31037	0.620000	0.30215	-0.351000	0.07748	GAT	.	.		0.323	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668	
ZIM2	23619	hgsc.bcm.edu	37	19	57286250	57286250	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:57286250T>C	ENST00000391708.3	-	12	1932	c.1390A>G	c.(1390-1392)Aga>Gga	p.R464G	AC006115.3_ENST00000595954.1_RNA|AC006115.3_ENST00000597946.1_RNA|AC006115.3_ENST00000594400.1_RNA|ZIM2_ENST00000593711.1_Missense_Mutation_p.R464G|ZIM2_ENST00000221722.5_Missense_Mutation_p.R464G|ZIM2_ENST00000599935.1_Missense_Mutation_p.R464G|ZIM2_ENST00000601070.1_Missense_Mutation_p.R464G	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	464					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)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		TGGCAGGCTCTCTCTCCAACG	0.478																																					p.R464G		Atlas-SNP	.											.	ZIM2	511	.	0			c.A1390G						.						88.0	70.0	76.0					19																	57286250		2203	4300	6503	SO:0001583	missense	23619	exon11			AGGCTCTCTCTCC	AF166122	CCDS33123.1	19q13.4	2012-10-31				ENSG00000269699		"""Zinc fingers, C2H2-type"""	12875	protein-coding gene	gene with protein product							Standard	NM_015363		Approved	ZNF656		Q9NZV7		ENST00000391708.3:c.1390A>G	chr19.hg19:g.57286250T>C	ENSP00000375589:p.Arg464Gly	86.0	0.0		79.0	4.0	NM_015363	Q2M3K1	Missense_Mutation	SNP	ENST00000391708.3	hg19	CCDS33123.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.288519	0.23478	.	.	ENSG00000198300	ENST00000391708;ENST00000221722	T;T	0.05081	3.5;3.5	4.96	2.8	0.32819	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08846	0.0219	L	0.52823	1.66	.	.	.	P	0.50272	0.933	B	0.42692	0.395	T	0.13308	-1.0514	8	0.87932	D	0	.	10.506	0.44834	0.0:0.0:0.5025:0.4975	.	464	Q9NZV7	ZIM2_HUMAN	G	464	ENSP00000375589:R464G;ENSP00000221722:R464G	ENSP00000221722:R464G	R	-	1	2	ZIM2	61978062	0.689000	0.27690	0.012000	0.15200	0.373000	0.29922	2.802000	0.47916	0.341000	0.23771	-0.316000	0.08728	AGA	.	.		0.478	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2		
ZNF543	125919	hgsc.bcm.edu	37	19	57839824	57839824	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:57839824A>G	ENST00000321545.4	+	4	1339	c.994A>G	c.(994-996)Atc>Gtc	p.I332V		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	332					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)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		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;0.0257)		ACACTACATCATCCACACGGG	0.512																																					p.I332V		Atlas-SNP	.											.	ZNF543	61	.	0			c.A994G						.						74.0	75.0	75.0					19																	57839824		2203	4300	6503	SO:0001583	missense	125919	exon4			TACATCATCCACA	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"""Zinc fingers, C2H2-type"", ""-"""	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.994A>G	chr19.hg19:g.57839824A>G	ENSP00000322545:p.Ile332Val	98.0	0.0		67.0	4.0	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	hg19	CCDS33130.1	.	.	.	.	.	.	.	.	.	.	A	9.782	1.175449	0.21704	.	.	ENSG00000178229	ENST00000321545	T	0.16324	2.35	3.0	1.9	0.25705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10208	0.0250	N	0.17379	0.485	0.19945	N	0.999942	B	0.21225	0.053	B	0.28849	0.095	T	0.34976	-0.9807	9	0.49607	T	0.09	.	3.0895	0.06289	0.6653:0.0:0.1218:0.2128	.	332	Q08ER8	ZN543_HUMAN	V	332	ENSP00000322545:I332V	ENSP00000322545:I332V	I	+	1	0	ZNF543	62531636	0.000000	0.05858	0.970000	0.41538	0.890000	0.51754	1.146000	0.31589	0.310000	0.22990	0.459000	0.35465	ATC	.	.		0.512	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
A1BG	1	hgsc.bcm.edu	37	19	58863849	58863849	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr19:58863849A>G	ENST00000263100.3	-	4	474	c.413T>C	c.(412-414)gTg>gCg	p.V138A	A1BG-AS1_ENST00000595302.1_RNA|A1BG-AS1_ENST00000593960.1_RNA|CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000599728.1_RNA	NM_130786.3	NP_570602.2	P04217	A1BG_HUMAN	alpha-1-B glycoprotein	138	Ig-like V-type 2.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|prostate(2)	15		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)		ACCTCGGCACACTGCTGTTGT	0.632																																					p.V138A		Atlas-SNP	.											.	A1BG	40	.	0			c.T413C						.						102.0	107.0	105.0					19																	58863849		2203	4300	6503	SO:0001583	missense	1	exon4			CGGCACACTGCTG		CCDS12976.1	19q13.43	2013-10-15			ENSG00000121410	ENSG00000121410		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5	protein-coding gene	gene with protein product		138670				2591067	Standard	NM_130786		Approved		uc002qsd.4	P04217	OTTHUMG00000183507	ENST00000263100.3:c.413T>C	chr19.hg19:g.58863849A>G	ENSP00000263100:p.Val138Ala	67.0	0.0		78.0	4.0	NM_130786	A8K052|Q68CK0|Q8IYJ6|Q96P39	Missense_Mutation	SNP	ENST00000263100.3	hg19	CCDS12976.1	.	.	.	.	.	.	.	.	.	.	A	7.800	0.713499	0.15306	.	.	ENSG00000121410	ENST00000263100;ENST00000453054	T	0.09538	2.97	3.39	-0.268	0.12934	Immunoglobulin-like fold (1);	1.307360	0.05638	N	0.582894	T	0.12561	0.0305	L	0.54323	1.7	0.09310	N	1	B	0.22146	0.065	B	0.29598	0.104	T	0.46303	-0.9201	10	0.15499	T	0.54	.	9.0994	0.36658	0.3965:0.6035:0.0:0.0	.	138	P04217	A1BG_HUMAN	A	138;16	ENSP00000263100:V138A	ENSP00000263100:V138A	V	-	2	0	A1BG	63555661	0.000000	0.05858	0.131000	0.22000	0.017000	0.09413	-0.751000	0.04803	-0.125000	0.11703	0.460000	0.39030	GTG	.	.		0.632	A1BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466930.1	NM_130786	
CHGB	1114	hgsc.bcm.edu	37	20	5903053	5903053	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:5903053A>G	ENST00000378961.4	+	4	467	c.263A>G	c.(262-264)gAc>gGc	p.D88G		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	88						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						TTGTTAAGAGACCCAGCTGAT	0.473																																					p.D88G		Atlas-SNP	.											.	CHGB	112	.	0			c.A263G						.						58.0	59.0	59.0					20																	5903053		2203	4300	6503	SO:0001583	missense	1114	exon4			TAAGAGACCCAGC		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.263A>G	chr20.hg19:g.5903053A>G	ENSP00000368244:p.Asp88Gly	121.0	0.0		116.0	5.0	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	hg19	CCDS13092.1	.	.	.	.	.	.	.	.	.	.	A	17.39	3.376473	0.61735	.	.	ENSG00000089199	ENST00000378961;ENST00000455042	T;T	0.02916	4.11;4.11	5.77	5.77	0.91146	.	0.290166	0.31082	N	0.008285	T	0.09468	0.0233	M	0.69823	2.125	0.31460	N	0.669675	D	0.56746	0.977	P	0.54889	0.763	T	0.02437	-1.1159	10	0.87932	D	0	-29.2125	10.1671	0.42886	0.9251:0.0:0.0749:0.0	.	88	P05060	SCG1_HUMAN	G	88;68	ENSP00000368244:D88G;ENSP00000416643:D68G	ENSP00000368244:D88G	D	+	2	0	CHGB	5851053	1.000000	0.71417	0.998000	0.56505	0.444000	0.32077	6.353000	0.73032	2.197000	0.70478	0.533000	0.62120	GAC	.	.		0.473	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
SPTLC3	55304	hgsc.bcm.edu	37	20	13071736	13071736	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:13071736T>A	ENST00000399002.2	+	5	887	c.613T>A	c.(613-615)Ttg>Atg	p.L205M	SPTLC3_ENST00000378194.4_Missense_Mutation_p.L205M	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	205					small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						TGCAGGCACCTTGGATAAGCA	0.428																																					p.L205M		Atlas-SNP	.											.	SPTLC3	78	.	0			c.T613A						.						170.0	169.0	169.0					20																	13071736		1900	4126	6026	SO:0001583	missense	55304	exon5			GGCACCTTGGATA	AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"""chromosome 20 open reading frame 38"", ""serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"""	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.613T>A	chr20.hg19:g.13071736T>A	ENSP00000381968:p.Leu205Met	201.0	0.0		158.0	53.0	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Missense_Mutation	SNP	ENST00000399002.2	hg19	CCDS13115.2	.	.	.	.	.	.	.	.	.	.	T	9.789	1.177390	0.21787	.	.	ENSG00000172296	ENST00000399002;ENST00000378194	D;D	0.90676	-2.71;-2.71	5.44	-1.46	0.08800	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.363501	0.25823	N	0.028065	T	0.80248	0.4588	L	0.33485	1.01	0.37988	D	0.933822	B	0.17667	0.023	B	0.28553	0.091	T	0.62300	-0.6883	10	0.27082	T	0.32	-6.3789	1.2822	0.02043	0.2561:0.3455:0.1195:0.2789	.	205	Q9NUV7	SPTC3_HUMAN	M	205	ENSP00000381968:L205M;ENSP00000367436:L205M	ENSP00000367436:L205M	L	+	1	2	SPTLC3	13019736	0.969000	0.33509	0.991000	0.47740	0.418000	0.31294	0.472000	0.22116	0.073000	0.16731	0.524000	0.50904	TTG	.	.		0.428	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327	
MACROD2	140733	hgsc.bcm.edu	37	20	15967784	15967784	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:15967784A>G	ENST00000310348.4	+	15	1134	c.1134A>G	c.(1132-1134)gaA>gaG	p.E378E	MACROD2_ENST00000402914.1_Silent_p.E143E|MACROD2_ENST00000217246.4_Silent_p.E378E|MACROD2_ENST00000378058.3_Silent_p.E143E|MACROD2_ENST00000407045.3_Silent_p.E29E			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	378	Glu-rich.				brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				AGGACCAAGAAGAAAAAGAAG	0.383																																					p.E378E		Atlas-SNP	.											.	MACROD2	34	.	0			c.A1134G						.						113.0	111.0	112.0					20																	15967784		2203	4300	6503	SO:0001819	synonymous_variant	140733	exon15			CCAAGAAGAAAAA	BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"""chromosome 20 open reading frame 133"""	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.1134A>G	chr20.hg19:g.15967784A>G		91.0	0.0		78.0	4.0	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Silent	SNP	ENST00000310348.4	hg19	CCDS13120.2																																																																																			.	.		0.383	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676	
GZF1	64412	hgsc.bcm.edu	37	20	23345920	23345920	+	Silent	SNP	A	A	G	rs547594353|rs146870841	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:23345920A>G	ENST00000338121.5	+	2	977	c.900A>G	c.(898-900)gaA>gaG	p.E300E	GZF1_ENST00000544236.1_Intron|GZF1_ENST00000542987.1_Intron|GZF1_ENST00000461789.1_3'UTR|GZF1_ENST00000377051.2_Silent_p.E300E			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	300					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					Cggaggaggaagaggaggagg	0.527																																					p.E300E		Atlas-SNP	.											.,1	GZF1	61	.	0			c.A900G						.	A		0,4406		0,0,2203	48.0	53.0	52.0		900	-8.0	0.0	20	dbSNP_134	52	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous	GZF1	NM_022482.3		0,3,6500	GG,GA,AA		0.0349,0.0,0.0231		300/712	23345920	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	64412	exon1			GGAGGAAGAGGAG	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	15808	protein-coding gene	gene with protein product		613842	"""zinc finger protein 336"""	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.900A>G	chr20.hg19:g.23345920A>G		69.0	0.0		74.0	3.0	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Silent	SNP	ENST00000338121.5	hg19	CCDS13151.1																																																																																			.	A|1.000;G|0.000		0.527	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482	
KIAA1755	85449	hgsc.bcm.edu	37	20	36851965	36851965	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:36851965T>C	ENST00000279024.4	-	9	2514	c.2243A>G	c.(2242-2244)aAg>aGg	p.K748R		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	748										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)				GGGGTCGGCCTTCTCGAATTC	0.612																																					p.K748R		Atlas-SNP	.											.	KIAA1755	145	.	0			c.A2243G						.						50.0	48.0	49.0					20																	36851965		2203	4300	6503	SO:0001583	missense	85449	exon9			TCGGCCTTCTCGA	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.2243A>G	chr20.hg19:g.36851965T>C	ENSP00000279024:p.Lys748Arg	94.0	0.0		82.0	4.0	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	hg19	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	T	4.279	0.050887	0.08243	.	.	ENSG00000149633	ENST00000279024;ENST00000373398;ENST00000435901	T;T	0.22945	3.34;1.93	4.46	3.36	0.38483	.	0.130493	0.34906	N	0.003596	T	0.15869	0.0382	L	0.29908	0.895	0.32929	D	0.516869	B	0.14012	0.009	B	0.09377	0.004	T	0.17992	-1.0351	10	0.20519	T	0.43	.	8.0775	0.30724	0.0:0.0979:0.0:0.9021	.	748	Q5JYT7	K1755_HUMAN	R	748;256;47	ENSP00000279024:K748R;ENSP00000393503:K47R	ENSP00000279024:K748R	K	-	2	0	KIAA1755	36285379	0.998000	0.40836	0.982000	0.44146	0.031000	0.12232	1.558000	0.36309	0.754000	0.32968	0.418000	0.28097	AAG	.	.		0.612	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
SLC12A5	57468	hgsc.bcm.edu	37	20	44685068	44685068	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:44685068A>G	ENST00000454036.2	+	23	3093	c.3044A>G	c.(3043-3045)gAg>gGg	p.E1015G	SLC12A5_ENST00000243964.3_Missense_Mutation_p.E992G	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	1015					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	CCAGGGGAGGAGCCTGAGGGG	0.607																																					p.E1015G		Atlas-SNP	.											.	SLC12A5	181	.	0			c.A3044G						.						39.0	37.0	38.0					20																	44685068		2203	4300	6503	SO:0001583	missense	57468	exon23			GGGAGGAGCCTGA	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"""Solute carriers"""	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.3044A>G	chr20.hg19:g.44685068A>G	ENSP00000387694:p.Glu1015Gly	80.0	0.0		87.0	4.0	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Missense_Mutation	SNP	ENST00000454036.2	hg19	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	A	7.247	0.602362	0.13939	.	.	ENSG00000124140	ENST00000454036;ENST00000243964	T;T	0.42131	0.98;0.98	5.14	5.14	0.70334	.	0.375027	0.27105	N	0.020908	T	0.24586	0.0596	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.10450	0.001;0.005	T	0.06935	-1.0799	10	0.24483	T	0.36	.	14.2969	0.66318	1.0:0.0:0.0:0.0	.	1015;992	Q9H2X9;Q9H2X9-2	S12A5_HUMAN;.	G	1015;992	ENSP00000387694:E1015G;ENSP00000243964:E992G	ENSP00000243964:E992G	E	+	2	0	SLC12A5	44118475	1.000000	0.71417	1.000000	0.80357	0.030000	0.12068	4.682000	0.61671	2.155000	0.67459	0.459000	0.35465	GAG	.	.		0.607	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		
STAU1	6780	hgsc.bcm.edu	37	20	47734536	47734536	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:47734536T>C	ENST00000371856.2	-	11	1697	c.1287A>G	c.(1285-1287)ggA>ggG	p.G429G	STAU1_ENST00000371802.1_Silent_p.G354G|STAU1_ENST00000371828.3_Silent_p.G354G|STAU1_ENST00000347458.5_Silent_p.G348G|STAU1_ENST00000340954.7_Silent_p.G348G|STAU1_ENST00000360426.4_Silent_p.G348G|STAU1_ENST00000371792.1_Silent_p.G346G	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	429					intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			CTTGACTAACTCCTACAGCCT	0.522																																					p.G429G		Atlas-SNP	.											.	STAU1	54	.	0			c.A1287G						.						126.0	123.0	124.0					20																	47734536		2203	4300	6503	SO:0001819	synonymous_variant	6780	exon11			ACTAACTCCTACA		CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214			11370	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 150"""	601716	"""staufen (Drosophila, RNA-binding protein)"", ""staufen, RNA binding protein (Drosophila)"", ""staufen, RNA binding protein, homolog 1 (Drosophila)"""	STAU		8884277, 15680326	Standard	XM_005260524		Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.1287A>G	chr20.hg19:g.47734536T>C		113.0	0.0		86.0	5.0	NM_017453	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	Silent	SNP	ENST00000371856.2	hg19	CCDS13414.1																																																																																			.	.		0.522	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079633.1	NM_017453	
TSHZ2	128553	hgsc.bcm.edu	37	20	51872705	51872705	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:51872705T>C	ENST00000371497.5	+	2	3595	c.2708T>C	c.(2707-2709)gTc>gCc	p.V903A	TSHZ2_ENST00000603338.2_Missense_Mutation_p.V900A|TSHZ2_ENST00000329613.6_Missense_Mutation_p.V900A|RP4-678D15.1_ENST00000606932.1_RNA	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	903					multicellular organismal development (GO:0007275)|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(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			CTGGCCAACGTCAAGTACCAG	0.488																																					p.V903A		Atlas-SNP	.											.	TSHZ2	209	.	0			c.T2708C						.						70.0	69.0	70.0					20																	51872705		2203	4300	6503	SO:0001583	missense	128553	exon2			CCAACGTCAAGTA	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2708T>C	chr20.hg19:g.51872705T>C	ENSP00000360552:p.Val903Ala	136.0	0.0		108.0	5.0	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	hg19	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.127114	0.77549	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.26810	1.72;1.71	5.8	5.8	0.92144	Homeobox (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.46425	0.1392	L	0.49126	1.545	0.80722	D	1	D	0.69078	0.997	D	0.72625	0.978	T	0.42155	-0.9468	10	0.87932	D	0	-18.2384	16.1354	0.81481	0.0:0.0:0.0:1.0	.	903	Q9NRE2	TSH2_HUMAN	A	903;900;429	ENSP00000360552:V903A;ENSP00000333114:V900A	ENSP00000333114:V900A	V	+	2	0	TSHZ2	51306112	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.693000	0.84214	2.206000	0.71126	0.523000	0.50628	GTC	.	.		0.488	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
CASS4	57091	hgsc.bcm.edu	37	20	55025710	55025710	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:55025710T>C	ENST00000360314.3	+	5	842	c.617T>C	c.(616-618)cTc>cCc	p.L206P	CASS4_ENST00000371336.3_Missense_Mutation_p.L206P|CASS4_ENST00000434344.1_Missense_Mutation_p.L206P	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	206					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						AAGGCAGGACTCCATCCCCCA	0.483																																					p.L206P		Atlas-SNP	.											.	CASS4	121	.	0			c.T617C						.						96.0	71.0	80.0					20																	55025710		2203	4300	6503	SO:0001583	missense	57091	exon4			CAGGACTCCATCC	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.617T>C	chr20.hg19:g.55025710T>C	ENSP00000353462:p.Leu206Pro	120.0	0.0		91.0	5.0	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	hg19	CCDS33492.1	.	.	.	.	.	.	.	.	.	.	T	9.102	1.004418	0.19199	.	.	ENSG00000087589	ENST00000360314;ENST00000371336;ENST00000434344	T;T;T	0.20881	2.54;2.54;2.04	4.99	1.41	0.22369	.	1.471490	0.04517	N	0.383859	T	0.38374	0.1038	M	0.63428	1.95	0.18873	N	0.999989	D;D;D;B	0.71674	0.991;0.994;0.998;0.016	P;P;D;B	0.63381	0.556;0.906;0.914;0.008	T	0.09228	-1.0684	10	0.34782	T	0.22	-1.8146	5.496	0.16804	0.0:0.0939:0.3955:0.5106	.	152;206;206;206	B4DII4;Q9NQ75-3;Q9NQ75-2;Q9NQ75	.;.;.;CASS4_HUMAN	P	206	ENSP00000353462:L206P;ENSP00000360387:L206P;ENSP00000410027:L206P	ENSP00000353462:L206P	L	+	2	0	CASS4	54459117	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	0.145000	0.16157	0.062000	0.16340	0.533000	0.62120	CTC	.	.		0.483	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356	
EDN3	1908	hgsc.bcm.edu	37	20	57896094	57896094	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:57896094T>C	ENST00000337938.2	+	3	774	c.388T>C	c.(388-390)Tcc>Ccc	p.S130P	EDN3_ENST00000371025.3_Missense_Mutation_p.S130P|EDN3_ENST00000395654.3_Missense_Mutation_p.S130P|EDN3_ENST00000311585.7_Missense_Mutation_p.S130P|EDN3_ENST00000371028.2_Missense_Mutation_p.S130P	NM_207034.1	NP_996917.1	P14138	EDN3_HUMAN	endothelin 3	130					blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inositol phosphate-mediated signaling (GO:0048016)|melanocyte differentiation (GO:0030318)|multicellular organismal development (GO:0007275)|neural crest cell migration (GO:0001755)|neuron differentiation (GO:0030182)|neutrophil chemotaxis (GO:0030593)|peptide hormone secretion (GO:0030072)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|regulation of developmental pigmentation (GO:0048070)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|signal transduction (GO:0007165)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	19	all_lung(29;0.0115)					CTATGGACTGTCCAACTACAG	0.612																																					p.S130P		Atlas-SNP	.											.	EDN3	83	.	0			c.T388C						.						89.0	77.0	81.0					20																	57896094		2203	4300	6503	SO:0001583	missense	1908	exon3			GGACTGTCCAACT	X52001	CCDS13477.1, CCDS13478.1, CCDS13479.1	20q13.2-q13.3	2013-02-26			ENSG00000124205	ENSG00000124205		"""Endogenous ligands"""	3178	protein-coding gene	gene with protein product		131242					Standard	NM_000114		Approved	ET3	uc002yaq.3	P14138	OTTHUMG00000032867	ENST00000337938.2:c.388T>C	chr20.hg19:g.57896094T>C	ENSP00000337128:p.Ser130Pro	118.0	0.0		95.0	4.0	NM_207034	E1P5I5|Q03229|Q7Z6D2|Q9UGT7	Missense_Mutation	SNP	ENST00000337938.2	hg19	CCDS13477.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.029868	0.75504	.	.	ENSG00000124205	ENST00000337938;ENST00000311585;ENST00000371028;ENST00000371025;ENST00000395654	D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18;-2.18	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	D	0.91181	0.7222	M	0.62723	1.935	0.38107	D	0.93745	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.72338	0.977;0.965;0.949;0.961	D	0.92226	0.5788	10	0.54805	T	0.06	-41.3052	11.1433	0.48415	0.0:0.0:0.0:1.0	.	130;130;130;130	P14138-2;Q7Z6D2;P14138;Q4FAT2	.;.;EDN3_HUMAN;.	P	130	ENSP00000337128:S130P;ENSP00000311854:S130P;ENSP00000360067:S130P;ENSP00000360064:S130P;ENSP00000379015:S130P	ENSP00000311854:S130P	S	+	1	0	EDN3	57329489	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	2.877000	0.48506	1.951000	0.56629	0.459000	0.35465	TCC	.	.		0.612	EDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079919.2	NM_000114	
COL9A3	1299	hgsc.bcm.edu	37	20	61460123	61460123	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:61460123C>T	ENST00000343916.3	+	18	911	c.908C>T	c.(907-909)cCg>cTg	p.P303L		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	303	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					CAGGGCATGCCGGGCAAGGAC	0.682																																					p.P303L		Atlas-SNP	.											COL9A3,right_lower_lobe,carcinoma,0,1	COL9A3	70	.	0			c.C908T						.						49.0	46.0	47.0					20																	61460123		2201	4299	6500	SO:0001583	missense	1299	exon18			GCATGCCGGGCAA	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2219	protein-coding gene	gene with protein product	"""collagen type IX proteoglycan"""	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.908C>T	chr20.hg19:g.61460123C>T	ENSP00000341640:p.Pro303Leu	59.0	0.0		56.0	4.0	NM_001853	Q13681|Q9H4G9|Q9UPE2	Missense_Mutation	SNP	ENST00000343916.3	hg19	CCDS13505.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.121043	0.77436	.	.	ENSG00000092758	ENST00000343916	D	0.97066	-4.23	3.93	3.93	0.45458	.	0.119276	0.64402	D	0.000019	D	0.97870	0.9300	M	0.82433	2.59	0.80722	D	1	D	0.76494	0.999	P	0.57283	0.817	D	0.98387	1.0561	10	0.66056	D	0.02	.	15.0251	0.71663	0.0:1.0:0.0:0.0	.	303	Q14050	CO9A3_HUMAN	L	303	ENSP00000341640:P303L	ENSP00000341640:P303L	P	+	2	0	COL9A3	60930568	0.989000	0.36119	0.995000	0.50966	0.740000	0.42216	2.883000	0.48554	2.200000	0.70718	0.448000	0.29417	CCG	.	.		0.682	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
YTHDF1	54915	hgsc.bcm.edu	37	20	61835049	61835049	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:61835049A>G	ENST00000370339.3	-	4	584	c.243T>C	c.(241-243)ccT>ccC	p.P81P	YTHDF1_ENST00000370333.4_Silent_p.P31P|YTHDF1_ENST00000370334.4_Intron	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	81							N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						ATGGAATCGGAGGGTCCCCTG	0.557																																					p.P81P		Atlas-SNP	.											.	YTHDF1	66	.	0			c.T243C						.						104.0	109.0	107.0					20																	61835049		2203	4300	6503	SO:0001819	synonymous_variant	54915	exon4			AATCGGAGGGTCC	AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"""YTH domain family 1"""	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.243T>C	chr20.hg19:g.61835049A>G		124.0	0.0		102.0	5.0	NM_017798	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Silent	SNP	ENST00000370339.3	hg19	CCDS13511.1																																																																																			.	.		0.557	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798	
OPRL1	4987	hgsc.bcm.edu	37	20	62729930	62729930	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr20:62729930C>T	ENST00000349451.3	+	6	1303	c.891C>T	c.(889-891)gcC>gcT	p.A297A	OPRL1_ENST00000355631.4_Silent_p.A297A|OPRL1_ENST00000336866.2_Silent_p.A297A	NM_001200019.1	NP_001186948.1	P41146	OPRX_HUMAN	opiate receptor-like 1	297					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavior (GO:0007610)|opioid receptor signaling pathway (GO:0038003)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|nociceptin receptor activity (GO:0001626)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)					GCGAGACTGCCGTGGCCATTC	0.632																																					p.A297A		Atlas-SNP	.											.	OPRL1	47	.	0			c.C891T						.						81.0	68.0	73.0					20																	62729930		2201	4295	6496	SO:0001819	synonymous_variant	4987	exon4			GACTGCCGTGGCC		CCDS13556.1	20q13.33	2012-08-08			ENSG00000125510	ENSG00000125510		"""GPCR / Class A : Opioid receptors"""	8155	protein-coding gene	gene with protein product	"""LC132 receptor-like"", ""orphanin FQ receptor"", ""kappa3-related opioid receptor"""	602548				8137918	Standard	NM_000913		Approved	NOCIR, ORL1, OOR, KOR-3	uc021wgs.1	P41146	OTTHUMG00000033027	ENST00000349451.3:c.891C>T	chr20.hg19:g.62729930C>T		104.0	0.0		96.0	38.0	NM_000913	Q8TD34|Q8WYH9|Q9H4K4	Silent	SNP	ENST00000349451.3	hg19	CCDS13556.1																																																																																			.	.		0.632	OPRL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080295.1	NM_182647	
CXADR	1525	hgsc.bcm.edu	37	21	18933790	18933790	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:18933790A>G	ENST00000284878.7	+	6	1577	c.829A>G	c.(829-831)Atc>Gtc	p.I277V	CXADR_ENST00000400166.1_Intron|CXADR_ENST00000356275.6_Intron|CXADR_ENST00000306618.10_Missense_Mutation_p.I236V|CXADR_ENST00000400165.1_Intron|CXADR_ENST00000400169.1_Missense_Mutation_p.I277V	NM_001338.4	NP_001329.1	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor	277					actin cytoskeleton reorganization (GO:0031532)|AV node cell to bundle of His cell communication (GO:0086067)|blood coagulation (GO:0007596)|cardiac muscle fiber development (GO:0048739)|cell-cell junction organization (GO:0045216)|defense response to virus (GO:0051607)|epithelial structure maintenance (GO:0010669)|gamma-delta T cell activation (GO:0046629)|germ cell migration (GO:0008354)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|homotypic cell-cell adhesion (GO:0034109)|leukocyte migration (GO:0050900)|mitochondrion organization (GO:0007005)|neutrophil chemotaxis (GO:0030593)|regulation of immune response (GO:0050776)|transepithelial transport (GO:0070633)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|adherens junction (GO:0005912)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|filopodium (GO:0030175)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|cell adhesion molecule binding (GO:0050839)|connexin binding (GO:0071253)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|virus receptor activity (GO:0001618)			endometrium(2)|large_intestine(5)|lung(1)|ovary(1)|prostate(2)	11				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		TCATCACGATATCAGGTAATT	0.363																																					p.I277V		Atlas-SNP	.											.	CXADR	44	.	0			c.A829G						.						71.0	70.0	71.0					21																	18933790		2203	4300	6503	SO:0001583	missense	1525	exon6			CACGATATCAGGT	Y07593	CCDS33519.1, CCDS56204.1, CCDS56205.1, CCDS56206.1, CCDS56207.1	21q21.1	2013-01-29			ENSG00000154639	ENSG00000154639		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2559	protein-coding gene	gene with protein product		602621				9036860, 9096397	Standard	NM_001338		Approved	CAR	uc002yki.3	P78310	OTTHUMG00000074508	ENST00000284878.7:c.829A>G	chr21.hg19:g.18933790A>G	ENSP00000284878:p.Ile277Val	240.0	0.0		179.0	11.0	NM_001207066	B2R8V8|B7WPI3|D3YHP0|O00694|Q8WWT6|Q8WWT7|Q8WWT8|Q9UKV4	Missense_Mutation	SNP	ENST00000284878.7	hg19	CCDS33519.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.983826	0.74474	.	.	ENSG00000154639	ENST00000284878;ENST00000400169;ENST00000306618	T;T;D	0.91237	-1.23;-1.26;-2.81	4.49	4.49	0.54785	.	0.045406	0.85682	D	0.000000	D	0.93966	0.8068	M	0.82517	2.595	0.53688	D	0.999978	D;D	0.65815	0.992;0.995	P;P	0.59761	0.729;0.863	D	0.93084	0.6494	10	0.30854	T	0.27	.	13.2808	0.60212	1.0:0.0:0.0:0.0	.	277;277	B7WPI3;P78310	.;CXAR_HUMAN	V	277;277;236	ENSP00000284878:I277V;ENSP00000383033:I277V;ENSP00000303395:I236V	ENSP00000284878:I277V	I	+	1	0	CXADR	17855661	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.030000	0.88816	1.799000	0.52666	0.482000	0.46254	ATC	.	.		0.363	CXADR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000158209.1		
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31692292	31692292	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:31692292T>G	ENST00000360542.3	-	1	315	c.62A>C	c.(61-63)cAt>cCt	p.H21P		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	21						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						GAGAGGAATATGGCGGGAGGT	0.532																																					p.H21P		Atlas-SNP	.											.	KRTAP26-1	58	.	0			c.A62C						.						53.0	56.0	55.0					21																	31692292		2203	4300	6503	SO:0001583	missense	388818	exon1			GGAATATGGCGGG	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"""Keratin associated proteins"""	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.62A>C	chr21.hg19:g.31692292T>G	ENSP00000353742:p.His21Pro	136.0	0.0		109.0	16.0	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	hg19	CCDS13588.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.877962	0.33162	.	.	ENSG00000197683	ENST00000360542	T	0.03272	3.99	4.95	2.34	0.29019	.	0.521049	0.18487	N	0.139742	T	0.04363	0.0120	L	0.47716	1.5	0.23260	N	0.998028	B	0.24721	0.11	B	0.27262	0.078	T	0.33854	-0.9852	10	0.36615	T	0.2	-11.6437	8.6875	0.34247	0.0:0.0:0.3806:0.6193	.	21	Q6PEX3	KR261_HUMAN	P	21	ENSP00000353742:H21P	ENSP00000353742:H21P	H	-	2	0	KRTAP26-1	30614163	0.892000	0.30473	0.262000	0.24481	0.260000	0.26232	1.198000	0.32223	0.949000	0.37715	-0.316000	0.08728	CAT	.	.		0.532	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405	
KRTAP27-1	643812	hgsc.bcm.edu	37	21	31709981	31709981	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:31709981A>G	ENST00000382835.2	-	1	31	c.6T>C	c.(4-6)ccT>ccC	p.P2P		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	2						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						AGTGGCTATGAGGCATATTGC	0.418																																					p.P2P		Atlas-SNP	.											.	KRTAP27-1	53	.	0			c.T6C						.						66.0	66.0	66.0					21																	31709981		2203	4299	6502	SO:0001819	synonymous_variant	643812	exon1			GCTATGAGGCATA	AB096937	CCDS33532.1	21q22.11	2007-11-23			ENSG00000206107	ENSG00000206107		"""Keratin associated proteins"""	33864	protein-coding gene	gene with protein product							Standard	NM_001077711		Approved		uc002ynx.1	Q3LI81	OTTHUMG00000059577	ENST00000382835.2:c.6T>C	chr21.hg19:g.31709981A>G		214.0	0.0		132.0	7.0	NM_001077711		Silent	SNP	ENST00000382835.2	hg19	CCDS33532.1																																																																																			.	.		0.418	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711	
C21orf62	56245	hgsc.bcm.edu	37	21	34166650	34166650	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:34166650T>C	ENST00000536776.1	-	2	223	c.83A>G	c.(82-84)aAg>aGg	p.K28R	C21orf62_ENST00000490358.1_Missense_Mutation_p.K28R|C21orf49_ENST00000382378.1_Intron|C21orf49_ENST00000453404.1_Intron|C21orf62_ENST00000487113.1_Missense_Mutation_p.K28R|C21orf49_ENST00000477513.1_Intron|C21orf49_ENST00000382375.4_Intron|C21orf49_ENST00000382377.3_Intron|C21orf62_ENST00000479548.1_Missense_Mutation_p.K28R	NM_001162495.2|NM_001162496.2|NM_019596.5	NP_001155967.2|NP_001155968.2|NP_062542.5	Q9NYP8	CU062_HUMAN	chromosome 21 open reading frame 62	28										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	6		Myeloproliferative disorder(46;0.0255)				CGTGCTGTTCTTCTGACCTTT	0.527																																					p.K28R		Atlas-SNP	.											.	C21orf62	26	.	0			c.A83G						.						88.0	88.0	88.0					21																	34166650		2026	4188	6214	SO:0001583	missense	56245	exon4			CTGTTCTTCTGAC	AF231922	CCDS42919.1, CCDS42919.2	21q22.1	2011-02-24			ENSG00000205929	ENSG00000205929			1305	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 120"""	C21orf120			Standard	NM_001162495		Approved	B37, PRED81	uc011adu.2	Q9NYP8	OTTHUMG00000163477	ENST00000536776.1:c.83A>G	chr21.hg19:g.34166650T>C	ENSP00000444950:p.Lys28Arg	140.0	0.0		98.0	5.0	NM_001162495	A8K4L8	Missense_Mutation	SNP	ENST00000536776.1	hg19	CCDS42919.2	.	.	.	.	.	.	.	.	.	.	T	9.826	1.187170	0.21870	.	.	ENSG00000205929	ENST00000536776;ENST00000490358;ENST00000487113;ENST00000382373;ENST00000479548	.	.	.	4.95	-9.9	0.00461	.	1.368940	0.05385	N	0.537977	T	0.34483	0.0899	L	0.50333	1.59	0.09310	N	0.999992	B	0.11235	0.004	B	0.08055	0.003	T	0.15065	-1.0450	9	0.35671	T	0.21	.	7.6993	0.28613	0.2964:0.466:0.0:0.2375	.	28	Q9NYP8	CU062_HUMAN	R	28;28;28;75;28	.	ENSP00000371810:K75R	K	-	2	0	C21orf62	33088520	0.130000	0.22417	0.329000	0.25429	0.605000	0.37080	-0.701000	0.05075	-2.319000	0.00643	0.379000	0.24179	AAG	.	.		0.527	C21orf62-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139598.5	NM_019596	
DONSON	29980	hgsc.bcm.edu	37	21	34957031	34957031	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:34957031C>A	ENST00000303071.5	-	4	716	c.650G>T	c.(649-651)aGc>aTc	p.S217I	DONSON_ENST00000453626.1_Missense_Mutation_p.S217I|DONSON_ENST00000303113.6_Splice_Site_p.S203I|DONSON_ENST00000432378.1_Missense_Mutation_p.S217I|AP000304.12_ENST00000429238.1_Missense_Mutation_p.E178D	NM_017613.3	NP_060083.1	Q9NYP3	DONS_HUMAN	downstream neighbor of SON	217					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|ovary(1)	11						ATAGATAAGGCTCTGCTGGAA	0.453																																					p.S217I		Atlas-SNP	.											.	DONSON	34	.	0			c.G650T						.						78.0	67.0	71.0					21																	34957031		2203	4300	6503	SO:0001583	missense	29980	exon4			ATAAGGCTCTGCT	AF000002	CCDS13632.1	21q22.1	2008-07-31			ENSG00000159147	ENSG00000159147			2993	protein-coding gene	gene with protein product		611428		C21orf60		10773462, 10950926	Standard	NM_017613		Approved	B17, C2TA, DKFZP434M035	uc002ysk.4	Q9NYP3	OTTHUMG00000065904	ENST00000303071.5:c.650G>T	chr21.hg19:g.34957031C>A	ENSP00000307143:p.Ser217Ile	134.0	0.0		100.0	4.0	NM_017613	Q8NC53|Q9NSR9|Q9NVZ5|Q9NYP1|Q9NYP2	Missense_Mutation	SNP	ENST00000303071.5	hg19	CCDS13632.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	25.7|25.7|25.7	4.665866|4.665866|4.665866	0.88251|0.88251|0.88251	.|.|.	.|.|.	ENSG00000159147|ENSG00000159147;ENSG00000249209|ENSG00000159147	ENST00000437395|ENST00000440810;ENST00000429238|ENST00000303113;ENST00000453626;ENST00000303071;ENST00000432378	.|.|.	.|.|.	.|.|.	5.99|5.99|5.99	4.14|4.14|4.14	0.48551|0.48551|0.48551	.|.|.	.|.|0.117155	.|.|0.85682	.|.|D	.|.|0.000000	T|T|T	0.61553|0.61553|0.61553	0.2356|0.2356|0.2356	M|M|M	0.64404|0.64404|0.64404	1.975|1.975|1.975	0.49687|0.49687|0.49687	D|D|D	0.999811|0.999811|0.999811	.|.|B;B;B	.|.|0.31209	.|.|0.313;0.168;0.313	.|.|B;B;B	.|.|0.36030	.|.|0.216;0.153;0.216	T|T|T	0.65569|0.65569|0.65569	-0.6136|-0.6136|-0.6136	5|5|9	.|.|0.72032	.|.|D	.|.|0.01	-36.6994|-36.6994|-36.6994	11.6527|11.6527|11.6527	0.51299|0.51299|0.51299	0.0:0.804:0.1274:0.0685|0.0:0.804:0.1274:0.0685|0.0:0.804:0.1274:0.0685	.|.|.	.|.|203;217;217	.|.|F8W8A5;C9J4K5;Q9NYP3	.|.|.;.;DONS_HUMAN	S|D|I	188|75;178|203;217;217;217	.|.|.	.|.|ENSP00000307143:S217I	A|E|S	-|-|-	1|3|2	0|2|0	DONSON|DONSON;AP000304.12|DONSON	33878901|33878901|33878901	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.999000|0.999000|0.999000	0.59377|0.59377|0.59377	0.974000|0.974000|0.974000	0.67602|0.67602|0.67602	2.976000|2.976000|2.976000	0.49289|0.49289|0.49289	1.499000|1.499000|1.499000	0.48617|0.48617|0.48617	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GCC|GAG|AGC	.	.		0.453	DONSON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141184.1	NM_017613	
HLCS	3141	hgsc.bcm.edu	37	21	38309237	38309237	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:38309237A>G	ENST00000399120.1	-	5	1738	c.508T>C	c.(508-510)Tcc>Ccc	p.S170P	HLCS_ENST00000336648.4_Missense_Mutation_p.S170P	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	170					biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	TGGGAGTCGGAGCCCACATAG	0.577																																					p.S170P		Atlas-SNP	.											.	HLCS	64	.	0			c.T508C						.						68.0	60.0	63.0					21																	38309237		2203	4300	6503	SO:0001583	missense	3141	exon5			AGTCGGAGCCCAC		CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"""holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)"", ""holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"""			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.508T>C	chr21.hg19:g.38309237A>G	ENSP00000382071:p.Ser170Pro	157.0	0.0		95.0	4.0	NM_000411	B2RAH1|D3DSG6|Q99451	Missense_Mutation	SNP	ENST00000399120.1	hg19	CCDS13647.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.429202	0.43122	.	.	ENSG00000159267	ENST00000399120;ENST00000336648	D;D	0.98345	-4.88;-4.88	5.91	-3.88	0.04205	.	0.648921	0.17681	N	0.165616	D	0.95046	0.8396	L	0.55481	1.735	0.20307	N	0.999915	B;B	0.11235	0.004;0.002	B;B	0.09377	0.004;0.003	D	0.87120	0.2190	10	0.26408	T	0.33	.	9.615	0.39685	0.3517:0.1252:0.5231:0.0	.	170;170	B2RAH1;P50747	.;BPL1_HUMAN	P	170	ENSP00000382071:S170P;ENSP00000338387:S170P	ENSP00000338387:S170P	S	-	1	0	HLCS	37231107	0.985000	0.35326	0.135000	0.22099	0.902000	0.53008	0.511000	0.22739	-0.582000	0.05929	-0.250000	0.11733	TCC	.	.		0.577	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2		
TTC3	7267	hgsc.bcm.edu	37	21	38573864	38573864	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:38573864T>C	ENST00000399017.2	+	46	8814	c.6067T>C	c.(6067-6069)Tct>Cct	p.S2023P	TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000355666.1_Missense_Mutation_p.S2023P|TTC3_ENST00000354749.2_Missense_Mutation_p.S2023P	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	2023					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GCCTTCCTGCTCTTCTAGGTA	0.498																																					p.S2023P	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.T6067C						.						58.0	56.0	57.0					21																	38573864		2203	4300	6503	SO:0001583	missense	7267	exon46			TCCTGCTCTTCTA	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.6067T>C	chr21.hg19:g.38573864T>C	ENSP00000381981:p.Ser2023Pro	86.0	0.0		74.0	4.0	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.46|12.46	1.944531|1.944531	0.34283|0.34283	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000428693|ENST00000355666;ENST00000399017;ENST00000354749	.|T;T;T	.|0.08984	.|3.03;3.03;3.03	3.95|3.95	1.52|1.52	0.23074|0.23074	.|.	.|.	.|.	.|.	.|.	T|T	0.07369|0.07369	0.0186|0.0186	L|L	0.46157|0.46157	1.445|1.445	0.09310|0.09310	N|N	1|1	.|B	.|0.29909	.|0.261	.|B	.|0.23018	.|0.043	T|T	0.31194|0.31194	-0.9952|-0.9952	5|9	.|0.87932	.|D	.|0	-0.0249|-0.0249	5.1189|5.1189	0.14851|0.14851	0.0:0.2776:0.0:0.7224|0.0:0.2776:0.0:0.7224	.|.	.|2023	.|P53804	.|TTC3_HUMAN	P|P	314|2023	.|ENSP00000347889:S2023P;ENSP00000381981:S2023P;ENSP00000346791:S2023P	.|ENSP00000346791:S2023P	L|S	+|+	2|1	0|0	TTC3|TTC3	37495734|37495734	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.199000|0.199000	0.17237|0.17237	0.205000|0.205000	0.20568|0.20568	-0.256000|-0.256000	0.11100|0.11100	CTC|TCT	.	.		0.498	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
ETS2	2114	hgsc.bcm.edu	37	21	40191431	40191431	+	Silent	SNP	T	T	C	rs457705	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:40191431T>C	ENST00000360214.3	+	9	1276	c.816T>C	c.(814-816)acT>acC	p.T272T	ETS2_ENST00000360938.3_Silent_p.T272T	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	272					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				TGCCAGGGACTCCCAAAGACC	0.547																																					p.T412T		Atlas-SNP	.											ETS2_ENST00000360214,NS,carcinoma,0,2	ETS2	87	.	0			c.T1236C						.						71.0	64.0	66.0					21																	40191431		2203	4300	6503	SO:0001819	synonymous_variant	2114	exon9			AGGGACTCCCAAA		CCDS13659.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157557	ENSG00000157557			3489	protein-coding gene	gene with protein product		164740	"""v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)"""			17986575	Standard	NM_001256295		Approved		uc002yxf.3	P15036	OTTHUMG00000090769	ENST00000360214.3:c.816T>C	chr21.hg19:g.40191431T>C		72.0	1.0		39.0	3.0	NM_001256295	A6NM68|D3DSH6|Q53Y89	Silent	SNP	ENST00000360214.3	hg19	CCDS13659.1																																																																																			.	T|0.298;G|0.702		0.547	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1		
TMPRSS3	64699	hgsc.bcm.edu	37	21	43808513	43808513	+	Splice_Site	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:43808513T>C	ENST00000291532.3	-	5	1400	c.445A>G	c.(445-447)Agc>Ggc	p.S149G	TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000433957.2_Splice_Site_p.S149G|TMPRSS3_ENST00000398405.1_Splice_Site_p.S147G|TMPRSS3_ENST00000380399.1_Splice_Site_p.S233G|TMPRSS3_ENST00000398397.3_Splice_Site_p.S149G	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	149	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						TTAACTTACCTTGGGAAACCC	0.473																																					p.S149G		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.A445G						.						116.0	108.0	111.0					21																	43808513		2203	4300	6503	SO:0001630	splice_region_variant	64699	exon5			CTTACCTTGGGAA	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.446+1A>G	chr21.hg19:g.43808513T>C		153.0	0.0		94.0	4.0	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	hg19	CCDS13686.1	.	.	.	.	.	.	.	.	.	.	T	17.15	3.316263	0.60524	.	.	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64	4.94	4.94	0.65067	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.050337	0.85682	D	0.000000	T	0.45558	0.1348	L	0.45581	1.43	0.80722	D	1	P;P;B	0.46142	0.724;0.873;0.153	B;B;B	0.44044	0.19;0.439;0.068	T	0.38735	-0.9647	9	.	.	.	.	14.601	0.68441	0.0:0.0:0.0:1.0	.	149;149;149	P57727-3;P57727-5;P57727	.;.;TMPS3_HUMAN	G	149;149;147;233;149	ENSP00000291532:S149G;ENSP00000411013:S149G;ENSP00000381442:S147G;ENSP00000369762:S233G;ENSP00000381434:S149G	.	S	-	1	0	TMPRSS3	42681582	1.000000	0.71417	1.000000	0.80357	0.783000	0.44284	6.190000	0.72057	1.849000	0.53698	0.402000	0.26972	AGC	.	.		0.473	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		Missense_Mutation
PDE9A	5152	hgsc.bcm.edu	37	21	44174131	44174131	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:44174131T>C	ENST00000291539.6	+	10	827	c.767T>C	c.(766-768)cTg>cCg	p.L256P	PDE9A_ENST00000398225.3_Missense_Mutation_p.L215P|PDE9A_ENST00000328862.6_Missense_Mutation_p.L230P|PDE9A_ENST00000398224.3_Missense_Mutation_p.L129P|PDE9A_ENST00000398232.3_Missense_Mutation_p.L189P|PDE9A_ENST00000539837.1_Missense_Mutation_p.L128P|PDE9A_ENST00000335440.6_Missense_Mutation_p.L154P|PDE9A_ENST00000398227.3_Missense_Mutation_p.L96P|PDE9A_ENST00000335512.4_Missense_Mutation_p.L196P|PDE9A_ENST00000380328.2_Missense_Mutation_p.L203P|PDE9A_ENST00000349112.3_Missense_Mutation_p.L128P|PDE9A_ENST00000398229.3_Missense_Mutation_p.L122P|PDE9A_ENST00000398234.3_Missense_Mutation_p.L155P|PDE9A_ENST00000398236.3_Missense_Mutation_p.L170P|PDE9A_ENST00000470987.1_3'UTR	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	256					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	ATCGAGGCCCTGCGGAAGCCG	0.597																																					p.L256P		Atlas-SNP	.											.	PDE9A	69	.	0			c.T767C						.						70.0	57.0	62.0					21																	44174131		2203	4300	6503	SO:0001583	missense	5152	exon10			AGGCCCTGCGGAA	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.767T>C	chr21.hg19:g.44174131T>C	ENSP00000291539:p.Leu256Pro	49.0	0.0		52.0	4.0	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Missense_Mutation	SNP	ENST00000291539.6	hg19	CCDS13690.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.170944	0.78452	.	.	ENSG00000160191	ENST00000335512;ENST00000539837;ENST00000291539;ENST00000380328;ENST00000398232;ENST00000398234;ENST00000398236;ENST00000328862;ENST00000335440;ENST00000398225;ENST00000398229;ENST00000398227;ENST00000349112;ENST00000398224	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.79554	-0.92;-1.13;-0.79;-1.28;-0.97;-0.89;-0.83;-0.93;-1.16;-0.79;-1.14;-1.14;-1.08;-0.85	4.54	4.54	0.55810	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.184656	0.38778	N	0.001564	D	0.89750	0.6805	M	0.85373	2.75	0.80722	D	1	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	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.85130	0.996;0.996;0.996;0.996;0.996;0.997;0.995;0.994;0.996;0.996;0.996;0.997;0.997;0.996;0.996;0.986	D	0.91202	0.4992	10	0.87932	D	0	.	12.5263	0.56087	0.0:0.0:0.0:1.0	.	128;189;170;155;230;215;148;196;39;96;122;128;154;203;129;256	F5GWD0;O76083-13;O76083-8;O76083-6;O76083-15;O76083-14;O76083-16;O76083-2;O76083-10;O76083-9;O76083-11;O76083-4;O76083-12;O76083-5;O76083-3;O76083	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;PDE9A_HUMAN	P	196;128;256;203;189;155;170;230;154;215;122;96;128;129	ENSP00000335242:L196P;ENSP00000441899:L128P;ENSP00000291539:L256P;ENSP00000369685:L203P;ENSP00000381287:L189P;ENSP00000381289:L155P;ENSP00000381291:L170P;ENSP00000328699:L230P;ENSP00000335365:L154P;ENSP00000381281:L215P;ENSP00000381285:L122P;ENSP00000381283:L96P;ENSP00000344730:L128P;ENSP00000381280:L129P	ENSP00000291539:L256P	L	+	2	0	PDE9A	43047200	1.000000	0.71417	0.467000	0.27180	0.944000	0.59088	7.205000	0.77881	1.705000	0.51264	0.454000	0.30748	CTG	.	.		0.597	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
PKNOX1	5316	hgsc.bcm.edu	37	21	44430256	44430256	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:44430256A>G	ENST00000291547.5	+	4	484	c.273A>G	c.(271-273)gtA>gtG	p.V91V	PKNOX1_ENST00000432907.2_Intron	NM_004571.3	NP_004562.2	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1	91					angiogenesis (GO:0001525)|camera-type eye development (GO:0043010)|erythrocyte differentiation (GO:0030218)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|prostate(1)	22						GTTTTGATGTAGACATCGAAA	0.338																																					p.V91V		Atlas-SNP	.											.	PKNOX1	40	.	0			c.A273G						.						68.0	67.0	67.0					21																	44430256		2203	4300	6503	SO:0001819	synonymous_variant	5316	exon4			TGATGTAGACATC		CCDS13692.1, CCDS68211.1	21q22.3	2011-06-20			ENSG00000160199	ENSG00000160199		"""Homeoboxes / TALE class"""	9022	protein-coding gene	gene with protein product		602100				9479508	Standard	NM_001286258		Approved	PREP1	uc002zcq.1	P55347	OTTHUMG00000086833	ENST00000291547.5:c.273A>G	chr21.hg19:g.44430256A>G		66.0	0.0		53.0	4.0	NM_004571	O00528|Q8IWT7	Silent	SNP	ENST00000291547.5	hg19	CCDS13692.1																																																																																			.	.		0.338	PKNOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195520.3		
SIK1	150094	hgsc.bcm.edu	37	21	44838374	44838374	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:44838374T>C	ENST00000270162.6	-	12	1642	c.1510A>G	c.(1510-1512)Agc>Ggc	p.S504G		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	504					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)	CTGTCAGAGCTGGTTCCCTCT	0.642																																					p.S504G		Atlas-SNP	.											.	SIK1	65	.	0			c.A1510G						.						37.0	39.0	38.0					21																	44838374		2202	4300	6502	SO:0001583	missense	150094	exon12			CAGAGCTGGTTCC	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.1510A>G	chr21.hg19:g.44838374T>C	ENSP00000270162:p.Ser504Gly	85.0	0.0		69.0	5.0	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	hg19	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	T	11.99	1.803053	0.31869	.	.	ENSG00000142178	ENST00000270162	T	0.73681	-0.77	4.79	4.79	0.61399	.	0.110591	0.64402	D	0.000005	T	0.71634	0.3363	M	0.72118	2.19	0.43313	D	0.995329	B	0.21071	0.051	B	0.14023	0.01	T	0.67929	-0.5543	10	0.22706	T	0.39	.	14.3387	0.66608	0.0:0.0:0.0:1.0	.	504	P57059	SIK1_HUMAN	G	504	ENSP00000270162:S504G	ENSP00000270162:S504G	S	-	1	0	SIK1	43662802	1.000000	0.71417	1.000000	0.80357	0.254000	0.26022	5.626000	0.67777	1.790000	0.52503	0.533000	0.62120	AGC	.	.		0.642	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354	
C21orf2	755	hgsc.bcm.edu	37	21	45755646	45755646	+	Silent	SNP	C	C	A	rs146104157	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:45755646C>A	ENST00000339818.4	-	3	345	c.138G>T	c.(136-138)acG>acT	p.T46T	C21orf2_ENST00000397956.3_Silent_p.T46T|C21orf2_ENST00000496321.1_5'UTR|C21orf2_ENST00000325223.7_Silent_p.T46T|AP001062.7_ENST00000448927.1_RNA	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	46					cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				endometrium(2)	2				Colorectal(79;0.0806)		GGTACCTGAGCGTGATCACCT	0.607																																					p.T46T		Atlas-SNP	.											.	C21orf2	10	.	0			c.G138T						.						65.0	42.0	50.0					21																	45755646		2202	4294	6496	SO:0001819	synonymous_variant	755	exon3			CCTGAGCGTGATC	Y11392	CCDS13709.1, CCDS59444.1, CCDS59445.1	21q22.3	2014-03-24			ENSG00000160226	ENSG00000160226			1260	protein-coding gene	gene with protein product	"""nuclear encoded mitochondrial protein"", ""leucine rich repeat containing 76"""	603191				9465297	Standard	NM_004928		Approved	YF5, A2, LRRC76	uc002zeq.2	O43822	OTTHUMG00000086909	ENST00000339818.4:c.138G>T	chr21.hg19:g.45755646C>A		139.0	0.0		100.0	4.0	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Silent	SNP	ENST00000339818.4	hg19	CCDS13709.1																																																																																			.	C|0.997;T|0.003		0.607	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
TRPM2	7226	hgsc.bcm.edu	37	21	45833912	45833912	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:45833912T>C	ENST00000397928.1	+	20	3546	c.3101T>C	c.(3100-3102)cTc>cCc	p.L1034P	AP001065.2_ENST00000456880.1_RNA|TRPM2_ENST00000300482.5_Missense_Mutation_p.L1034P|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.L1034P|TRPM2_ENST00000300481.9_Missense_Mutation_p.L1014P|AP001065.2_ENST00000423310.1_RNA	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	1034					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						CTCTACCTGCTCTTCACCAAC	0.652																																					p.L1034P		Atlas-SNP	.											.	TRPM2	196	.	0			c.T3101C						.						230.0	229.0	230.0					21																	45833912		2203	4300	6503	SO:0001583	missense	7226	exon20			ACCTGCTCTTCAC	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.3101T>C	chr21.hg19:g.45833912T>C	ENSP00000381023:p.Leu1034Pro	75.0	0.0		52.0	4.0	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	hg19	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.503139	0.85176	.	.	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	D;D;D;D	0.98732	-5.1;-5.1;-5.1;-5.1	4.65	4.65	0.58169	Ion transport (1);	0.000000	0.64402	D	0.000002	D	0.99275	0.9747	M	0.93016	3.37	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	0.98974	1.0802	10	0.87932	D	0	-36.9905	14.3827	0.66921	0.0:0.0:0.0:1.0	.	1034;820;1034	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	P	1034;1034;1014;1034	ENSP00000300482:L1034P;ENSP00000381023:L1034P;ENSP00000300481:L1014P;ENSP00000381026:L1034P	ENSP00000300481:L1014P	L	+	2	0	TRPM2	44658340	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.652000	0.83633	1.868000	0.54150	0.482000	0.46254	CTC	.	.		0.652	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
PCNT	5116	hgsc.bcm.edu	37	21	47786943	47786943	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr21:47786943A>G	ENST00000359568.5	+	15	3161	c.3054A>G	c.(3052-3054)aaA>aaG	p.K1018K	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1018					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					AGTTGGAGAAACTGAAGCGGA	0.547																																					p.K1018K		Atlas-SNP	.											.	PCNT	283	.	0			c.A3054G						.						91.0	100.0	97.0					21																	47786943		2203	4300	6503	SO:0001819	synonymous_variant	5116	exon15			GGAGAAACTGAAG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.3054A>G	chr21.hg19:g.47786943A>G		94.0	0.0		77.0	4.0	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	hg19	CCDS33592.1																																																																																			.	.		0.547	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
CDC45	8318	hgsc.bcm.edu	37	22	19502321	19502321	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:19502321C>T	ENST00000407835.1	+	15	1523	c.1267C>T	c.(1267-1269)Ctg>Ttg	p.L423L	CDC45_ENST00000404724.3_Silent_p.L377L|CDC45_ENST00000437685.2_Silent_p.L455L|CDC45_ENST00000263201.1_Silent_p.L423L			O75419	CDC45_HUMAN	cell division cycle 45	423					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	19						CAAGAAGCAGCTGCGAGCCAC	0.572																																					p.L455L		Atlas-SNP	.											.	CDC45	48	.	0			c.C1363T						.						109.0	93.0	99.0					22																	19502321		2203	4300	6503	SO:0001819	synonymous_variant	8318	exon15			AAGCAGCTGCGAG	AF053074	CCDS13762.1, CCDS54499.1, CCDS54500.1	22q11.21	2013-01-17	2013-01-17	2010-03-24	ENSG00000093009	ENSG00000093009			1739	protein-coding gene	gene with protein product	"""human CDC45"""	603465	"""CDC45 (cell division cycle 45, S.cerevisiae, homolog)-like"", ""CDC45 cell division cycle 45-like (S. cerevisiae)"", ""cell division cycle 45 homolog (S. cerevisiae)"""	CDC45L2, CDC45L		9660782, 9724329, 17608804	Standard	NM_001178010		Approved		uc011aha.2	O75419	OTTHUMG00000150386	ENST00000407835.1:c.1267C>T	chr22.hg19:g.19502321C>T		74.0	0.0		59.0	4.0	NM_001178010	B4DDB4|B4DDU3|E9PDH7|O60856|Q20WK8|Q6UW54|Q9UP68	Silent	SNP	ENST00000407835.1	hg19	CCDS13762.1																																																																																			.	.		0.572	CDC45-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317903.1	NM_003504	
ZNF74	7625	hgsc.bcm.edu	37	22	20755034	20755034	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:20755034A>G	ENST00000400451.2	+	3	747	c.233A>G	c.(232-234)aAc>aGc	p.N78S	ZNF74_ENST00000405993.1_Missense_Mutation_p.N78S|ZNF74_ENST00000357502.5_Silent_p.E83E|ZNF74_ENST00000403682.3_Silent_p.E49E|ZNF74_ENST00000356671.5_Missense_Mutation_p.N78S	NM_003426.3	NP_003417.2	Q16587	ZNF74_HUMAN	zinc finger protein 74	78	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			AACTACCAGAACCTTCTTGCC	0.552																																					p.N78S		Atlas-SNP	.											.	ZNF74	54	.	0			c.A233G						.						100.0	116.0	111.0					22																	20755034		2197	4295	6492	SO:0001583	missense	7625	exon3			ACCAGAACCTTCT	X71623	CCDS42982.1, CCDS58794.1	22q11.2	2013-01-08	2006-05-12		ENSG00000185252	ENSG00000185252		"""Zinc fingers, C2H2-type"", ""-"""	13144	protein-coding gene	gene with protein product		194548	"""zinc finger protein 74 (Cos52)"""			1639391, 10591208	Standard	NM_003426		Approved	Cos52, Zfp520, ZNF520	uc010gsm.4	Q16587	OTTHUMG00000150687	ENST00000400451.2:c.233A>G	chr22.hg19:g.20755034A>G	ENSP00000383301:p.Asn78Ser	157.0	0.0		123.0	5.0	NM_003426	B5MCE3|B7Z5Y2|Q6IBV2|Q6PJP1|Q9UC04|Q9UF05|Q9UF06|Q9UF07	Missense_Mutation	SNP	ENST00000400451.2	hg19	CCDS42982.1	.	.	.	.	.	.	.	.	.	.	A	15.83	2.949996	0.53186	.	.	ENSG00000185252	ENST00000400451;ENST00000356671;ENST00000405993	T;T;T	0.02525	4.26;4.26;4.26	3.37	3.37	0.38596	Krueppel-associated box (4);	0.000000	0.38436	N	0.001686	T	0.08492	0.0211	M	0.81802	2.56	0.22280	N	0.999237	D	0.59767	0.986	P	0.56612	0.802	T	0.14615	-1.0466	10	0.28530	T	0.3	.	5.3694	0.16131	0.8724:0.0:0.1276:0.0	.	78	Q16587	ZNF74_HUMAN	S	78	ENSP00000383301:N78S;ENSP00000349098:N78S;ENSP00000385855:N78S	ENSP00000349098:N78S	N	+	2	0	ZNF74	19085034	0.997000	0.39634	1.000000	0.80357	0.992000	0.81027	3.557000	0.53741	1.768000	0.52137	0.533000	0.62120	AAC	.	.		0.552	ZNF74-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319648.2	NM_003426	
CCDC116	164592	hgsc.bcm.edu	37	22	21990761	21990761	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:21990761T>C	ENST00000292779.3	+	5	1405	c.1244T>C	c.(1243-1245)cTg>cCg	p.L415P		NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	415										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					AAGAAGCCGCTGCCCTCCATC	0.607																																					p.L415P		Atlas-SNP	.											.	CCDC116	56	.	0			c.T1244C						.						51.0	48.0	49.0					22																	21990761		2203	4300	6503	SO:0001583	missense	164592	exon5			AGCCGCTGCCCTC	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.1244T>C	chr22.hg19:g.21990761T>C	ENSP00000292779:p.Leu415Pro	94.0	0.0		68.0	4.0	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	hg19	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.628058	0.46944	.	.	ENSG00000161180	ENST00000292779	T	0.19394	2.15	4.47	-0.138	0.13464	.	1.652160	0.03980	N	0.293173	T	0.17323	0.0416	L	0.38175	1.15	0.09310	N	0.999995	P	0.39157	0.662	B	0.38655	0.278	T	0.22138	-1.0225	10	0.87932	D	0	.	3.027	0.06094	0.1883:0.3181:0.0:0.4936	.	415	Q8IYX3-2	.	P	415	ENSP00000292779:L415P	ENSP00000292779:L415P	L	+	2	0	CCDC116	20320761	0.000000	0.05858	0.091000	0.20842	0.086000	0.17979	0.154000	0.16343	0.020000	0.15106	-0.361000	0.07541	CTG	.	.		0.607	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
SEZ6L	23544	hgsc.bcm.edu	37	22	26771552	26771552	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:26771552G>T	ENST00000248933.6	+	15	2934	c.2839G>T	c.(2839-2841)Gca>Tca	p.A947S	SEZ6L_ENST00000404234.3_Missense_Mutation_p.A946S|SEZ6L_ENST00000494013.1_3'UTR|SEZ6L_ENST00000343706.4_Missense_Mutation_p.A871S|SEZ6L_ENST00000411842.2_Intron|SEZ6L_ENST00000360929.3_Missense_Mutation_p.A872S|SEZ6L_ENST00000403121.1_Missense_Mutation_p.A643S|SEZ6L_ENST00000402979.1_Missense_Mutation_p.A719S|SEZ6L_ENST00000529632.2_Missense_Mutation_p.A936S			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	947					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)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						AGCAGAAGCGGCAGCAGAGAC	0.567																																					p.A947S		Atlas-SNP	.											.	SEZ6L	174	.	0			c.G2839T						.						87.0	72.0	77.0					22																	26771552		2203	4300	6503	SO:0001583	missense	23544	exon15			GAAGCGGCAGCAG	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.2839G>T	chr22.hg19:g.26771552G>T	ENSP00000248933:p.Ala947Ser	114.0	0.0		64.0	26.0	NM_021115	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	hg19	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.248544	0.39797	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.29655	1.9;2.0;2.12;1.87;1.69;1.56;1.88	5.33	5.33	0.75918	.	0.000000	0.56097	D	0.000031	T	0.43809	0.1264	L	0.34521	1.04	0.80722	D	1	D;D;B;D;P;D;D	0.89917	1.0;0.989;0.0;0.995;0.628;0.989;0.989	D;P;B;P;B;P;P	0.80764	0.994;0.804;0.0;0.814;0.415;0.804;0.804	T	0.11108	-1.0601	10	0.16420	T	0.52	.	18.0393	0.89314	0.0:0.0:1.0:0.0	.	934;936;643;871;872;946;947	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	S	946;936;872;947;871;643;719	ENSP00000384772:A946S;ENSP00000437037:A936S;ENSP00000354185:A872S;ENSP00000248933:A947S;ENSP00000342661:A871S;ENSP00000384838:A643S;ENSP00000384733:A719S	ENSP00000248933:A947S	A	+	1	0	SEZ6L	25101552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.214000	0.65236	2.502000	0.84385	0.555000	0.69702	GCA	.	.		0.567	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
THOC5	8563	hgsc.bcm.edu	37	22	29917065	29917065	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:29917065A>G	ENST00000490103.1	-	13	1321	c.1199T>C	c.(1198-1200)gTc>gCc	p.V400A	THOC5_ENST00000397872.1_Missense_Mutation_p.V400A|THOC5_ENST00000397873.2_Missense_Mutation_p.V400A|CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397871.1_Missense_Mutation_p.V400A	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	400					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						GCAACTCAGGACTGAGTCAGG	0.453																																					p.V400A		Atlas-SNP	.											.	THOC5	58	.	0			c.T1199C						.						133.0	136.0	135.0					22																	29917065		2203	4300	6503	SO:0001583	missense	8563	exon14			CTCAGGACTGAGT	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.1199T>C	chr22.hg19:g.29917065A>G	ENSP00000420306:p.Val400Ala	92.0	0.0		93.0	4.0	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	hg19	CCDS13859.1	.	.	.	.	.	.	.	.	.	.	A	19.77	3.889409	0.72524	.	.	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	5.82	5.82	0.92795	.	0.175441	0.49916	D	0.000130	T	0.24275	0.0588	L	0.34521	1.04	0.46478	D	0.999061	B	0.23185	0.081	B	0.25506	0.061	T	0.02852	-1.1102	10	0.66056	D	0.02	-20.9404	15.8454	0.78883	1.0:0.0:0.0:0.0	.	400	Q13769	THOC5_HUMAN	A	400	ENSP00000420306:V400A;ENSP00000380970:V400A;ENSP00000380969:V400A;ENSP00000380971:V400A	ENSP00000380969:V400A	V	-	2	0	THOC5	28247065	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.530000	0.90606	2.222000	0.72286	0.533000	0.62120	GTC	.	.		0.453	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678	
UQCR10	29796	hgsc.bcm.edu	37	22	30165668	30165668	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:30165668A>G	ENST00000330029.6	+	2	182	c.152A>G	c.(151-153)aAg>aGg	p.K51R	ZMAT5_ENST00000397781.3_5'Flank|UQCR10_ENST00000401406.3_3'UTR|ZMAT5_ENST00000344318.3_5'Flank	NM_001003684.1|NM_013387.3	NP_001003684.1|NP_037519.2	Q9UDW1	QCR9_HUMAN	ubiquinol-cytochrome c reductase, complex III subunit X	51					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)	ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	5						AAAATGCAGAAGCTGTGGAAA	0.493																																					p.K51R		Atlas-SNP	.											.	UQCR10	10	.	0			c.A152G						.						65.0	70.0	68.0					22																	30165668		1897	4118	6015	SO:0001630	splice_region_variant	29796	exon2			TGCAGAAGCTGTG	AB028598	CCDS46680.1, CCDS46681.1	22q12.2	2011-07-04			ENSG00000184076	ENSG00000184076		"""Mitochondrial respiratory chain complex / Complex III"""	30863	protein-coding gene	gene with protein product	"""ubiquinol-cytochrome c reductase, complex III subunit X, 7.2kDa"", ""complex III subunit 9"""	610843				11042152	Standard	NM_013387		Approved	HSPC051, UCRC, QCR9, UCCR7.2	uc003agq.1	Q9UDW1	OTTHUMG00000151283	ENST00000330029.6:c.151-1A>G	chr22.hg19:g.30165668A>G		154.0	0.0		134.0	6.0	NM_013387	B5MCM5|Q9T2V6	Missense_Mutation	SNP	ENST00000330029.6	hg19	CCDS46680.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.91|13.91	2.378985|2.378985	0.42207|0.42207	.|.	.|.	ENSG00000184076|ENSG00000184076	ENST00000330029;ENST00000406782|ENST00000332801	T|.	0.57107|.	0.42|.	4.72|4.72	4.72|4.72	0.59763|0.59763	.|.	.|0.289711	.|0.25006	.|N	.|0.033872	T|T	0.67021|0.67021	0.2849|0.2849	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	P|.	0.39157|.	0.662|.	P|.	0.48654|.	0.585|.	T|T	0.70565|0.70565	-0.4837|-0.4837	8|6	0.33141|0.87932	T|D	0.24|0	-0.9291|-0.9291	10.795|10.795	0.46455|0.46455	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	51|.	Q9UDW1|.	QCR9_HUMAN|.	R|G	51;70|51	ENSP00000332887:K51R|.	ENSP00000332887:K51R|ENSP00000333278:S51G	K|S	+|+	2|1	0|0	UQCR10|UQCR10	28495668|28495668	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	6.697000|6.697000	0.74603|0.74603	2.110000|2.110000	0.64415|0.64415	0.529000|0.529000	0.55759|0.55759	AAG|AGC	.	.		0.493	UQCR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322081.1	NM_013387	Missense_Mutation
PES1	23481	hgsc.bcm.edu	37	22	30975865	30975865	+	Silent	SNP	G	G	T	rs200700442|rs140808409	byFrequency	TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:30975865G>T	ENST00000405677.1	-	14	1753	c.810C>A	c.(808-810)ccC>ccA	p.P270P	PES1_ENST00000402281.1_Silent_p.P270P|PES1_ENST00000335214.6_Silent_p.P404P|PES1_ENST00000354694.7_Silent_p.P409P|PES1_ENST00000402284.3_Silent_p.P392P	NM_001282328.1	NP_001269257.1			pescadillo ribosomal biogenesis factor 1											breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	29						ACTCTGCCACGGGGAGAAGGA	0.582																																					p.P409P		Atlas-SNP	.											.	PES1	55	.	0			c.C1227A						.						88.0	93.0	92.0					22																	30975865		2203	4300	6503	SO:0001819	synonymous_variant	23481	exon12			TGCCACGGGGAGA	U78310	CCDS13880.1, CCDS58802.1, CCDS74842.1	22q12.1	2012-02-23	2012-02-23		ENSG00000100029	ENSG00000100029			8848	protein-coding gene	gene with protein product		605819	"""pescadillo (zebrafish) homolog 1, containing BRCT domain"", ""pescadillo homolog 1, containing BRCT domain (zebrafish)"""			8985183, 10591208, 17353269	Standard	NM_014303		Approved	PES	uc003aij.2	O00541	OTTHUMG00000151077	ENST00000405677.1:c.810C>A	chr22.hg19:g.30975865G>T		79.0	0.0		81.0	6.0	NM_014303		Silent	SNP	ENST00000405677.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.288	1.049937	0.19827	.	.	ENSG00000100029	ENST00000441668	.	.	.	4.89	-9.78	0.00496	.	.	.	.	.	T	0.46580	0.1400	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55872	-0.8072	4	.	.	.	-10.6129	8.5608	0.33509	0.6373:0.2022:0.0906:0.0699	.	.	.	.	S	16	.	.	R	-	1	0	PES1	29305865	0.000000	0.05858	0.638000	0.29380	0.978000	0.69477	-3.878000	0.00344	-2.072000	0.00879	-0.878000	0.02970	CGT	.	G|0.980;A|0.020		0.582	PES1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000321189.2	NM_014303	
SMTN	6525	hgsc.bcm.edu	37	22	31487265	31487265	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:31487265G>T	ENST00000347557.2	+	10	1474	c.1256G>T	c.(1255-1257)cGg>cTg	p.R419L	SMTN_ENST00000358743.1_Missense_Mutation_p.R419L|SMTN_ENST00000333137.7_Missense_Mutation_p.R419L|SMTN_ENST00000404574.1_5'Flank	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	419					muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)	p.R419Q(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						CCCAGGGGGCGGGGCTTGGCT	0.697																																					p.R475L		Atlas-SNP	.											SMTN_ENST00000404496,NS,carcinoma,+1,1	SMTN	219	.	1	Substitution - Missense(1)	pancreas(1)	c.G1424T						.						6.0	7.0	7.0					22																	31487265		2091	4144	6235	SO:0001583	missense	6525	exon9			GGGGGCGGGGCTT	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.1256G>T	chr22.hg19:g.31487265G>T	ENSP00000328635:p.Arg419Leu	37.0	0.0		37.0	2.0	NM_001207018	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Missense_Mutation	SNP	ENST00000347557.2	hg19	CCDS13886.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.223322	0.79464	.	.	ENSG00000183963	ENST00000358743;ENST00000347557;ENST00000333137;ENST00000329852;ENST00000404496	T;T;T	0.69435	0.02;-0.4;-0.39	5.22	4.21	0.49690	.	.	.	.	.	T	0.76442	0.3988	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D;D	0.76494	0.998;0.998;0.997;0.998;0.997;0.999	D;D;D;D;D;D	0.78314	0.991;0.936;0.987;0.936;0.987;0.968	T	0.78247	-0.2278	9	0.72032	D	0.01	-23.7183	11.995	0.53196	0.0818:0.0:0.9182:0.0	.	475;473;411;419;419;419	E7ETT8;B4E229;B5MC56;E7EWD0;P53814;P53814-5	.;.;.;.;SMTN_HUMAN;.	L	419;419;419;417;411	ENSP00000351593:R419L;ENSP00000328635:R419L;ENSP00000329532:R419L	ENSP00000329393:R417L	R	+	2	0	SMTN	29817265	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	4.107000	0.57811	1.354000	0.45846	0.491000	0.48974	CGG	.	.		0.697	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270	
PRR14L	253143	hgsc.bcm.edu	37	22	32109192	32109192	+	Missense_Mutation	SNP	T	T	C	rs532999755		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:32109192T>C	ENST00000327423.6	-	4	4822	c.4633A>G	c.(4633-4635)Aga>Gga	p.R1545G	PRR14L_ENST00000397493.2_Missense_Mutation_p.R1545G|PRR14L_ENST00000434485.1_Missense_Mutation_p.R1545G	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1545										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						GCAGAACTTCTGATTTTACCT	0.418																																					p.R1545G		Atlas-SNP	.											.	PRR14L	198	.	0			c.A4633G						.						69.0	61.0	64.0					22																	32109192		692	1591	2283	SO:0001583	missense	253143	exon4			AACTTCTGATTTT	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.4633A>G	chr22.hg19:g.32109192T>C	ENSP00000331845:p.Arg1545Gly	92.0	0.0		85.0	4.0	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	hg19	CCDS13900.2	.	.	.	.	.	.	.	.	.	.	T	11.60	1.685573	0.29962	.	.	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.09445	2.98;3.0;2.98	5.38	0.273	0.15650	.	0.534999	0.17011	N	0.190526	T	0.07818	0.0196	L	0.44542	1.39	0.09310	N	1	B;B;B	0.22003	0.063;0.01;0.063	B;B;B	0.19946	0.027;0.006;0.027	T	0.32719	-0.9896	9	.	.	.	-0.6826	5.0789	0.14646	0.0:0.1719:0.2524:0.5757	.	1545;1545;1545	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	G	1545	ENSP00000380630:R1545G;ENSP00000331845:R1545G;ENSP00000388314:R1545G	.	R	-	1	2	PRR14L	30439192	0.000000	0.05858	0.008000	0.14137	0.975000	0.68041	0.213000	0.17521	0.345000	0.23873	0.533000	0.62120	AGA	.	.		0.418	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	
RTCB	51493	hgsc.bcm.edu	37	22	32795593	32795593	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:32795593A>G	ENST00000216038.5	-	6	749	c.651T>C	c.(649-651)ccT>ccC	p.P217P	RTCB_ENST00000476619.1_5'UTR|RTCB_ENST00000451746.2_Intron	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		GAGTTACCTGAGGAAGGCCTC	0.418																																					p.P217P		Atlas-SNP	.											.	C22orf28	43	.	0			c.T651C						.						136.0	131.0	133.0					22																	32795593		2203	4300	6503	SO:0001819	synonymous_variant	51493	exon6			TACCTGAGGAAGG	BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"""focal adhesion-associated protein"""	613901	"""chromosome 22 open reading frame 28"""	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.651T>C	chr22.hg19:g.32795593A>G		129.0	0.0		124.0	5.0	NM_014306		Silent	SNP	ENST00000216038.5	hg19	CCDS13905.1																																																																																			.	.		0.418	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306	
HMGXB4	10042	hgsc.bcm.edu	37	22	35661108	35661108	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:35661108A>G	ENST00000216106.5	+	5	855	c.727A>G	c.(727-729)Agc>Ggc	p.S243G	HMGXB4_ENST00000444518.2_Missense_Mutation_p.S134G	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	243					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGAGTTACAGAGCTTTCTGAA	0.498																																					p.S243G		Atlas-SNP	.											.	HMGXB4	52	.	0			c.A727G						.						80.0	86.0	84.0					22																	35661108		2203	4300	6503	SO:0001583	missense	10042	exon5			TTACAGAGCTTTC	AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"""High mobility group / Non-canonical"""	5003	protein-coding gene	gene with protein product		604702	"""high-mobility group protein 2-like 1"""	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.727A>G	chr22.hg19:g.35661108A>G	ENSP00000216106:p.Ser243Gly	142.0	0.0		132.0	16.0	NM_001003681	O75672|O75673|Q9UMT5	Missense_Mutation	SNP	ENST00000216106.5	hg19	CCDS33641.1	.	.	.	.	.	.	.	.	.	.	A	10.08	1.252352	0.22880	.	.	ENSG00000100281	ENST00000420166;ENST00000444518;ENST00000455359;ENST00000216106	T;T;T;T	0.49720	0.77;2.12;0.78;2.12	5.81	3.7	0.42460	.	0.062472	0.64402	N	0.000002	T	0.33352	0.0860	L	0.27053	0.805	0.28140	N	0.929847	B	0.02656	0.0	B	0.04013	0.001	T	0.27839	-1.0062	10	0.87932	D	0	-5.6282	8.9631	0.35860	0.7914:0.0:0.2086:0.0	.	243	Q9UGU5	HMGX4_HUMAN	G	134;134;134;243	ENSP00000401658:S134G;ENSP00000398302:S134G;ENSP00000415500:S134G;ENSP00000216106:S243G	ENSP00000216106:S243G	S	+	1	0	HMGXB4	33991108	1.000000	0.71417	0.998000	0.56505	0.019000	0.09904	3.133000	0.50531	0.483000	0.27608	-0.256000	0.11100	AGC	.	.		0.498	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318104.2	NM_005487	
APOL3	80833	hgsc.bcm.edu	37	22	36537572	36537572	+	Silent	SNP	G	G	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:36537572G>T	ENST00000349314.2	-	3	922	c.885C>A	c.(883-885)atC>atA	p.I295I	APOL3_ENST00000361710.2_Silent_p.I95I|APOL3_ENST00000487423.1_5'Flank|APOL3_ENST00000397293.2_Silent_p.I224I|APOL3_ENST00000397287.2_Silent_p.I95I|APOL3_ENST00000424878.2_Silent_p.I95I	NM_145640.2	NP_663615.1	O95236	APOL3_HUMAN	apolipoprotein L, 3	295					inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|signal transducer activity (GO:0004871)			endometrium(2)|large_intestine(1)|lung(1)|stomach(1)	5						TGATGGCACGGATTTCACTCC	0.493																																					p.I295I		Atlas-SNP	.											.	APOL3	60	.	0			c.C885A						.						74.0	74.0	74.0					22																	36537572		2203	4300	6503	SO:0001819	synonymous_variant	80833	exon3			GGCACGGATTTCA	AF305227	CCDS13922.1, CCDS13924.1	22q13.1	2013-01-24			ENSG00000128284	ENSG00000128284		"""Apolipoproteins"""	14868	protein-coding gene	gene with protein product		607253				11374903	Standard	NM_145640		Approved	CG12-1, APOLIII	uc003aot.3	O95236	OTTHUMG00000150632	ENST00000349314.2:c.885C>A	chr22.hg19:g.36537572G>T		91.0	0.0		83.0	4.0	NM_145640	B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3	Silent	SNP	ENST00000349314.2	hg19	CCDS13922.1																																																																																			.	.		0.493	APOL3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319268.1	NM_145641	
CSF2RB	1439	hgsc.bcm.edu	37	22	37334252	37334252	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:37334252C>T	ENST00000403662.3	+	14	2624	c.2402C>T	c.(2401-2403)gCa>gTa	p.A801V	CSF2RB_ENST00000536485.1_Missense_Mutation_p.A748V|CSF2RB_ENST00000406230.1_Missense_Mutation_p.A807V|CSF2RB_ENST00000262825.5_Missense_Mutation_p.A807V			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	801					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	GAACGCCCGGCAGATGTGTCC	0.662																																					p.A801V		Atlas-SNP	.											.	CSF2RB	104	.	0			c.C2402T						.						65.0	69.0	67.0					22																	37334252		2203	4300	6503	SO:0001583	missense	1439	exon14			GCCCGGCAGATGT	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"""CD molecules"", ""Fibronectin type III domain containing"""	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.2402C>T	chr22.hg19:g.37334252C>T	ENSP00000384053:p.Ala801Val	54.0	0.0		51.0	4.0	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	hg19	CCDS13936.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.047510	0.36085	.	.	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000536485	D;D;D;D	0.91945	-2.43;-2.94;-2.94;-2.94	5.4	-7.21	0.01490	.	0.777720	0.10890	N	0.622791	D	0.82435	0.5036	L	0.57536	1.79	0.09310	N	1	B;B	0.28783	0.222;0.067	B;B	0.17433	0.018;0.005	T	0.69068	-0.5243	10	0.23891	T	0.37	-2.2166	0.2917	0.00259	0.3202:0.1836:0.1457:0.3505	.	807;801	P32927-2;P32927	.;IL3RB_HUMAN	V	801;801;807;807;748	ENSP00000384053:A801V;ENSP00000262825:A807V;ENSP00000385271:A807V;ENSP00000440003:A748V	ENSP00000262825:A807V	A	+	2	0	CSF2RB	35664198	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.728000	0.04925	-0.846000	0.04174	-0.300000	0.09419	GCA	.	.		0.662	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395	
CARD10	29775	hgsc.bcm.edu	37	22	37888763	37888763	+	Silent	SNP	C	C	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:37888763C>A	ENST00000403299.1	-	18	2739	c.2523G>T	c.(2521-2523)ctG>ctT	p.L841L	CARD10_ENST00000406271.3_Silent_p.L555L|CARD10_ENST00000251973.5_Silent_p.L841L			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	841					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					GGGCAGACACCAGTAGCGGCC	0.657																																					p.L841L		Atlas-SNP	.											.	CARD10	55	.	0			c.G2523T						.						31.0	31.0	31.0					22																	37888763		2203	4299	6502	SO:0001819	synonymous_variant	29775	exon17			AGACACCAGTAGC	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.2523G>T	chr22.hg19:g.37888763C>A		108.0	0.0		92.0	5.0	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	hg19	CCDS13948.1																																																																																			.	.		0.657	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
FAM83F	113828	hgsc.bcm.edu	37	22	40415308	40415308	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:40415308A>G	ENST00000333407.6	+	2	720	c.626A>G	c.(625-627)cAg>cGg	p.Q209R	FAM83F_ENST00000473717.1_Missense_Mutation_p.Q41R	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	209										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						GAGATGTGTCAGGACCTGCAG	0.542																																					p.Q209R		Atlas-SNP	.											.	FAM83F	29	.	0			c.A626G						.						153.0	117.0	129.0					22																	40415308		2203	4300	6503	SO:0001583	missense	113828	exon2			TGTGTCAGGACCT		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.626A>G	chr22.hg19:g.40415308A>G	ENSP00000330432:p.Gln209Arg	114.0	0.0		116.0	5.0	NM_138435	Q96FD6	Missense_Mutation	SNP	ENST00000333407.6	hg19	CCDS14000.2	.	.	.	.	.	.	.	.	.	.	A	8.026	0.760733	0.15914	.	.	ENSG00000133477	ENST00000333407	T	0.11712	2.75	4.94	0.291	0.15732	.	0.554792	0.18621	N	0.135853	T	0.06142	0.0159	N	0.16478	0.41	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.36407	-0.9749	10	0.31617	T	0.26	-7.835	9.5473	0.39288	0.6013:0.0:0.3987:0.0	.	209	Q8NEG4	FA83F_HUMAN	R	209	ENSP00000330432:Q209R	ENSP00000330432:Q209R	Q	+	2	0	FAM83F	38745254	0.439000	0.25610	0.977000	0.42913	0.703000	0.40648	0.212000	0.17497	0.068000	0.16574	-0.379000	0.06801	CAG	.	.		0.542	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435	
EP300	2033	hgsc.bcm.edu	37	22	41513713	41513713	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:41513713A>G	ENST00000263253.7	+	2	1836	c.617A>G	c.(616-618)cAg>cGg	p.Q206R		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	206					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CAGAATATGCAGTACCCAAAC	0.532			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																												p.Q206R		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.A617G						.						84.0	67.0	73.0					22																	41513713		2203	4300	6503	SO:0001583	missense	2033	exon2	Familial Cancer Database	Broad Thumb-Hallux syndrome	ATATGCAGTACCC	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.617A>G	chr22.hg19:g.41513713A>G	ENSP00000263253:p.Gln206Arg	115.0	0.0		73.0	5.0	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	hg19	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	16.45	3.125639	0.56721	.	.	ENSG00000100393	ENST00000263253	D	0.84146	-1.81	6.11	5.05	0.67936	.	0.153176	0.29587	N	0.011734	D	0.85287	0.5662	L	0.43152	1.355	0.31138	N	0.706986	D	0.53745	0.962	P	0.55055	0.767	T	0.82778	-0.0289	10	0.25106	T	0.35	-6.0963	12.3775	0.55289	0.778:0.222:0.0:0.0	.	206	Q09472	EP300_HUMAN	R	206	ENSP00000263253:Q206R	ENSP00000263253:Q206R	Q	+	2	0	EP300	39843659	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.694000	0.47035	2.343000	0.79666	0.496000	0.49642	CAG	.	.		0.532	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
ACO2	50	hgsc.bcm.edu	37	22	41913597	41913597	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:41913597A>G	ENST00000216254.4	+	7	924	c.902A>G	c.(901-903)cAc>cGc	p.H301R	ACO2_ENST00000466237.1_3'UTR|ACO2_ENST00000396512.3_Missense_Mutation_p.H326R	NM_001098.2	NP_001089.1	Q99798	ACON_HUMAN	aconitase 2, mitochondrial	301					cell death (GO:0008219)|cellular metabolic process (GO:0044237)|citrate metabolic process (GO:0006101)|generation of precursor metabolites and energy (GO:0006091)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron ion binding (GO:0005506)			breast(3)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	23						CCTTACAACCACAGGATGAAG	0.607											OREG0026588	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H301R		Atlas-SNP	.											.	ACO2	58	.	0			c.A902G						.						84.0	63.0	70.0					22																	41913597		2203	4300	6503	SO:0001583	missense	50	exon7			ACAACCACAGGAT	AH006514	CCDS14017.1	22q13.2	2013-05-21			ENSG00000100412	ENSG00000100412	4.2.1.3		118	protein-coding gene	gene with protein product	"""aconitate hydratase, mitochondrial"""	100850				10591208	Standard	NM_001098		Approved	ACONM	uc003bac.3	Q99798	OTTHUMG00000030544	ENST00000216254.4:c.902A>G	chr22.hg19:g.41913597A>G	ENSP00000216254:p.His301Arg	77.0	0.0	904	78.0	4.0	NM_001098	O75809|Q5JZ41|Q6FHX0|Q8TAQ6	Missense_Mutation	SNP	ENST00000216254.4	hg19	CCDS14017.1	.	.	.	.	.	.	.	.	.	.	A	14.04	2.416156	0.42918	.	.	ENSG00000100412	ENST00000541439;ENST00000544234;ENST00000216254;ENST00000396512	T;T	0.75704	-0.96;-0.96	5.86	5.86	0.93980	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 2 (1);	0.133241	0.64402	D	0.000002	T	0.66733	0.2819	L	0.39514	1.22	0.44129	D	0.996916	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.63056	-0.6722	10	0.49607	T	0.09	.	13.0777	0.59097	0.7998:0.2002:0.0:0.0	.	326;301	A2A274;Q99798	.;ACON_HUMAN	R	22;282;301;326	ENSP00000216254:H301R;ENSP00000379769:H326R	ENSP00000216254:H301R	H	+	2	0	ACO2	40243543	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	3.832000	0.55783	2.241000	0.73720	0.482000	0.46254	CAC	.	.		0.607	ACO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259151.1	NM_001098	
SHANK3	85358	hgsc.bcm.edu	37	22	51160246	51160246	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr22:51160246T>C	ENST00000414786.2	+	21	4170	c.3943T>C	c.(3943-3945)Tcg>Ccg	p.S1315P	SHANK3_ENST00000445220.2_Missense_Mutation_p.S1331P|SHANK3_ENST00000262795.3_Missense_Mutation_p.S1345P			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1329	Pro-rich.				adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CCCGGGCCCCTCGCCCACCAC	0.706																																					p.S1315P		Atlas-SNP	.											.	SHANK3	96	.	0			c.T3943C						.						6.0	8.0	7.0					22																	51160246		1881	4040	5921	SO:0001583	missense	85358	exon21			GGCCCCTCGCCCA	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.3943T>C	chr22.hg19:g.51160246T>C	ENSP00000464552:p.Ser1315Pro	53.0	0.0		23.0	4.0	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	T	8.260	0.810974	0.16537	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.20738	2.05;2.05	4.93	1.46	0.22682	.	1.561710	0.03411	N	0.204853	T	0.17066	0.0410	N	0.25890	0.77	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.26985	-1.0087	10	0.34782	T	0.22	.	8.2873	0.31937	0.0:0.2586:0.0:0.7414	.	1329;1330;1345	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	P	1345;1331	ENSP00000442518:S1345P;ENSP00000446078:S1331P	ENSP00000442518:S1345P	S	+	1	0	SHANK3	49507112	0.002000	0.14202	0.394000	0.26270	0.484000	0.33280	0.402000	0.20965	0.212000	0.20703	0.379000	0.24179	TCG	.	.		0.706	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
AKAP17A	8227	hgsc.bcm.edu	37	X	1712975	1712975	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:1712975T>C	ENST00000313871.3	+	2	816	c.620T>C	c.(619-621)tTc>tCc	p.F207S	AKAP17A_ENST00000381261.3_Missense_Mutation_p.F207S	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	207	RRM.				B cell activation (GO:0042113)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)			breast(2)|endometrium(5)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)	26						TTCCACACCTTCAGTTTCGGG	0.587																																					p.F207S		Atlas-SNP	.											.	AKAP17A	46	.	0			c.T620C						.						132.0	122.0	125.0					X																	1712975		2203	4296	6499	SO:0001583	missense	8227	exon2			ACACCTTCAGTTT	L03426	CCDS14116.1	Xp22.33 and Yp11.32	2010-09-08	2010-09-08	2010-09-08	ENSG00000197976	ENSG00000197976		"""Pseudoautosomal regions / PAR1"", ""A-kinase anchor proteins"""	18783	protein-coding gene	gene with protein product		312095, 465000	"""chromosome X and Y open reading frame 3"", ""splicing factor, arginine/serine-rich 17A"""	CXYorf3, SFRS17A		9736779, 1438229, 19840947	Standard	NR_027383		Approved	XE7, XE7Y, DXYS155E, MGC39904, 721P, CCDC133	uc004cqa.3	Q02040	OTTHUMG00000021063	ENST00000313871.3:c.620T>C	chrX.hg19:g.1712975T>C	ENSP00000324827:p.Phe207Ser	87.0	0.0		93.0	4.0	NM_005088	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Missense_Mutation	SNP	ENST00000313871.3	hg19	CCDS14116.1	.	.	.	.	.	.	.	.	.	.	t	10.68	1.419356	0.25552	.	.	ENSG00000197976	ENST00000313871;ENST00000381261	T;T	0.29917	1.55;1.55	1.83	1.83	0.25207	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	U	0.000000	T	0.49541	0.1563	.	.	.	0.31688	N	0.642274	D;D	0.71674	0.998;0.997	D;D	0.83275	0.943;0.996	T	0.56715	-0.7933	9	0.59425	D	0.04	.	9.5435	0.39266	0.0:0.0:0.0:1.0	.	207;207	Q02040-3;Q02040	.;AK17A_HUMAN	S	207	ENSP00000324827:F207S;ENSP00000370660:F207S	ENSP00000324827:F207S	F	+	2	0	AKAP17A	1672975	1.000000	0.71417	0.018000	0.16275	0.362000	0.29581	5.773000	0.68898	0.582000	0.29556	0.084000	0.15446	TTC	.	.		0.587	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088	
ARSH	347527	hgsc.bcm.edu	37	X	2928166	2928166	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:2928166T>C	ENST00000381130.2	+	2	188	c.188T>C	c.(187-189)cTg>cCg	p.L63P		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	63					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(3)|endometrium(8)|kidney(2)|large_intestine(6)|lung(13)|skin(1)|stomach(1)	34		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				GCTGCCTTCCTGACCGGCCGG	0.502																																					p.L63P		Atlas-SNP	.											.	ARSH	72	.	0			c.T188C						.						59.0	45.0	49.0					X																	2928166		2203	4300	6503	SO:0001583	missense	347527	exon2			CCTTCCTGACCGG	AY875940	CCDS35198.1	Xp22.33	2013-02-14	2006-03-07		ENSG00000205667	ENSG00000205667		"""Arylsulfatase family"""	32488	protein-coding gene	gene with protein product		300586	"""arylsulfatase H"""			16174644	Standard	NM_001011719		Approved		uc011mhj.2	Q5FYA8	OTTHUMG00000159612	ENST00000381130.2:c.188T>C	chrX.hg19:g.2928166T>C	ENSP00000370522:p.Leu63Pro	124.0	0.0		106.0	5.0	NM_001011719		Missense_Mutation	SNP	ENST00000381130.2	hg19	CCDS35198.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.617479	0.46736	.	.	ENSG00000205667	ENST00000381130	D	0.99338	-5.76	3.58	3.58	0.41010	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase, conserved site (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.061108	0.64402	D	0.000004	D	0.99674	0.9878	H	0.99444	4.57	0.52501	D	0.99995	D	0.89917	1.0	D	0.87578	0.998	D	0.97411	1.0002	10	0.87932	D	0	.	11.7444	0.51811	0.0:0.0:0.0:1.0	.	63	Q5FYA8	ARSH_HUMAN	P	63	ENSP00000370522:L63P	ENSP00000370522:L63P	L	+	2	0	ARSH	2938166	1.000000	0.71417	0.576000	0.28549	0.213000	0.24496	3.578000	0.53892	1.273000	0.44346	0.486000	0.48141	CTG	.	.		0.502	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719	
GPR143	4935	hgsc.bcm.edu	37	X	9711666	9711666	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:9711666T>C	ENST00000467482.1	-	6	852	c.706A>G	c.(706-708)Agg>Ggg	p.R236G	GPR143_ENST00000380929.2_Missense_Mutation_p.R256G			P51810	GP143_HUMAN	G protein-coupled receptor 143	236	Necessary for its G protein-activation ability and normal distribution of melanosomes.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|eye pigment biosynthetic process (GO:0006726)|G-protein coupled receptor signaling pathway (GO:0007186)|melanosome localization (GO:0032400)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|neuropeptide signaling pathway (GO:0007218)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of calcium-mediated signaling (GO:0050848)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|G-protein coupled receptor activity (GO:0004930)|L-DOPA binding (GO:0072544)|L-DOPA receptor activity (GO:0035643)|tyrosine binding (GO:0072545)			endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Hepatocellular(5;0.000888)				CCCATCCTCCTCTCGTTCTCC	0.378																																					p.R236G		Atlas-SNP	.											.	GPR143	37	.	0			c.A706G						.						164.0	141.0	149.0					X																	9711666		2203	4300	6503	SO:0001583	missense	4935	exon6			TCCTCCTCTCGTT	Z48804	CCDS14134.1, CCDS14134.2	Xp22.3	2013-09-27	2003-12-01		ENSG00000101850	ENSG00000101850		"""GPCR / Unclassified : 7TM orphan receptors"""	20145	protein-coding gene	gene with protein product	"""ocular albinism 1"""	300808	"""ocular albinism 1 (Nettleship-Falls)"""	OA1		7647783, 10471510	Standard	NM_000273		Approved		uc004cst.2	P51810	OTTHUMG00000021118	ENST00000467482.1:c.706A>G	chrX.hg19:g.9711666T>C	ENSP00000417161:p.Arg236Gly	67.0	0.0		70.0	4.0	NM_000273	Q6NTI7	Missense_Mutation	SNP	ENST00000467482.1	hg19	CCDS14134.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.13|18.13	3.556439|3.556439	0.65425|0.65425	.|.	.|.	ENSG00000101850|ENSG00000101850	ENST00000447366|ENST00000467482;ENST00000380929;ENST00000431126	D|D;D;D	0.99399|0.99413	-5.83|-5.86;-5.86;-5.86	5.15|5.15	3.95|3.95	0.45737|0.45737	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99384|0.99384	0.9783|0.9783	M|M	0.80616|0.80616	2.505|2.505	0.53688|0.53688	D|D	0.999976|0.999976	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.99204|0.99204	1.0874|1.0874	6|10	.|0.62326	.|D	.|0.03	-9.3567|-9.3567	10.3836|10.3836	0.44125|0.44125	0.0:0.0:0.1626:0.8374|0.0:0.0:0.1626:0.8374	.|.	.|236	.|P51810	.|GP143_HUMAN	G|G	171|236;256;152	ENSP00000390546:E171G|ENSP00000417161:R236G;ENSP00000370316:R256G;ENSP00000406138:R152G	.|ENSP00000370316:R256G	E|R	-|-	2|1	0|2	GPR143|GPR143	9671666|9671666	1.000000|1.000000	0.71417|0.71417	0.957000|0.957000	0.39632|0.39632	0.777000|0.777000	0.43975|0.43975	2.492000|2.492000	0.45311|0.45311	0.594000|0.594000	0.29761|0.29761	0.417000|0.417000	0.27973|0.27973	GAG|AGG	.	.		0.378	GPR143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055714.2	NM_000273	
TLR8	51311	hgsc.bcm.edu	37	X	12938298	12938298	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:12938298A>G	ENST00000218032.6	+	2	1226	c.1139A>G	c.(1138-1140)cAg>cGg	p.Q380R	TLR8_ENST00000311912.5_Missense_Mutation_p.Q398R	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	380					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	TATGTGTTCCAGGAACTCAGA	0.358																																					p.Q380R		Atlas-SNP	.											.	TLR8	134	.	0			c.A1139G						.						82.0	85.0	84.0					X																	12938298		2201	4300	6501	SO:0001583	missense	51311	exon2			TGTTCCAGGAACT	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1139A>G	chrX.hg19:g.12938298A>G	ENSP00000218032:p.Gln380Arg	63.0	0.0		59.0	4.0	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	hg19	CCDS14152.1	.	.	.	.	.	.	.	.	.	.	A	7.190	0.591284	0.13812	.	.	ENSG00000101916	ENST00000218032;ENST00000311912	T;T	0.30448	1.53;1.7	5.67	4.51	0.55191	.	0.198166	0.24856	N	0.035058	T	0.19644	0.0472	N	0.25060	0.705	0.24994	N	0.991519	B;B	0.22746	0.074;0.074	B;B	0.17979	0.02;0.02	T	0.16719	-1.0393	10	0.22706	T	0.39	.	10.7201	0.46036	0.9244:0.0:0.0756:0.0	.	380;398	Q9NR97;D1CS70	TLR8_HUMAN;.	R	380;398	ENSP00000218032:Q380R;ENSP00000312082:Q398R	ENSP00000218032:Q380R	Q	+	2	0	TLR8	12848219	0.976000	0.34144	0.914000	0.36105	0.437000	0.31866	2.446000	0.44908	0.877000	0.35895	0.486000	0.48141	CAG	.	.		0.358	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
PIR	8544	hgsc.bcm.edu	37	X	15477841	15477841	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:15477841C>T	ENST00000380421.3	-	4	672	c.212G>A	c.(211-213)gGc>gAc	p.G71D	PIR_ENST00000476381.1_5'UTR|PIR_ENST00000380420.5_Missense_Mutation_p.G71D	NM_001018109.2|NM_003662.3	NP_001018119.1|NP_003653.1	O00625	PIR_HUMAN	pirin (iron-binding nuclear protein)	71					monocyte differentiation (GO:0030224)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|quercetin 2,3-dioxygenase activity (GO:0008127)|transcription cofactor activity (GO:0003712)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9	Hepatocellular(33;0.183)					GGCCATGCTGCCCCCTTCCAG	0.413																																					p.G71D	Ovarian(180;1587 2015 10555 34192 51653)	Atlas-SNP	.											.	PIR	22	.	0			c.G212A						.						205.0	200.0	202.0					X																	15477841		2203	4300	6503	SO:0001583	missense	8544	exon4			ATGCTGCCCCCTT	Y07868	CCDS14167.1	Xp22.31	2008-02-05			ENSG00000087842	ENSG00000087842			30048	protein-coding gene	gene with protein product		300931				9079676	Standard	NM_003662		Approved		uc004cwv.3	O00625	OTTHUMG00000021176	ENST00000380421.3:c.212G>A	chrX.hg19:g.15477841C>T	ENSP00000369786:p.Gly71Asp	112.0	0.0		84.0	4.0	NM_001018109	Q5U0G0|Q6FHD2	Missense_Mutation	SNP	ENST00000380421.3	hg19	CCDS14167.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.425097	0.83667	.	.	ENSG00000087842	ENST00000380420;ENST00000380421	T;T	0.43294	0.95;0.95	5.98	5.98	0.97165	Cupin, RmlC-type (1);RmlC-like jelly roll fold (1);Pirin, N-terminal (1);	0.063149	0.64402	D	0.000007	T	0.81777	0.4894	H	0.99874	4.875	0.46521	D	0.999083	D	0.89917	1.0	D	0.97110	1.0	D	0.90115	0.4195	10	0.72032	D	0.01	-23.1464	16.5188	0.84308	0.0:1.0:0.0:0.0	.	71	O00625	PIR_HUMAN	D	71	ENSP00000369785:G71D;ENSP00000369786:G71D	ENSP00000369785:G71D	G	-	2	0	PIR	15387762	0.987000	0.35691	0.946000	0.38457	0.992000	0.81027	4.445000	0.60007	2.508000	0.84585	0.600000	0.82982	GGC	.	.		0.413	PIR-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055863.1	NM_003662	
PDK3	5165	hgsc.bcm.edu	37	X	24521601	24521601	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:24521601T>C	ENST00000379162.4	+	4	713	c.478T>C	c.(478-480)Tct>Cct	p.S160P	PDK3_ENST00000441463.2_Missense_Mutation_p.S160P	NM_005391.4	NP_005382.1	Q15120	PDK3_HUMAN	pyruvate dehydrogenase kinase, isozyme 3	160	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cell death (GO:0008219)|cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to glucose stimulus (GO:0071333)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|peptidyl-serine phosphorylation (GO:0018105)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|regulation of reactive oxygen species metabolic process (GO:2000377)|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)			NS(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						CAACCGCATCTCTTTCCGCAT	0.388																																					p.S160P		Atlas-SNP	.											.	PDK3	86	.	0			c.T478C						.						114.0	103.0	107.0					X																	24521601		2203	4300	6503	SO:0001583	missense	5165	exon4			CGCATCTCTTTCC	L42452	CCDS14212.1, CCDS48088.1	Xp22.12	2008-02-05	2005-11-16		ENSG00000067992	ENSG00000067992			8811	protein-coding gene	gene with protein product		300906	"""pyruvate dehydrogenase kinase, isoenzyme 3"""			7499431	Standard	NM_001142386		Approved		uc004dbh.3	Q15120	OTTHUMG00000021269	ENST00000379162.4:c.478T>C	chrX.hg19:g.24521601T>C	ENSP00000368460:p.Ser160Pro	115.0	0.0		98.0	4.0	NM_005391	B4DXG6	Missense_Mutation	SNP	ENST00000379162.4	hg19	CCDS14212.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.846122	0.71603	.	.	ENSG00000067992	ENST00000379162;ENST00000441463	T;T	0.35605	1.36;1.3	5.94	5.94	0.96194	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal (3);	0.098003	0.64402	D	0.000001	T	0.51753	0.1693	M	0.83603	2.65	0.80722	D	1	B;B	0.26147	0.143;0.143	B;B	0.38056	0.264;0.177	T	0.54186	-0.8331	10	0.59425	D	0.04	.	15.3771	0.74615	0.0:0.0:0.0:1.0	.	160;160	B4DXG6;Q15120	.;PDK3_HUMAN	P	160	ENSP00000368460:S160P;ENSP00000387536:S160P	ENSP00000368460:S160P	S	+	1	0	PDK3	24431522	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.013000	0.88655	2.015000	0.59207	0.483000	0.47432	TCT	.	.		0.388	PDK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056097.1	NM_005391	
DMD	1756	hgsc.bcm.edu	37	X	32366626	32366626	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:32366626T>C	ENST00000357033.4	-	38	5551	c.5345A>G	c.(5344-5346)gAa>gGa	p.E1782G	DMD_ENST00000378677.2_Missense_Mutation_p.E1778G	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	1782	Interaction with SYNM. {ECO:0000250}.				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)				CTGCTCCAATTCCTTCAAAGG	0.323																																					p.E1782G		Atlas-SNP	.											.	DMD	2127	.	0			c.A5345G						.						73.0	65.0	68.0					X																	32366626		2202	4298	6500	SO:0001583	missense	1756	exon38			TCCAATTCCTTCA	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.5345A>G	chrX.hg19:g.32366626T>C	ENSP00000354923:p.Glu1782Gly	106.0	0.0		74.0	5.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.088119	0.55968	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000493412	T;T;T	0.62105	0.05;0.06;0.93	5.49	5.49	0.81192	.	0.000000	0.38111	U	0.001819	T	0.61476	0.2350	N	0.08118	0	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.979;0.998;0.998;0.998	D;P;D;D;D	0.78314	0.991;0.702;0.979;0.991;0.991	T	0.65837	-0.6071	10	0.34782	T	0.22	.	14.6635	0.68891	0.0:0.0:0.0:1.0	.	1774;1782;1778;441;438	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	G	1774;441;438;1778;1782;1782;1659;1	ENSP00000367948:E1778G;ENSP00000354923:E1782G;ENSP00000417725:E1G	ENSP00000354923:E1782G	E	-	2	0	DMD	32276547	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.332000	0.72934	1.844000	0.53588	0.376000	0.23039	GAA	.	.		0.323	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
SYN1	6853	hgsc.bcm.edu	37	X	47464463	47464463	+	Missense_Mutation	SNP	C	C	T	rs143341539		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:47464463C>T	ENST00000295987.7	-	5	812	c.688G>A	c.(688-690)Gcc>Acc	p.A230T	SYN1_ENST00000340666.4_Missense_Mutation_p.A230T	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	230	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						ACCATCTGGGCAAACTATGAG	0.468																																					p.A230T		Atlas-SNP	.											.	SYN1	84	.	0			c.G688A						.	C	THR/ALA,THR/ALA	0,3835		0,0,1632,571	89.0	76.0	80.0		688,688	4.9	1.0	X	dbSNP_134	80	1,6727		0,1,2427,1872	no	missense,missense	SYN1	NM_006950.3,NM_133499.2	58,58	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	probably-damaging,probably-damaging	230/706,230/670	47464463	1,10562	2203	4300	6503	SO:0001583	missense	6853	exon5			TCTGGGCAAACTA		CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.688G>A	chrX.hg19:g.47464463C>T	ENSP00000295987:p.Ala230Thr	114.0	0.0		95.0	4.0	NM_006950	B1AJQ1|O75825|Q5H9A9	Missense_Mutation	SNP	ENST00000295987.7	hg19	CCDS14280.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.862415	0.71949	0.0	1.49E-4	ENSG00000008056	ENST00000295987;ENST00000340666	T;T	0.34072	1.81;1.38	4.88	4.88	0.63580	ATP-grasp fold, subdomain 2 (1);Synapsin, ATP-binding domain (1);	0.000000	0.64402	D	0.000002	T	0.57917	0.2086	M	0.84219	2.685	0.44110	D	0.99688	D;D	0.67145	0.993;0.996	D;P	0.63703	0.917;0.817	T	0.63673	-0.6584	10	0.72032	D	0.01	-2.8311	10.0826	0.42399	0.2005:0.7995:0.0:0.0	.	230;230	P17600;P17600-2	SYN1_HUMAN;.	T	230	ENSP00000295987:A230T;ENSP00000343206:A230T	ENSP00000295987:A230T	A	-	1	0	SYN1	47349407	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	1.617000	0.36943	2.152000	0.67230	0.544000	0.68410	GCC	.	C|1.000;T|0.000		0.468	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950	
ZNF182	7569	hgsc.bcm.edu	37	X	47842408	47842408	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:47842408A>G	ENST00000396965.1	-	6	580	c.230T>C	c.(229-231)cTc>cCc	p.L77P	ZNF182_ENST00000376943.3_Missense_Mutation_p.L58P|ZNF182_ENST00000305127.6_Missense_Mutation_p.L77P	NM_001178099.1	NP_001171570.1	P17025	ZN182_HUMAN	zinc finger protein 182	77	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)			endometrium(5)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)	22						CTCCAACTTGAGGATGAGGTT	0.458																																					p.L77P		Atlas-SNP	.											.	ZNF182	117	.	0			c.T230C						.						128.0	100.0	110.0					X																	47842408		2203	4300	6503	SO:0001583	missense	7569	exon6			AACTTGAGGATGA	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.230T>C	chrX.hg19:g.47842408A>G	ENSP00000380165:p.Leu77Pro	81.0	0.0		75.0	4.0	NM_006962	A2IDD7|Q3KP67|Q96QH7	Missense_Mutation	SNP	ENST00000396965.1	hg19	CCDS35236.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.221206	0.39201	.	.	ENSG00000147118	ENST00000376943;ENST00000396965;ENST00000305127	T;T;T	0.00892	5.57;5.57;5.57	4.42	4.42	0.53409	Krueppel-associated box (3);	.	.	.	.	T	0.01765	0.0056	L	0.29908	0.895	0.49389	D	0.999781	P;P;D	0.57571	0.874;0.823;0.98	B;B;P	0.58013	0.24;0.392;0.831	T	0.74420	-0.3671	9	0.33141	T	0.24	.	9.0057	0.36111	1.0:0.0:0.0:0.0	.	58;58;77	B4DRM0;Q96QH7;P17025	.;.;ZN182_HUMAN	P	58;77;77	ENSP00000366142:L58P;ENSP00000380165:L77P;ENSP00000306351:L77P	ENSP00000306351:L77P	L	-	2	0	ZNF182	47727352	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	1.542000	0.36137	1.948000	0.56530	0.486000	0.48141	CTC	.	.		0.458	ZNF182-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277055.1	NM_006962	
WDR13	64743	hgsc.bcm.edu	37	X	48458002	48458002	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:48458002A>G	ENST00000218056.5	+	4	925	c.420A>G	c.(418-420)tcA>tcG	p.S140S	WDR13_ENST00000492715.1_3'UTR|WDR13_ENST00000376729.5_Silent_p.S140S	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	140						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						TGCCCACGTCAGCAGCAGAGG	0.612																																					p.S140S		Atlas-SNP	.											.	WDR13	96	.	0			c.A420G						.						82.0	71.0	74.0					X																	48458002		2203	4300	6503	SO:0001819	synonymous_variant	64743	exon4			CACGTCAGCAGCA	AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"""WD repeat domain containing"""	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.420A>G	chrX.hg19:g.48458002A>G		92.0	0.0		84.0	4.0	NM_017883	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Silent	SNP	ENST00000218056.5	hg19	CCDS14302.1																																																																																			.	.		0.612	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2		
USP27X	389856	hgsc.bcm.edu	37	X	49644929	49644929	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:49644929T>C	ENST00000508866.2	+	1	460	c.19T>C	c.(19-21)Tat>Cat	p.Y7H	USP27X-AS1_ENST00000437322.2_lincRNA	NM_001145073.1	NP_001138545.1	A6NNY8	UBP27_HUMAN	ubiquitin specific peptidase 27, X-linked	7					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			endometrium(7)	7						GGACTATGTATATGACAAAGA	0.423																																					p.Y7H		Atlas-SNP	.											.	USP27X	25	.	0			c.T19C						.						59.0	49.0	52.0					X																	49644929		692	1591	2283	SO:0001583	missense	389856	exon1			TATGTATATGACA	AW851065	CCDS65260.1	Xp11.23	2007-10-05	2005-08-08			ENSG00000273820		"""Ubiquitin-specific peptidases"""	13486	protein-coding gene	gene with protein product			"""ubiquitin specific protease 27, X chromosome"", ""ubiquitin specific protease 27, X-linked"""			12838346	Standard	NM_001145073		Approved	USP27	uc004dop.3	A6NNY8		ENST00000508866.2:c.19T>C	chrX.hg19:g.49644929T>C	ENSP00000475071:p.Tyr7His	92.0	0.0		56.0	4.0	NM_001145073		Missense_Mutation	SNP	ENST00000508866.2	hg19																																																																																				.	.		0.423	USP27X-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000060837.3	XM_372213	
CCNB3	85417	hgsc.bcm.edu	37	X	50053332	50053332	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:50053332A>G	ENST00000376042.1	+	6	2461	c.2163A>G	c.(2161-2163)gaA>gaG	p.E721E	CCNB3_ENST00000376038.1_Intron|CCNB3_ENST00000348603.2_Intron|CCNB3_ENST00000276014.7_Silent_p.E721E			Q8WWL7	CCNB3_HUMAN	cyclin B3	721					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					CCATGGAAGAAGAGTCCCTTA	0.453																																					p.E721E		Atlas-SNP	.											.	CCNB3	367	.	0			c.A2163G						.						38.0	36.0	37.0					X																	50053332		2203	4300	6503	SO:0001819	synonymous_variant	85417	exon5			GGAAGAAGAGTCC	AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.2163A>G	chrX.hg19:g.50053332A>G		194.0	0.0		177.0	8.0	NM_033031	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Silent	SNP	ENST00000376042.1	hg19	CCDS14331.1																																																																																			.	.		0.453	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1		
KDM5C	8242	hgsc.bcm.edu	37	X	53223019	53223019	+	Silent	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:53223019C>T	ENST00000375401.3	-	24	4585	c.4053G>A	c.(4051-4053)ctG>ctA	p.L1351L	KDM5C_ENST00000375379.3_Silent_p.L1351L|KDM5C_ENST00000452825.3_Silent_p.L1284L|KDM5C_ENST00000375383.3_Silent_p.L1310L|KDM5C_ENST00000404049.3_Silent_p.L1350L	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	1351					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|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)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						CTCCATTCTCCAGTAAGCCCT	0.567			"""N, F, S"""		clear cell renal carcinoma																																p.L1351L		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.G4053A						.						109.0	80.0	90.0					X																	53223019		2203	4300	6503	SO:0001819	synonymous_variant	8242	exon24			ATTCTCCAGTAAG	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11114	protein-coding gene	gene with protein product		314690	"""Jumonji, AT rich interactive domain 1C (RBP2-like)"", ""Smcy homolog, X-linked (mouse)"", ""jumonji, AT rich interactive domain 1C"", ""mental retardation, X-linked 13"""	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.4053G>A	chrX.hg19:g.53223019C>T		93.0	0.0		79.0	4.0	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Silent	SNP	ENST00000375401.3	hg19	CCDS14351.1																																																																																			.	.		0.567	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187	
PHF8	23133	hgsc.bcm.edu	37	X	54011486	54011486	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:54011486A>G	ENST00000357988.5	-	18	2770	c.2412T>C	c.(2410-2412)agT>agC	p.S804S	PHF8_ENST00000338946.6_Silent_p.S667S|PHF8_ENST00000322659.8_Silent_p.S751S|PHF8_ENST00000338154.6_Silent_p.S768S	NM_001184896.1	NP_001171825.1	Q9UPP1	PHF8_HUMAN	PHD finger protein 8	804	Ser-rich.				brain development (GO:0007420)|G1/S transition of mitotic cell cycle (GO:0000082)|histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of chromatin silencing at rDNA (GO:0061188)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|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)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	40						GGGAAGCAGGACTGTTAGACA	0.637																																					p.S804S		Atlas-SNP	.											.	PHF8	198	.	0			c.T2412C						.						68.0	55.0	60.0					X																	54011486		2203	4300	6503	SO:0001819	synonymous_variant	23133	exon18			AGCAGGACTGTTA	AB029034	CCDS14355.1, CCDS55418.1, CCDS55419.1, CCDS55420.1	Xp11.22	2013-01-28			ENSG00000172943	ENSG00000172943		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	20672	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1F"""	300560				10470851, 20023638, 20644565	Standard	NM_015107		Approved	ZNF422, KIAA1111, JHDM1F	uc004dsu.3	Q9UPP1	OTTHUMG00000021622	ENST00000357988.5:c.2412T>C	chrX.hg19:g.54011486A>G		52.0	0.0		46.0	4.0	NM_001184896	B3KMV4|B7Z911|Q5H9U5|Q5JPR9|Q5JPS0|Q5JPS2|Q5JPS3|Q5VUJ4|Q7Z6D4|Q9HAH2	Silent	SNP	ENST00000357988.5	hg19	CCDS55420.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.979|9.979	1.227489|1.227489	0.22542|0.22542	.|.	.|.	ENSG00000172943|ENSG00000172943	ENST00000443302|ENST00000396282;ENST00000375189	T|.	0.48836|.	0.8|.	5.74|5.74	1.88|1.88	0.25563|0.25563	.|.	0.341060|.	0.37577|.	N|.	0.002036|.	T|T	0.38295|0.38295	0.1035|0.1035	.|.	.|.	.|.	0.30323|0.30323	N|N	0.78743|0.78743	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.46610|0.46610	-0.9179|-0.9179	7|5	0.24483|0.87932	T|D	0.36|0	-13.8079|-13.8079	3.2386|3.2386	0.06773|0.06773	0.4701:0.2157:0.3142:0.0|0.4701:0.2157:0.3142:0.0	.|.	.|.	.|.	.|.	P|A	532|672;244	ENSP00000397129:S532P|.	ENSP00000397129:S532P|ENSP00000364335:V244A	S|V	-|-	1|2	0|0	PHF8|PHF8	54028211|54028211	0.108000|0.108000	0.22018|0.22018	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	0.561000|0.561000	0.23515|0.23515	0.804000|0.804000	0.34136|0.34136	0.486000|0.486000	0.48141|0.48141	TCC|GTC	.	.		0.637	PHF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056784.2	NM_015107	
ITIH6	347365	hgsc.bcm.edu	37	X	54786268	54786268	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:54786268T>C	ENST00000218436.6	-	7	1025	c.996A>G	c.(994-996)aaA>aaG	p.K332K		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	332	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										AGCCTCCAGCTTTCCAAACAT	0.478																																					p.K332K		Atlas-SNP	.											.	.	.	.	0			c.A996G						.						162.0	121.0	135.0					X																	54786268		2203	4300	6503	SO:0001819	synonymous_variant	347365	exon7			TCCAGCTTTCCAA	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.996A>G	chrX.hg19:g.54786268T>C		119.0	0.0		93.0	4.0	NM_198510	A6NN03	Silent	SNP	ENST00000218436.6	hg19	CCDS14361.1																																																																																			.	.		0.478	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
ZC3H12B	340554	hgsc.bcm.edu	37	X	64709115	64709115	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:64709115T>C	ENST00000338957.4	+	1	501	c.434T>C	c.(433-435)cTt>cCt	p.L145P	ZC3H12B_ENST00000423889.3_Missense_Mutation_p.L134P	NM_001010888.3	NP_001010888.3	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	145							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TTGGCAGAGCTTGTCAGACTT	0.478																																					p.L145P		Atlas-SNP	.											.	ZC3H12B	144	.	0			c.T434C						.						86.0	83.0	84.0					X																	64709115		1938	4128	6066	SO:0001583	missense	340554	exon1			CAGAGCTTGTCAG	BX647241	CCDS48131.1, CCDS48131.2	Xq12	2012-07-05	2005-06-14	2005-06-14	ENSG00000102053	ENSG00000102053		"""Zinc fingers, CCCH-type domain containing"""	17407	protein-coding gene	gene with protein product	"""MCP induced protein 2"""	300889	"""chromosome X open reading frame 32"""	CXorf32		18178554	Standard	NM_001010888		Approved	MCPIP2	uc010nko.3	Q5HYM0	OTTHUMG00000021719	ENST00000338957.4:c.434T>C	chrX.hg19:g.64709115T>C	ENSP00000340839:p.Leu145Pro	78.0	0.0		74.0	4.0	NM_001010888	B2RTQ3|E9PAJ6|Q5H9C0	Missense_Mutation	SNP	ENST00000338957.4	hg19	CCDS48131.2	.	.	.	.	.	.	.	.	.	.	T	19.20	3.781242	0.70222	.	.	ENSG00000102053	ENST00000338957;ENST00000423889	T;T	0.61627	0.09;0.11	5.36	5.36	0.76844	.	0.458821	0.17941	N	0.156844	T	0.75280	0.3828	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77587	-0.2532	10	0.87932	D	0	-28.8678	13.1206	0.59325	0.0:0.0:0.0:1.0	.	134	Q5HYM0	ZC12B_HUMAN	P	145;134	ENSP00000340839:L145P;ENSP00000408077:L134P	ENSP00000340839:L145P	L	+	2	0	ZC3H12B	64625840	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.423000	0.80229	1.983000	0.57843	0.412000	0.27726	CTT	.	.		0.478	ZC3H12B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378734.2	XM_293334	
FOXO4	4303	hgsc.bcm.edu	37	X	70320733	70320733	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:70320733T>C	ENST00000374259.3	+	2	985	c.653T>C	c.(652-654)gTg>gCg	p.V218A	FOXO4_ENST00000341558.3_Missense_Mutation_p.V163A	NM_001170931.1|NM_005938.3	NP_001164402.1|NP_005929.2	P98177	FOXO4_HUMAN	forkhead box O4	218					cell cycle arrest (GO:0007050)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mitotic G2 DNA damage checkpoint (GO:0007095)|muscle organ development (GO:0007517)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of smooth muscle cell differentiation (GO:0051151)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)	18	Renal(35;0.156)					AAACCATCTGTGCTGCCAGCT	0.642											OREG0019856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V218A		Atlas-SNP	.											.	FOXO4	60	.	0			c.T653C						.						21.0	22.0	22.0					X																	70320733		1952	4136	6088	SO:0001583	missense	4303	exon2			CATCTGTGCTGCC		CCDS43969.1, CCDS55440.1	Xq13.1	2008-02-05	2007-05-02	2007-05-02	ENSG00000184481	ENSG00000184481		"""Forkhead boxes"""	7139	protein-coding gene	gene with protein product		300033	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 7"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 7"""	MLLT7		7529552	Standard	NM_005938		Approved	AFX1	uc004dys.2	P98177	OTTHUMG00000021789	ENST00000374259.3:c.653T>C	chrX.hg19:g.70320733T>C	ENSP00000363377:p.Val218Ala	33.0	0.0	1121	39.0	4.0	NM_005938	B7WPJ7|O43821|Q13720|Q3KPF1|Q8TDK9	Missense_Mutation	SNP	ENST00000374259.3	hg19	CCDS43969.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.210425	0.00292	.	.	ENSG00000184481	ENST00000374259;ENST00000341558	D;D	0.95412	-3.48;-3.7	5.11	1.14	0.20703	.	0.325828	0.26776	N	0.022542	D	0.83751	0.5322	N	0.04880	-0.145	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.002;0.001	T	0.71090	-0.4693	10	0.09338	T	0.73	-19.6219	4.8266	0.13419	0.0:0.1744:0.1557:0.6699	.	218;163;218	B4DTB6;P98177-2;P98177	.;.;FOXO4_HUMAN	A	218;163	ENSP00000363377:V218A;ENSP00000342209:V163A	ENSP00000342209:V163A	V	+	2	0	FOXO4	70237458	0.852000	0.29690	0.019000	0.16419	0.005000	0.04900	0.608000	0.24223	0.232000	0.21100	0.422000	0.28245	GTG	.	.		0.642	FOXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057115.1	NM_005938	
TAF1	6872	hgsc.bcm.edu	37	X	70601683	70601683	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:70601683A>G	ENST00000373790.4	+	9	1499	c.1448A>G	c.(1447-1449)aAt>aGt	p.N483S	TAF1_ENST00000276072.3_Missense_Mutation_p.N504S|TAF1_ENST00000423759.1_Missense_Mutation_p.N504S|TAF1_ENST00000449580.1_Missense_Mutation_p.N483S	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	483					cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|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)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				TGGGAGGACAATATCATTTGG	0.458																																					p.N504S		Atlas-SNP	.											.	TAF1	439	.	0			c.A1511G						.						144.0	115.0	125.0					X																	70601683		2203	4300	6503	SO:0001583	missense	6872	exon9			AGGACAATATCAT		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.1448A>G	chrX.hg19:g.70601683A>G	ENSP00000362895:p.Asn483Ser	110.0	0.0		70.0	4.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	hg19	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	16.72	3.200855	0.58234	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.10860	2.83;2.91;2.88;2.83	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.14700	0.0355	L	0.54323	1.7	0.58432	D	0.999999	B;B	0.28584	0.138;0.216	B;B	0.33846	0.119;0.171	T	0.03728	-1.1009	10	0.30854	T	0.27	.	14.5732	0.68226	1.0:0.0:0.0:0.0	.	483;504	P21675;P21675-2	TAF1_HUMAN;.	S	483;483;504;504	ENSP00000362895:N483S;ENSP00000389000:N483S;ENSP00000406549:N504S;ENSP00000276072:N504S	ENSP00000276072:N504S	N	+	2	0	TAF1	70518408	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.125000	0.77193	1.821000	0.53095	0.481000	0.45027	AAT	.	.		0.458	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
RGAG4	340526	hgsc.bcm.edu	37	X	71349868	71349868	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:71349868T>C	ENST00000545866.1	-	1	1890	c.1523A>G	c.(1522-1524)aAc>aGc	p.N508S	NHSL2_ENST00000540800.1_Intron|RGAG4_ENST00000609883.1_Missense_Mutation_p.N508S	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	508										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					TCGATTCTGGTTCCTCCGTCT	0.557																																					p.N508S		Atlas-SNP	.											.	RGAG4	63	.	0			c.A1523G						.						53.0	55.0	54.0					X																	71349868		2030	4148	6178	SO:0001583	missense	340526	exon1			TTCTGGTTCCTCC	AB082532	CCDS55446.1	Xq13.1	2008-02-05			ENSG00000242732	ENSG00000242732			29430	protein-coding gene	gene with protein product						12056414, 15716091, 16093683	Standard	NM_001024455		Approved	KIAA2001, Mar5, Mart5	uc004eaj.2	Q5HYW3	OTTHUMG00000021808	ENST00000545866.1:c.1523A>G	chrX.hg19:g.71349868T>C	ENSP00000441366:p.Asn508Ser	140.0	0.0		122.0	5.0	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Missense_Mutation	SNP	ENST00000545866.1	hg19	CCDS55446.1	.	.	.	.	.	.	.	.	.	.	T	11.26	1.587655	0.28268	.	.	ENSG00000242732	ENST00000545866;ENST00000479991	T;T	0.14893	2.47;2.47	3.89	0.0353	0.14187	.	.	.	.	.	T	0.07007	0.0178	N	0.08118	0	0.21220	N	0.999754	B	0.17038	0.02	B	0.09377	0.004	T	0.42015	-0.9476	8	.	.	.	.	5.8822	0.18862	0.0:0.3757:0.0:0.6243	.	508	Q5HYW3	RGAG4_HUMAN	S	508	ENSP00000441366:N508S;ENSP00000418667:N508S	.	N	-	2	0	RGAG4	71266593	0.998000	0.40836	0.997000	0.53966	0.720000	0.41350	0.012000	0.13287	-0.091000	0.12440	0.417000	0.27973	AAC	.	.		0.557	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455	
DACH2	117154	hgsc.bcm.edu	37	X	86069720	86069720	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:86069720A>G	ENST00000373125.4	+	10	1567	c.1567A>G	c.(1567-1569)Aaa>Gaa	p.K523E	DACH2_ENST00000510272.1_Missense_Mutation_p.K304E|DACH2_ENST00000373131.1_Missense_Mutation_p.K510E|DACH2_ENST00000508860.1_Missense_Mutation_p.K356E	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	523	DACHbox-C.				development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						GAAGAAGGAGAAAAAAACCAA	0.428																																					p.K523E		Atlas-SNP	.											.	DACH2	263	.	0			c.A1567G						.						58.0	55.0	56.0					X																	86069720		2203	4300	6503	SO:0001583	missense	117154	exon10			AAGGAGAAAAAAA	AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"""dachshund homolog 2 (Drosophila)"""				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.1567A>G	chrX.hg19:g.86069720A>G	ENSP00000362217:p.Lys523Glu	41.0	0.0		46.0	4.0	NM_053281	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	hg19	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.970788	0.74246	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000510272;ENST00000400297;ENST00000484479	D;D	0.88741	-2.37;-2.42	4.76	4.76	0.60689	.	0.000000	0.64402	D	0.000001	D	0.93416	0.7900	M	0.72894	2.215	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;0.998;0.998	D;D;D;D	0.87578	0.998;0.998;0.991;0.989	D	0.93778	0.7081	10	0.62326	D	0.03	.	13.4743	0.61299	1.0:0.0:0.0:0.0	.	389;523;510;523	Q1RMF5;A8K3I1;Q96NX9-2;Q96NX9	.;.;.;DACH2_HUMAN	E	523;510;523;356;304;356;188	ENSP00000362223:K510E;ENSP00000362217:K523E	ENSP00000345134:K523E	K	+	1	0	DACH2	85956376	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	8.793000	0.91862	1.553000	0.49476	0.339000	0.21740	AAA	.	.		0.428	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281	
NXF3	56000	hgsc.bcm.edu	37	X	102339711	102339711	+	Silent	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:102339711A>G	ENST00000395065.3	-	2	230	c.129T>C	c.(127-129)tcT>tcC	p.S43S	NXF3_ENST00000425644.1_5'UTR|NXF3_ENST00000425463.2_Intron	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	43					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)			NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						GATGGGATGAAGAATGCATGC	0.458																																					p.S43S		Atlas-SNP	.											.	NXF3	81	.	0			c.T129C						.						254.0	204.0	221.0					X																	102339711		2203	4300	6503	SO:0001819	synonymous_variant	56000	exon2			GGATGAAGAATGC	AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.129T>C	chrX.hg19:g.102339711A>G		130.0	0.0		113.0	5.0	NM_022052	B4DYS7|Q5H9I1|Q9H1A9	Silent	SNP	ENST00000395065.3	hg19	CCDS14503.1																																																																																			.	.		0.458	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052	
SLC25A53	401612	hgsc.bcm.edu	37	X	103349276	103349276	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:103349276C>T	ENST00000357421.4	-	2	845	c.665G>A	c.(664-666)gGa>gAa	p.G222E		NM_001012755.3	NP_001012773.2	Q5H9E4	S2553_HUMAN	solute carrier family 25, member 53	222					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											GGTGATTGTTCCATTGACACT	0.522																																					p.G222E		Atlas-SNP	.											.	.	.	.	0			c.G665A						.						71.0	69.0	69.0					X																	103349276		2203	4300	6503	SO:0001583	missense	401612	exon2			ATTGTTCCATTGA		CCDS35363.1	Xq22.2	2013-05-22	2012-03-29	2012-03-29	ENSG00000176274	ENSG00000269743		"""Solute carriers"""	31894	protein-coding gene	gene with protein product			"""mitochondrial carrier triple repeat 6"""	MCART6			Standard	NM_001012755		Approved		uc004elu.3	Q5H9E4	OTTHUMG00000022124	ENST00000357421.4:c.665G>A	chrX.hg19:g.103349276C>T	ENSP00000361681:p.Gly222Glu	107.0	0.0		82.0	5.0	NM_001012755	B2RTT9	Missense_Mutation	SNP	ENST00000357421.4	hg19	CCDS35363.1	.	.	.	.	.	.	.	.	.	.	c	13.17	2.158299	0.38119	.	.	ENSG00000176274	ENST00000357421	D	0.85171	-1.95	4.18	4.18	0.49190	Mitochondrial carrier domain (2);	0.145961	0.46442	D	0.000293	D	0.84101	0.5398	M	0.72894	2.215	0.42889	D	0.994194	B	0.15719	0.014	B	0.20184	0.028	D	0.83794	0.0232	10	0.72032	D	0.01	-19.2128	13.1831	0.59666	0.0:1.0:0.0:0.0	.	222	Q5H9E4	MCAR6_HUMAN	E	222	ENSP00000361681:G222E	ENSP00000361681:G222E	G	-	2	0	MCART6	103235932	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.415000	0.52700	2.061000	0.61500	0.594000	0.82650	GGA	.	.		0.522	SLC25A53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057761.1	NM_001012755	
GUCY2F	2986	hgsc.bcm.edu	37	X	108628445	108628445	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:108628445T>C	ENST00000218006.2	-	16	3314	c.3023A>G	c.(3022-3024)aAc>aGc	p.N1008S		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	1008	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						AGAAGCTGTGTTCACAGTGTC	0.488																																					p.N1008S		Atlas-SNP	.											.	GUCY2F	178	.	0			c.A3023G						.						139.0	99.0	113.0					X																	108628445		2203	4300	6503	SO:0001583	missense	2986	exon16			GCTGTGTTCACAG	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"""guanylate cyclase 2D-like, membrane (retina-specific)"""	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.3023A>G	chrX.hg19:g.108628445T>C	ENSP00000218006:p.Asn1008Ser	97.0	0.0		99.0	4.0	NM_001522	Q9UJF1	Missense_Mutation	SNP	ENST00000218006.2	hg19	CCDS14545.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.968721	0.53614	.	.	ENSG00000101890	ENST00000218006	D	0.88124	-2.34	3.97	3.97	0.46021	Adenylyl cyclase class-3/4/guanylyl cyclase, conserved site (1);Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.153676	0.56097	D	0.000031	D	0.92773	0.7702	M	0.91249	3.19	0.34090	D	0.660587	D	0.63046	0.992	P	0.58331	0.837	D	0.95788	0.8822	10	0.87932	D	0	.	10.2551	0.43392	0.0:0.0:0.0:1.0	.	1008	P51841	GUC2F_HUMAN	S	1008	ENSP00000218006:N1008S	ENSP00000218006:N1008S	N	-	2	0	GUCY2F	108515101	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	3.898000	0.56281	1.781000	0.52344	0.486000	0.48141	AAC	.	.		0.488	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522	
AMOT	154796	hgsc.bcm.edu	37	X	112021881	112021881	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:112021881A>G	ENST00000524145.1	-	12	3243	c.3169T>C	c.(3169-3171)Ttc>Ctc	p.F1057L	AMOT_ENST00000371962.1_Missense_Mutation_p.F825L|AMOT_ENST00000371959.3_Missense_Mutation_p.F1057L|MIR4329_ENST00000582643.1_RNA|AMOT_ENST00000304758.1_Missense_Mutation_p.F648L			Q4VCS5	AMOT_HUMAN	angiomotin	1057					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						TTGGAGTGGAACACAGGCCCA	0.433																																					p.F1057L		Atlas-SNP	.											.	AMOT	204	.	0			c.T3169C						.						169.0	156.0	160.0					X																	112021881		2203	4300	6503	SO:0001583	missense	154796	exon11			AGTGGAACACAGG	AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.3169T>C	chrX.hg19:g.112021881A>G	ENSP00000429013:p.Phe1057Leu	89.0	0.0		79.0	4.0	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	hg19	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	A	15.22	2.768448	0.49680	.	.	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145	T;T;T;T	0.18657	2.2;2.24;2.48;2.24	6.01	3.52	0.40303	.	0.235189	0.32343	N	0.006229	T	0.10680	0.0261	N	0.19112	0.55	0.33031	D	0.53019	B	0.02656	0.0	B	0.06405	0.002	T	0.16541	-1.0399	10	0.08599	T	0.76	-7.9949	8.5959	0.33714	0.7442:0.1289:0.0:0.1268	.	1057	Q4VCS5	AMOT_HUMAN	L	648;1057;825;1057	ENSP00000305557:F648L;ENSP00000361027:F1057L;ENSP00000361030:F825L;ENSP00000429013:F1057L	ENSP00000305557:F648L	F	-	1	0	AMOT	111908537	1.000000	0.71417	0.978000	0.43139	0.965000	0.64279	5.024000	0.64090	2.020000	0.59435	0.486000	0.48141	TTC	.	.		0.433	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265	
KLHL13	90293	hgsc.bcm.edu	37	X	117079481	117079481	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:117079481C>T	ENST00000262820.3	-	2	1065	c.156G>A	c.(154-156)atG>atA	p.M52I	KLHL13_ENST00000371876.1_Start_Codon_SNP_p.M1I|KLHL13_ENST00000371878.1_Start_Codon_SNP_p.M1I|KLHL13_ENST00000469946.1_Start_Codon_SNP_p.M1I|KLHL13_ENST00000545703.1_Missense_Mutation_p.M10I|KLHL13_ENST00000539496.1_Missense_Mutation_p.M55I|KLHL13_ENST00000540167.1_Missense_Mutation_p.M36I|KLHL13_ENST00000541812.1_Missense_Mutation_p.M36I|KLHL13_ENST00000371882.1_Start_Codon_SNP_p.M1I	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	52					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						ATGAGAGGCCCATTTCGCTGC	0.433																																					p.M55I		Atlas-SNP	.											.	KLHL13	87	.	0			c.G165A						.						104.0	85.0	92.0					X																	117079481		2203	4300	6503	SO:0001583	missense	90293	exon3			GAGGCCCATTTCG	AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"""Kelch-like"", ""BTB/POZ domain containing"""	22931	protein-coding gene	gene with protein product		300655	"""BTB and kelch domain containing 2, KIAA1309"", ""kelch-like 13 (Drosophila)"""	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.156G>A	chrX.hg19:g.117079481C>T	ENSP00000262820:p.Met52Ile	126.0	0.0		97.0	4.0	NM_001168299	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Missense_Mutation	SNP	ENST00000262820.3	hg19	CCDS14571.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.372477	0.61624	.	.	ENSG00000003096	ENST00000371882;ENST00000371876;ENST00000371878;ENST00000447671;ENST00000541812;ENST00000540167;ENST00000539496;ENST00000262820;ENST00000545703;ENST00000469946;ENST00000453826	T;T;T;T;T;T;T;T;T;T	0.70282	-0.38;-0.38;-0.38;-0.38;-0.36;-0.36;-0.47;-0.47;-0.44;-0.38	5.09	5.09	0.68999	.	0.077063	0.85682	D	0.000000	T	0.52517	0.1739	N	0.08118	0	0.80722	D	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.48433	-0.9036	10	0.35671	T	0.21	.	16.4339	0.83864	0.0:1.0:0.0:0.0	.	36;55;46;52	Q9P2N7-3;Q9P2N7-5;Q9P2N7-4;Q9P2N7	.;.;.;KLH13_HUMAN	I	1;1;1;1;36;36;55;52;10;1;1	ENSP00000360949:M1I;ENSP00000360943:M1I;ENSP00000360945:M1I;ENSP00000412640:M1I;ENSP00000444450:M36I;ENSP00000441029:M36I;ENSP00000443191:M55I;ENSP00000262820:M52I;ENSP00000440707:M10I;ENSP00000419803:M1I	ENSP00000262820:M52I	M	-	3	0	KLHL13	116963509	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.209000	0.65208	2.490000	0.84030	0.594000	0.82650	ATG	.	.		0.433	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495	
KIAA1210	57481	hgsc.bcm.edu	37	X	118284386	118284386	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:118284386T>C	ENST00000402510.2	-	1	156	c.157A>G	c.(157-159)Act>Gct	p.T53A		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	53										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						CCTTTGTAAGTCAACCAAAGA	0.597																																					p.T53A		Atlas-SNP	.											.	KIAA1210	171	.	0			c.A157G						.						47.0	51.0	50.0					X																	118284386		2000	4151	6151	SO:0001583	missense	57481	exon1			TGTAAGTCAACCA	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.157A>G	chrX.hg19:g.118284386T>C	ENSP00000384670:p.Thr53Ala	88.0	0.0		87.0	5.0	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	T	9.486	1.099506	0.20552	.	.	ENSG00000250423	ENST00000402510	T	0.11169	2.8	3.74	1.19	0.21007	.	.	.	.	.	T	0.03871	0.0109	N	0.08118	0	0.09310	N	1	P	0.40731	0.728	B	0.30105	0.111	T	0.35674	-0.9779	9	0.87932	D	0	.	3.5273	0.07763	0.2208:0.0:0.2583:0.521	.	53	Q9ULL0	K1210_HUMAN	A	53	ENSP00000384670:T53A	ENSP00000384670:T53A	T	-	1	0	RP13-347D8.6	118168414	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.164000	0.09983	0.117000	0.18138	0.486000	0.48141	ACT	.	.		0.597	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721	
ZDHHC9	51114	hgsc.bcm.edu	37	X	128975901	128975901	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:128975901T>C	ENST00000357166.6	-	3	412	c.21A>G	c.(19-21)agA>agG	p.R7R	ZDHHC9_ENST00000371064.3_Silent_p.R7R	NM_016032.3	NP_057116.2	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC-type containing 9	7					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|palmitoyltransferase complex (GO:0002178)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|Ras palmitoyltransferase activity (GO:0043849)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)	19						TCACCTTCTTTCTCACCACCA	0.498																																					p.R7R		Atlas-SNP	.											.	ZDHHC9	41	.	0			c.A21G						.						171.0	137.0	148.0					X																	128975901		2203	4300	6503	SO:0001819	synonymous_variant	51114	exon2			CTTCTTTCTCACC	AF151847	CCDS35395.1	Xq26.1	2008-02-05			ENSG00000188706	ENSG00000188706		"""Zinc fingers, DHHC-type"""	18475	protein-coding gene	gene with protein product		300646	"""zinc finger, DHHC-type containing 10"", ""chromosome X open reading frame 11"""	ZDHHC10, CXorf11		10810093	Standard	NM_001008222		Approved	ZNF379, CGI-89, ZNF380	uc004euw.3	Q9Y397	OTTHUMG00000022375	ENST00000357166.6:c.21A>G	chrX.hg19:g.128975901T>C		112.0	0.0		103.0	6.0	NM_001008222	B4F6G2|D3DTF9|Q59EK4|Q5JSW5|Q8WWS7|Q9BPY4|Q9NSP0|Q9NVL0|Q9NVR6	Silent	SNP	ENST00000357166.6	hg19	CCDS35395.1																																																																																			.	.		0.498	ZDHHC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058213.1	NM_016032	
CT55	54967	hgsc.bcm.edu	37	X	134292208	134292208	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:134292208T>C	ENST00000276241.6	-	4	679	c.453A>G	c.(451-453)ttA>ttG	p.L151L	CXorf48_ENST00000344129.2_Silent_p.L151L	NM_001031705.2	NP_001026875.1	Q8WUE5	CT55_HUMAN		151										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)	5	Acute lymphoblastic leukemia(192;0.000127)					ATTCAACTTCTAACAAGTCAC	0.383																																					p.L151L		Atlas-SNP	.											.	CXorf48	17	.	0			c.A453G						.						101.0	90.0	94.0					X																	134292208		2203	4300	6503	SO:0001819	synonymous_variant	54967	exon4			AACTTCTAACAAG																												ENST00000276241.6:c.453A>G	chrX.hg19:g.134292208T>C		97.0	0.0		98.0	4.0	NM_017863	Q9NWY8	Silent	SNP	ENST00000276241.6	hg19	CCDS35400.1																																																																																			.	.		0.383	CXorf48-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058404.1		
GPR112	139378	hgsc.bcm.edu	37	X	135430116	135430116	+	Silent	SNP	T	T	C			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:135430116T>C	ENST00000394143.1	+	6	4542	c.4251T>C	c.(4249-4251)gaT>gaC	p.D1417D	GPR112_ENST00000370652.1_Silent_p.D1417D|GPR112_ENST00000394141.1_Silent_p.D1212D|GPR112_ENST00000412101.1_Silent_p.D1212D|GPR112_ENST00000287534.4_Silent_p.D1354D	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1417					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CATTTGTAGATACCACAACTT	0.428																																					p.D1417D		Atlas-SNP	.											.	GPR112	459	.	0			c.T4251C						.						147.0	139.0	142.0					X																	135430116		2203	4300	6503	SO:0001819	synonymous_variant	139378	exon6			TGTAGATACCACA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4251T>C	chrX.hg19:g.135430116T>C		106.0	0.0		86.0	4.0	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	hg19	CCDS35409.1																																																																																			.	.		0.428	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
AFF2	2334	hgsc.bcm.edu	37	X	148069086	148069086	+	Splice_Site	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:148069086A>G	ENST00000370460.2	+	20	4292	c.3813A>G	c.(3811-3813)aaA>aaG	p.K1271K	AFF2_ENST00000342251.3_Splice_Site_p.K1238K|AFF2_ENST00000370457.5_Splice_Site_p.K1236K|AFF2_ENST00000286437.5_Splice_Site_p.K912K	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	1271					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)					GAGAAAACAAAGGTATGCTCA	0.453																																					p.K1271K		Atlas-SNP	.											.	AFF2	679	.	0			c.A3813G						.						158.0	122.0	134.0					X																	148069086		2203	4300	6503	SO:0001630	splice_region_variant	2334	exon20			AAACAAAGGTATG	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.3814+1A>G	chrX.hg19:g.148069086A>G		124.0	0.0		97.0	4.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	hg19	CCDS14684.1																																																																																			.	.		0.453	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	Silent
MTMR1	8776	hgsc.bcm.edu	37	X	149905886	149905886	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrX:149905886A>G	ENST00000370390.3	+	11	1572	c.1415A>G	c.(1414-1416)aAg>aGg	p.K472R	MTMR1_ENST00000451863.2_Missense_Mutation_p.K472R|MTMR1_ENST00000541925.1_Missense_Mutation_p.K378R|MTMR1_ENST00000445323.2_Missense_Mutation_p.K480R|MTMR1_ENST00000538506.1_Missense_Mutation_p.K297R|MTMR1_ENST00000544228.1_Missense_Mutation_p.K472R	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	472	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					CTCGTAGAAAAGGAGTGGATA	0.453																																					p.K472R		Atlas-SNP	.											.	MTMR1	82	.	0			c.A1415G						.						145.0	123.0	130.0					X																	149905886		2203	4300	6503	SO:0001583	missense	8776	exon11			TAGAAAAGGAGTG	U58032	CCDS14695.1	Xq28	2011-06-09			ENSG00000063601	ENSG00000063601		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7449	protein-coding gene	gene with protein product		300171				9828128	Standard	XM_005274765		Approved		uc004fei.3	Q13613	OTTHUMG00000024159	ENST00000370390.3:c.1415A>G	chrX.hg19:g.149905886A>G	ENSP00000359417:p.Lys472Arg	103.0	0.0		88.0	4.0	NM_003828	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Missense_Mutation	SNP	ENST00000370390.3	hg19	CCDS14695.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.332574	0.81801	.	.	ENSG00000063601	ENST00000541925;ENST00000370390;ENST00000445323;ENST00000544228;ENST00000451863;ENST00000538506	D;D;D;D;D;D	0.94376	-3.41;-3.41;-3.41;-3.41;-3.41;-3.41	4.88	4.88	0.63580	Myotubularin phosphatase domain (1);	0.000000	0.85682	D	0.000000	D	0.95915	0.8670	M	0.76574	2.34	0.53005	D	0.999966	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.989	D	0.95296	0.8399	10	0.41790	T	0.15	.	12.327	0.55018	1.0:0.0:0.0:0.0	.	472;480	Q13613;F8WA39	MTMR1_HUMAN;.	R	378;472;480;472;472;297	ENSP00000441879:K378R;ENSP00000359417:K472R;ENSP00000414178:K480R;ENSP00000440534:K472R;ENSP00000387446:K472R;ENSP00000443444:K297R	ENSP00000359417:K472R	K	+	2	0	MTMR1	149656544	1.000000	0.71417	0.999000	0.59377	0.945000	0.59286	9.339000	0.96797	1.619000	0.50296	0.441000	0.28932	AAG	.	.		0.453	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789	
MT-ND1	4535	hgsc.bcm.edu	37	M	3745	3745	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chrM:3745G>A	ENST00000361390.2	+	1	439	c.439G>A	c.(439-441)Gcc>Acc	p.A147T	MT-CO1_ENST00000361624.2_5'Flank|MT-RNR1_ENST00000389680.2_RNA|MT-TI_ENST00000387365.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-ND2_ENST00000361453.3_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TA_ENST00000387392.1_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	147					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	AAGTCACCCTAGCCATCATTC	0.453																																					p.A147T		Atlas-SNP	.											.	.	.	.	0			c.G439A						.																																			SO:0001583	missense	10625	exon1			ACCCTAGCCATCA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.439G>A	chrM.hg19:g.3745G>A	ENSP00000354687:p.Ala147Thr	179.0	0.0		244.0	15.0	ENST00000361390	C0JKH6|Q37523	Missense_Mutation	SNP	ENST00000361390.2	hg19																																																																																				.	.		0.453	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
LRRC8A	56262	hgsc.bcm.edu	37	9	131670854	131670855	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr9:131670854_131670855delCT	ENST00000259324.5	+	3	1934_1935	c.1411_1412delCT	c.(1411-1413)ctcfs	p.L471fs	LRRC8A_ENST00000372599.3_Frame_Shift_Del_p.L471fs|LRRC8A_ENST00000372600.4_Frame_Shift_Del_p.L471fs	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	471					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						GCTCACGGGCCTCAAGGAGCTG	0.629																																					p.470_471del		Atlas-INDEL	.											.	LRRC8A	69	.	0			c.1410_1411del						.																																			SO:0001589	frameshift_variant	56262	exon3			.	AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"""leucine rich repeat containing 8"""	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.1411_1412delCT	chr9.hg19:g.131670854_131670855delCT	ENSP00000259324:p.Leu471fs	68.0	0.0		40.0	11.0	NM_001127244	Q6UXM2|Q8NCI0|Q9P2B1	Frame_Shift_Del	DEL	ENST00000259324.5	hg19	CCDS35155.1																																																																																			.	.		0.629	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594	
NCAM1	4684	hgsc.bcm.edu	37	11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-DD-A119-01A-11D-A12Z-10	TCGA-DD-A119-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	754b7a64-4a00-4461-a2e6-938ef1365f5d	91043a26-f026-4f25-86a7-7c7ab718c95b	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				RP11-629G13.1_ENST00000500537.2_RNA|NCAM1_ENST00000397957.4_3'UTR|RP11-629G13.1_ENST00000532002.1_RNA	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		1.0	1.0		32.0	32.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615	
