#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
H6PD	9563	hgsc.bcm.edu	37	1	9305494	9305494	+	Nonsense_Mutation	SNP	G	G	A	rs559063919		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:9305494G>A	ENST00000377403.2	+	2	803	c.501G>A	c.(499-501)tgG>tgA	p.W167*	H6PD_ENST00000602477.1_Nonsense_Mutation_p.W178*	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	167	Glucose 1-dehydrogenase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		CGGGCGCCTGGCTGCGGGTTG	0.597																																					p.W167X		Atlas-SNP	.											.	H6PD	71	.	0			c.G501A						.						46.0	55.0	52.0					1																	9305494		2203	4300	6503	SO:0001587	stop_gained	9563	exon2			CGCCTGGCTGCGG	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"""glucose dehyrogenase"""	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.501G>A	chr1.hg19:g.9305494G>A	ENSP00000366620:p.Trp167*	30.0	0.0		42.0	20.0	NM_004285	Q4TT33|Q66I35|Q68DT3	Nonsense_Mutation	SNP	ENST00000377403.2	hg19	CCDS101.1	.	.	.	.	.	.	.	.	.	.	G	40	8.156138	0.98680	.	.	ENSG00000049239	ENST00000377403	.	.	.	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.7585	18.3309	0.90268	0.0:0.0:1.0:0.0	.	.	.	.	X	167	.	ENSP00000366620:W167X	W	+	3	0	H6PD	9228081	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.358000	0.97109	2.641000	0.89580	0.591000	0.81541	TGG	.	.		0.597	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
CLSTN1	22883	hgsc.bcm.edu	37	1	9795606	9795606	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:9795606G>T	ENST00000377298.4	-	13	2594	c.1802C>A	c.(1801-1803)gCc>gAc	p.A601D	CLSTN1_ENST00000361311.4_Missense_Mutation_p.A591D|CLSTN1_ENST00000477264.1_5'Flank|CLSTN1_ENST00000377288.3_Missense_Mutation_p.A582D	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	601					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		GTGCTGCATGGCCTTATCCAA	0.517																																					p.A601D		Atlas-SNP	.											.	CLSTN1	88	.	0			c.C1802A						.						164.0	154.0	157.0					1																	9795606		2203	4300	6503	SO:0001583	missense	22883	exon13			TGCATGGCCTTAT	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"""Cadherins / Cadherin-related"""	17447	protein-coding gene	gene with protein product	"""cadherin-related family member 12"""	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.1802C>A	chr1.hg19:g.9795606G>T	ENSP00000366513:p.Ala601Asp	98.0	0.0		215.0	92.0	NM_001009566	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Missense_Mutation	SNP	ENST00000377298.4	hg19	CCDS30580.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.354559	0.61293	.	.	ENSG00000171603	ENST00000377298;ENST00000361311;ENST00000435891;ENST00000377288;ENST00000539822	T;T;T;T	0.36520	1.25;1.25;1.25;1.25	5.91	5.91	0.95273	.	0.053126	0.85682	D	0.000000	T	0.63780	0.2540	M	0.78049	2.395	0.58432	D	0.999996	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.68943	0.914;0.961;0.914	T	0.64748	-0.6334	10	0.66056	D	0.02	-49.4122	20.2985	0.98592	0.0:0.0:1.0:0.0	.	582;591;601	B4E3Q1;O94985-2;O94985	.;.;CSTN1_HUMAN	D	601;591;402;582;582	ENSP00000366513:A601D;ENSP00000354997:A591D;ENSP00000401934:A402D;ENSP00000366502:A582D	ENSP00000354997:A591D	A	-	2	0	CLSTN1	9718193	1.000000	0.71417	0.994000	0.49952	0.089000	0.18198	4.609000	0.61148	2.793000	0.96121	0.655000	0.94253	GCC	.	.		0.517	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1		
IL12RB2	3595	hgsc.bcm.edu	37	1	67861669	67861669	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:67861669T>C	ENST00000262345.1	+	16	3126	c.2486T>C	c.(2485-2487)cTt>cCt	p.L829P	IL12RB2_ENST00000544434.1_Missense_Mutation_p.L743P|IL12RB2_ENST00000371000.1_3'UTR	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	829					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						CACATCTCCCTTTCTGTTTTC	0.512																																					p.L829P		Atlas-SNP	.											.	IL12RB2	94	.	0			c.T2486C						.						310.0	295.0	300.0					1																	67861669		2203	4300	6503	SO:0001583	missense	3595	exon16			TCTCCCTTTCTGT	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.2486T>C	chr1.hg19:g.67861669T>C	ENSP00000262345:p.Leu829Pro	130.0	0.0		335.0	124.0	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	hg19	CCDS638.1	.	.	.	.	.	.	.	.	.	.	T	12.93	2.085356	0.36758	.	.	ENSG00000081985	ENST00000262345;ENST00000544434	T;T	0.49139	0.79;1.71	5.29	4.15	0.48705	.	0.892298	0.09923	N	0.738230	T	0.16769	0.0403	L	0.27053	0.805	0.20196	N	0.999927	B;B	0.33637	0.42;0.028	B;B	0.29176	0.099;0.014	T	0.10132	-1.0643	10	0.66056	D	0.02	-6.8301	7.2723	0.26264	0.0:0.0981:0.0:0.9019	.	743;829	F5H7L6;Q99665	.;I12R2_HUMAN	P	829;743	ENSP00000262345:L829P;ENSP00000442443:L743P	ENSP00000262345:L829P	L	+	2	0	IL12RB2	67634257	0.013000	0.17824	0.012000	0.15200	0.388000	0.30384	2.086000	0.41643	2.135000	0.66039	0.482000	0.46254	CTT	.	.		0.512	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	
AMY2A	279	hgsc.bcm.edu	37	1	104160673	104160673	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:104160673G>C	ENST00000414303.2	+	2	330	c.266G>C	c.(265-267)gGa>gCa	p.G89A		NM_000699.2	NP_000690.1	P04746	AMYP_HUMAN	amylase, alpha 2A (pancreatic)	89					carbohydrate catabolic process (GO:0016052)|carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|calcium ion binding (GO:0005509)|chloride ion binding (GO:0031404)			endometrium(3)|kidney(1)|large_intestine(5)|liver(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)	Acarbose(DB00284)|Icodextrin(DB00702)|Miglitol(DB00491)	ACAAGATCTGGAAATGAAGAT	0.353																																					p.G89A		Atlas-SNP	.											.	AMY2A	36	.	0			c.G266C						.						131.0	122.0	125.0					1																	104160673		2201	4275	6476	SO:0001583	missense	279	exon2			GATCTGGAAATGA	BC007060	CCDS783.1	1p21.1	2012-10-02	2007-05-03		ENSG00000243480	ENSG00000243480	3.2.1.1		477	protein-coding gene	gene with protein product		104650	"""amylase, alpha 2A; pancreatic"""	AMY2		3260028	Standard	NM_000699		Approved		uc001dut.3	P04746	OTTHUMG00000011023	ENST00000414303.2:c.266G>C	chr1.hg19:g.104160673G>C	ENSP00000397582:p.Gly89Ala	189.0	0.0		1043.0	374.0	NM_000699	B9EJG1|Q9UBH3	Missense_Mutation	SNP	ENST00000414303.2	hg19	CCDS783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	20.8|20.8	4.045045|4.045045	0.75846|0.75846	.|.	.|.	ENSG00000243480|ENSG00000243480	ENST00000414303;ENST00000393932|ENST00000423678	D|.	0.99929|.	-8.14|.	3.47|3.47	3.47|3.47	0.39725|0.39725	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87728|0.87728	0.6250|0.6250	H|H	0.99104|0.99104	4.43|4.43	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|D	0.92796|0.92796	0.6252|0.6252	10|5	0.87932|.	D|.	0|.	.|.	15.0729|15.0729	0.72053|0.72053	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	89;89|.	B9EJG1;P04746|.	.;AMYP_HUMAN|.	A|C	89|87	ENSP00000397582:G89A|.	ENSP00000377509:G89A|.	G|W	+|+	2|3	0|0	AMY2A|AMY2A	103962196|103962196	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.163000|9.163000	0.94750|0.94750	1.927000|1.927000	0.55829|0.55829	0.455000|0.455000	0.32223|0.32223	GGA|TGG	.	.		0.353	AMY2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030315.1	NM_000699	
FNDC7	163479	hgsc.bcm.edu	37	1	109270564	109270564	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:109270564G>A	ENST00000370017.3	+	7	1523	c.1246G>A	c.(1246-1248)Gac>Aac	p.D416N	FNDC7_ENST00000271311.2_Missense_Mutation_p.D417N	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	416	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		TGAGTGCAATGACACTACTCC	0.488																																					p.D416N		Atlas-SNP	.											.	FNDC7	113	.	0			c.G1246A						.						288.0	244.0	259.0					1																	109270564		2203	4300	6503	SO:0001583	missense	163479	exon7			TGCAATGACACTA		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"""Fibronectin type III domain containing"""	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.1246G>A	chr1.hg19:g.109270564G>A	ENSP00000359034:p.Asp416Asn	96.0	0.0		200.0	91.0	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	hg19	CCDS44185.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.933047	0.92458	.	.	ENSG00000143107	ENST00000370017;ENST00000271311	T;T	0.23950	1.88;1.88	5.73	5.73	0.89815	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.041024	0.85682	D	0.000000	T	0.41073	0.1143	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.03875	-1.0996	10	0.19147	T	0.46	-16.3329	19.9068	0.97010	0.0:0.0:1.0:0.0	.	417;416	Q5VTL7;E9PAZ5	FNDC7_HUMAN;.	N	416;417	ENSP00000359034:D416N;ENSP00000271311:D417N	ENSP00000271311:D417N	D	+	1	0	FNDC7	109072087	1.000000	0.71417	1.000000	0.80357	0.619000	0.37552	9.068000	0.93961	2.710000	0.92621	0.561000	0.74099	GAC	.	.		0.488	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
ATP1A1	476	hgsc.bcm.edu	37	1	116933025	116933025	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:116933025A>C	ENST00000295598.5	+	9	1466	c.1214A>C	c.(1213-1215)aAt>aCt	p.N405T	ATP1A1_ENST00000369496.4_Missense_Mutation_p.N374T|ATP1A1_ENST00000537345.1_Missense_Mutation_p.N405T	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	405					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	ACGACAGAGAATCAGAGTGGT	0.423																																					p.N405T		Atlas-SNP	.											.	ATP1A1	87	.	0			c.A1214C						.						59.0	58.0	58.0					1																	116933025		2203	4300	6503	SO:0001583	missense	476	exon9			CAGAGAATCAGAG	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"""ATPases / P-type"""	799	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-1"", ""sodium pump subunit alpha-1"", ""sodium-potassium ATPase catalytic subunit alpha-1"""	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.1214A>C	chr1.hg19:g.116933025A>C	ENSP00000295598:p.Asn405Thr	88.0	0.0		191.0	66.0	NM_001160233	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	hg19	CCDS887.1	.	.	.	.	.	.	.	.	.	.	A	18.43	3.622723	0.66787	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000339159;ENST00000369496	T;T;T	0.78816	-1.21;-1.21;-1.21	4.87	4.87	0.63330	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	T	0.59252	0.2180	N	0.20881	0.62	0.80722	D	1	B;B	0.14805	0.009;0.011	B;B	0.33960	0.108;0.173	T	0.61753	-0.6998	10	0.45353	T	0.12	.	14.6423	0.68734	1.0:0.0:0.0:0.0	.	405;405	F5H3A1;P05023	.;AT1A1_HUMAN	T	405;405;404;374	ENSP00000295598:N405T;ENSP00000445306:N405T;ENSP00000358508:N374T	ENSP00000295598:N405T	N	+	2	0	ATP1A1	116734548	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.126000	0.94411	2.068000	0.61886	0.528000	0.53228	AAT	.	.		0.423	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233	
NBPF10	100132406	hgsc.bcm.edu	37	1	145367777	145367777	+	Missense_Mutation	SNP	G	G	T	rs200743139		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	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	6.0	2.0		24.0	10.0	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	
TRIM46	80128	hgsc.bcm.edu	37	1	155151089	155151089	+	Splice_Site	SNP	G	G	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:155151089G>T	ENST00000334634.4	+	7	1285	c.1285G>T	c.(1285-1287)Gtg>Ttg	p.V429L	TRIM46_ENST00000368382.1_Splice_Site_p.V406L|TRIM46_ENST00000392451.2_Splice_Site_p.G429C|TRIM46_ENST00000468878.1_3'UTR|TRIM46_ENST00000368383.3_Splice_Site_p.V429L|TRIM46_ENST00000545012.1_Splice_Site_p.V303L|TRIM46_ENST00000543729.1_Splice_Site_p.G436C|TRIM46_ENST00000368385.4_Splice_Site_p.V429L|RP11-201K10.3_ENST00000473363.2_Intron	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	429	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CTTCCTGCGAGGTAAGGAGAT	0.657																																					p.V429L		Atlas-SNP	.											.	TRIM46	79	.	0			c.G1285T						.						77.0	69.0	72.0					1																	155151089		2203	4300	6503	SO:0001630	splice_region_variant	80128	exon7			CTGCGAGGTAAGG		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19019	protein-coding gene	gene with protein product		600986	"""tripartite motif-containing 46"""				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.1285+1G>T	chr1.hg19:g.155151089G>T		22.0	0.0		81.0	19.0	NM_025058	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Missense_Mutation	SNP	ENST00000334634.4	hg19	CCDS1097.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.82|13.82	2.351221|2.351221	0.41700|0.41700	.|.	.|.	ENSG00000163462|ENSG00000163462	ENST00000543729;ENST00000392451|ENST00000430513;ENST00000368385;ENST00000545012;ENST00000368383;ENST00000368382;ENST00000334634	T;T|T;T;T;T;T	0.50548|0.43294	0.8;0.74|0.95;0.95;0.95;0.95;0.95	3.51|3.51	3.51|3.51	0.40186|0.40186	.|Fibronectin, type III (1);	.|0.168925	.|0.37955	.|U	.|0.001863	T|T	0.11367|0.11367	0.0277|0.0277	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|B;B;B;P	.|0.37500	.|0.329;0.143;0.176;0.597	.|B;B;B;B	.|0.34779	.|0.148;0.039;0.096;0.189	T|T	0.08106|0.08106	-1.0738|-1.0738	7|10	0.72032|0.51188	D|T	0.01|0.08	.|.	10.7031|10.7031	0.45939|0.45939	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|429;406;429;429	.|Q5VT61;B1AVQ4;Q7Z4K8;Q7Z4K8-2	.|.;.;TRI46_HUMAN;.	C|L	436;429|387;429;303;429;406;429	ENSP00000442719:G436C;ENSP00000376245:G429C|ENSP00000357369:V429L;ENSP00000440254:V303L;ENSP00000357367:V429L;ENSP00000357366:V406L;ENSP00000334657:V429L	ENSP00000376245:G429C|ENSP00000334657:V429L	G|V	+|+	1|1	0|0	TRIM46|TRIM46	153417713|153417713	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.944000|0.944000	0.59088|0.59088	6.194000|6.194000	0.72082|0.72082	1.952000|1.952000	0.56665|0.56665	0.313000|0.313000	0.20887|0.20887	GGC|GTG	.	.		0.657	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058	Missense_Mutation
KCNT2	343450	hgsc.bcm.edu	37	1	196309631	196309631	+	Silent	SNP	T	T	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:196309631T>C	ENST00000294725.9	-	16	2538	c.1623A>G	c.(1621-1623)cgA>cgG	p.R541R	KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000367431.4_Silent_p.R491R|KCNT2_ENST00000451324.2_Silent_p.R152R|KCNT2_ENST00000367433.5_Silent_p.R541R|KCNT2_ENST00000609185.1_Silent_p.R491R			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	541	RCK N-terminal.				potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						TCATAATGTATCGAGGACCTG	0.328																																					p.R541R		Atlas-SNP	.											.	KCNT2	243	.	0			c.A1623G						.						73.0	73.0	73.0					1																	196309631		2203	4299	6502	SO:0001819	synonymous_variant	343450	exon16			AATGTATCGAGGA	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18866	protein-coding gene	gene with protein product	"""sodium and chloride activated ATP sensitive potassium channel"""	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.1623A>G	chr1.hg19:g.196309631T>C		70.0	0.0		199.0	42.0	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Silent	SNP	ENST00000294725.9	hg19	CCDS1384.1																																																																																			.	.		0.328	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503	
DDX59	83479	hgsc.bcm.edu	37	1	200635118	200635118	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:200635118A>T	ENST00000331314.6	-	2	964	c.751T>A	c.(751-753)Tca>Aca	p.S251T	DDX59_ENST00000447706.2_Missense_Mutation_p.S251T|DDX59_ENST00000367348.3_Missense_Mutation_p.S251T	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	251	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						GTTTTTCCTGAGCCAGTATCT	0.418																																					p.S251T		Atlas-SNP	.											.	DDX59	117	.	0			c.T751A						.						90.0	90.0	90.0					1																	200635118		2203	4300	6503	SO:0001583	missense	83479	exon2			TTCCTGAGCCAGT	BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197		"""Zinc fingers, HIT-type"", ""DEAD-boxes"""	25360	protein-coding gene	gene with protein product		615464					Standard	NM_001031725		Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000331314.6:c.751T>A	chr1.hg19:g.200635118A>T	ENSP00000330460:p.Ser251Thr	114.0	0.0		442.0	102.0	NM_001031725	Q6PJL2|Q8IVW3|Q9H0W3	Missense_Mutation	SNP	ENST00000331314.6	hg19	CCDS30964.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.724387	0.89298	.	.	ENSG00000118197	ENST00000447706;ENST00000367348;ENST00000331314	T;T;T	0.51574	0.7;0.7;0.7	5.33	5.33	0.75918	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.56217	0.1970	L	0.27944	0.81	0.80722	D	1	D;D	0.65815	0.995;0.995	D;D	0.71656	0.974;0.974	T	0.61491	-0.7052	10	0.87932	D	0	-18.7333	15.3466	0.74343	1.0:0.0:0.0:0.0	.	251;251	B7Z5N6;Q5T1V6	.;DDX59_HUMAN	T	251	ENSP00000394367:S251T;ENSP00000356317:S251T;ENSP00000330460:S251T	ENSP00000330460:S251T	S	-	1	0	DDX59	198901741	1.000000	0.71417	0.990000	0.47175	0.976000	0.68499	9.320000	0.96346	2.021000	0.59480	0.529000	0.55759	TCA	.	.		0.418	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086883.2	NM_001031725.4	
DYRK3	8444	hgsc.bcm.edu	37	1	206820946	206820946	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:206820946G>T	ENST00000367109.2	+	3	571	c.403G>T	c.(403-405)Gca>Tca	p.A135S	DYRK3_ENST00000367106.1_Missense_Mutation_p.A115S|DYRK3_ENST00000489878.1_Intron|DYRK3_ENST00000367108.3_Missense_Mutation_p.A115S	NM_003582.2	NP_003573.2	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	135					erythrocyte differentiation (GO:0030218)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2)	25	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			TTCATCCAAGGCACCCAAAGT	0.413																																					p.A135S	Melanoma(164;427 2622 26826 51707)	Atlas-SNP	.											.	DYRK3	146	.	0			c.G403T						.						79.0	79.0	79.0					1																	206820946		2203	4300	6503	SO:0001583	missense	8444	exon3			TCCAAGGCACCCA	Y12735	CCDS30999.1, CCDS31000.1	1q32	2008-07-18			ENSG00000143479	ENSG00000143479	2.7.12.1		3094	protein-coding gene	gene with protein product	"""regulatory erythroid kinase"", ""dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 5"", ""protein kinase Dyrk3"""	603497				9748265	Standard	NM_003582		Approved	RED, REDK, hYAK3-2	uc001hej.3	O43781	OTTHUMG00000036339	ENST00000367109.2:c.403G>T	chr1.hg19:g.206820946G>T	ENSP00000356076:p.Ala135Ser	79.0	0.0		287.0	177.0	NM_003582	D3DT79|Q7Z752|Q9HBY6|Q9HBY7	Missense_Mutation	SNP	ENST00000367109.2	hg19	CCDS30999.1	.	.	.	.	.	.	.	.	.	.	G	0.108	-1.142325	0.01728	.	.	ENSG00000143479	ENST00000367109;ENST00000367108;ENST00000441486;ENST00000367106	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	5.09	0.837	0.18896	.	0.946011	0.09044	N	0.856863	T	0.20618	0.0496	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.23190	-1.0195	10	0.12430	T	0.62	.	1.6353	0.02740	0.1512:0.1642:0.3442:0.3405	.	135;115	O43781;O43781-2	DYRK3_HUMAN;.	S	135;115;115;115	ENSP00000356076:A135S;ENSP00000356075:A115S;ENSP00000410187:A115S;ENSP00000356073:A115S	ENSP00000356073:A115S	A	+	1	0	DYRK3	204887569	0.007000	0.16637	0.004000	0.12327	0.759000	0.43091	-0.275000	0.08525	-0.005000	0.14395	0.579000	0.79373	GCA	.	.		0.413	DYRK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088458.1	NM_003582	
CHRM3	1131	hgsc.bcm.edu	37	1	240071370	240071370	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:240071370T>A	ENST00000255380.4	+	5	1398	c.619T>A	c.(619-621)Tgg>Agg	p.W207R		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	207					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CATCTTGTTCTGGCAATACTT	0.517																																					p.W207R		Atlas-SNP	.											.	CHRM3	118	.	0			c.T619A						.						186.0	191.0	189.0					1																	240071370		2203	4300	6503	SO:0001583	missense	1131	exon5			TTGTTCTGGCAAT	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1952	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 3"""	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.619T>A	chr1.hg19:g.240071370T>A	ENSP00000255380:p.Trp207Arg	124.0	0.0		570.0	352.0	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	hg19	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.892572	0.72524	.	.	ENSG00000133019	ENST00000255380	T	0.37915	1.17	5.79	5.79	0.91817	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.61776	0.2374	M	0.73753	2.245	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.65853	-0.6067	10	0.87932	D	0	-8.7528	16.1388	0.81509	0.0:0.0:0.0:1.0	.	207	P20309	ACM3_HUMAN	R	207	ENSP00000255380:W207R	ENSP00000255380:W207R	W	+	1	0	CHRM3	238137993	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.040000	0.89188	2.205000	0.71048	0.528000	0.53228	TGG	.	.		0.517	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740	
ZNF672	79894	hgsc.bcm.edu	37	1	249142604	249142604	+	Silent	SNP	C	C	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr1:249142604C>T	ENST00000306562.3	+	4	1877	c.1131C>T	c.(1129-1131)agC>agT	p.S377S		NM_024836.1	NP_079112.1	Q499Z4	ZN672_HUMAN	zinc finger protein 672	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(2)|kidney(2)|large_intestine(1)	5	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			AGGCCTTCAGCGTCGCCTCCA	0.647																																					p.S377S		Atlas-SNP	.											.	ZNF672	32	.	0			c.C1131T						.						40.0	37.0	38.0					1																	249142604		2201	4300	6501	SO:0001819	synonymous_variant	79894	exon4			CTTCAGCGTCGCC	AK027476	CCDS1638.1	1q44	2013-01-08			ENSG00000171161	ENSG00000171161		"""Zinc fingers, C2H2-type"""	26179	protein-coding gene	gene with protein product	"""hypothetical protein FLJ22301"""					12477932	Standard	NM_024836		Approved	FLJ22301	uc001iex.3	Q499Z4	OTTHUMG00000040377	ENST00000306562.3:c.1131C>T	chr1.hg19:g.249142604C>T		5.0	0.0		30.0	18.0	NM_024836	Q96H65|Q96IM3|Q9H6G5	Silent	SNP	ENST00000306562.3	hg19	CCDS1638.1																																																																																			.	.		0.647	ZNF672-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097125.2	NM_024836	
APOB	338	hgsc.bcm.edu	37	2	21231053	21231053	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr2:21231053G>A	ENST00000233242.1	-	26	8814	c.8687C>T	c.(8686-8688)cCc>cTc	p.P2896L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2896					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTCCAGTTTGGGGATGTTCAA	0.433																																					p.P2896L		Atlas-SNP	.											.	APOB	761	.	0			c.C8687T						.						176.0	173.0	174.0					2																	21231053		2203	4299	6502	SO:0001583	missense	338	exon26			AGTTTGGGGATGT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8687C>T	chr2.hg19:g.21231053G>A	ENSP00000233242:p.Pro2896Leu	110.0	0.0		232.0	100.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.677007	0.88445	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01527	4.8	5.73	5.73	0.89815	.	0.000000	0.51477	D	0.000088	T	0.11623	0.0283	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00061	-1.2161	10	0.87932	D	0	.	19.5098	0.95137	0.0:0.0:1.0:0.0	.	2896	P04114	APOB_HUMAN	L	2896	ENSP00000233242:P2896L	ENSP00000233242:P2896L	P	-	2	0	APOB	21084558	1.000000	0.71417	0.975000	0.42487	0.996000	0.88848	9.803000	0.99136	2.707000	0.92482	0.555000	0.69702	CCC	.	.		0.433	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
MEIS1	4211	hgsc.bcm.edu	37	2	66667100	66667100	+	Missense_Mutation	SNP	C	C	A	rs561384504		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr2:66667100C>A	ENST00000272369.9	+	3	822	c.365C>A	c.(364-366)gCc>gAc	p.A122D	MEIS1-AS1_ENST00000454595.1_RNA|MEIS1_ENST00000488550.1_Missense_Mutation_p.A122D|MEIS1_ENST00000495021.2_Missense_Mutation_p.A57D|MEIS1_ENST00000398506.2_Missense_Mutation_p.A120D|MEIS1-AS2_ENST00000439433.1_RNA|MEIS1_ENST00000444274.2_Missense_Mutation_p.A90D|MEIS1_ENST00000407092.2_Missense_Mutation_p.A122D|MEIS1_ENST00000560281.2_Missense_Mutation_p.A122D	NM_002398.2	NP_002389.1	O00470	MEIS1_HUMAN	Meis homeobox 1	122					angiogenesis (GO:0001525)|definitive hemopoiesis (GO:0060216)|lens morphogenesis in camera-type eye (GO:0002089)|megakaryocyte development (GO:0035855)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron differentiation (GO:0045665)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	24						GAAGATATAGCCGTGTTCGCC	0.532																																					p.A122D		Atlas-SNP	.											.	MEIS1	52	.	0			c.C365A						.						40.0	38.0	38.0					2																	66667100		1836	4082	5918	SO:0001583	missense	4211	exon3			ATATAGCCGTGTT		CCDS46309.1	2p14	2011-06-20	2007-02-15		ENSG00000143995	ENSG00000143995		"""Homeoboxes / TALE class"""	7000	protein-coding gene	gene with protein product		601739	"""Meis1 (mouse) homolog"", ""Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)"""			7565694	Standard	NM_002398		Approved		uc002sdu.3	O00470	OTTHUMG00000150714	ENST00000272369.9:c.365C>A	chr2.hg19:g.66667100C>A	ENSP00000272369:p.Ala122Asp	45.0	0.0		87.0	26.0	NM_002398	A8MV50	Missense_Mutation	SNP	ENST00000272369.9	hg19	CCDS46309.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.650991	0.67472	.	.	ENSG00000143995	ENST00000272369;ENST00000407092;ENST00000398506;ENST00000444274;ENST00000495021	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.49253	0.1546	L	0.49571	1.57	0.80722	D	1	B;D;P;D	0.63046	0.016;0.992;0.895;0.984	B;D;P;D	0.65140	0.017;0.932;0.652;0.917	T	0.26950	-1.0088	9	.	.	.	.	18.7057	0.91637	0.0:1.0:0.0:0.0	.	57;120;122;122	F5GYS8;O00470-2;O00470;F8W8U3	.;.;MEIS1_HUMAN;.	D	122;122;120;90;57	ENSP00000272369:A122D;ENSP00000384461:A122D;ENSP00000381518:A120D;ENSP00000403206:A90D;ENSP00000440571:A57D	.	A	+	2	0	MEIS1	66520604	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.623000	0.83113	2.735000	0.93741	0.655000	0.94253	GCC	.	.		0.532	MEIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319725.4	NM_002398	
CNOT11	55571	hgsc.bcm.edu	37	2	101885756	101885756	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr2:101885756A>T	ENST00000289382.3	+	7	1577	c.1414A>T	c.(1414-1416)Ata>Tta	p.I472L	RNF149_ENST00000485752.1_5'Flank	NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11	472					cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)											GGATTTGTTTATAGAAGTGCA	0.383																																					p.I472L		Atlas-SNP	.											.	.	.	.	0			c.A1414T						.						87.0	90.0	89.0					2																	101885756		2203	4300	6503	SO:0001583	missense	55571	exon7			TTGTTTATAGAAG	AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 29"""	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686	ENST00000289382.3:c.1414A>T	chr2.hg19:g.101885756A>T	ENSP00000289382:p.Ile472Leu	94.0	0.0		188.0	74.0	NM_017546	Q6P2M9|Q8N681	Missense_Mutation	SNP	ENST00000289382.3	hg19	CCDS2050.1	.	.	.	.	.	.	.	.	.	.	A	34	5.383985	0.95967	.	.	ENSG00000158435	ENST00000289382	.	.	.	5.96	5.96	0.96718	.	0.087263	0.85682	D	0.000000	D	0.84234	0.5427	M	0.88310	2.945	0.80722	D	1	D	0.67145	0.996	D	0.68353	0.957	D	0.87008	0.2121	9	0.66056	D	0.02	-26.6738	16.4484	0.83959	1.0:0.0:0.0:0.0	.	472	Q9UKZ1	CB029_HUMAN	L	472	.	ENSP00000289382:I472L	I	+	1	0	C2orf29	101252188	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.210000	0.95106	2.285000	0.76669	0.533000	0.62120	ATA	.	.		0.383	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1	NM_017546	
CAB39	51719	hgsc.bcm.edu	37	2	231624746	231624746	+	Silent	SNP	A	A	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr2:231624746A>G	ENST00000258418.5	+	2	459	c.30A>G	c.(28-30)aaA>aaG	p.K10K	CAB39_ENST00000410084.3_Silent_p.K10K|CAB39_ENST00000409788.3_Silent_p.K10K	NM_016289.3	NP_057373.1	Q9Y376	CAB39_HUMAN	calcium binding protein 39	10					activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cellular hypotonic response (GO:0071476)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein heterooligomerization (GO:0051291)|signal transduction by phosphorylation (GO:0023014)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activator activity (GO:0043539)			central_nervous_system(1)|large_intestine(1)|skin(1)	3		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)		AGTCTCACAAATCTCCAGCAG	0.498																																					p.K10K		Atlas-SNP	.											.	CAB39	30	.	0			c.A30G						.						89.0	92.0	91.0					2																	231624746		2203	4300	6503	SO:0001819	synonymous_variant	51719	exon2			TCACAAATCTCCA	AF113536	CCDS2478.1	2q37.1	2008-02-05			ENSG00000135932	ENSG00000135932			20292	protein-coding gene	gene with protein product		612174					Standard	NM_016289		Approved	CGI-66, MO25	uc002vqx.3	Q9Y376	OTTHUMG00000133220	ENST00000258418.5:c.30A>G	chr2.hg19:g.231624746A>G		100.0	0.0		267.0	114.0	NM_001130849	A8K8L7	Silent	SNP	ENST00000258418.5	hg19	CCDS2478.1																																																																																			.	.		0.498	CAB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256955.2	NM_016289	
ATP2B2	491	hgsc.bcm.edu	37	3	10443888	10443888	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:10443888C>A	ENST00000352432.4	-	3	611	c.542G>T	c.(541-543)gGc>gTc	p.G181V	ATP2B2_ENST00000397077.1_Missense_Mutation_p.G181V|ATP2B2_ENST00000383800.4_Missense_Mutation_p.G181V|ATP2B2_ENST00000360273.2_Missense_Mutation_p.G181V|ATP2B2_ENST00000343816.4_Missense_Mutation_p.G181V			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	181					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						GCTCTGCAGGCCCCGGAACTG	0.592																																					p.G181V	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.G542T						.						131.0	142.0	138.0					3																	10443888		2203	4300	6503	SO:0001583	missense	491	exon4			TGCAGGCCCCGGA	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"""ATPases / P-type"""	815	protein-coding gene	gene with protein product	"""plasma membrane Ca2+ pump 2"", ""plasma membrane calcium-transporting ATPase 2"""	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.542G>T	chr3.hg19:g.10443888C>A	ENSP00000324172:p.Gly181Val	45.0	0.0		95.0	40.0	NM_001683	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.013607	0.93404	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4;-2.4	5.44	5.44	0.79542	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.92935	0.7752	L	0.47078	1.49	0.80722	D	1	D;D;P	0.89917	1.0;0.991;0.946	D;D;P	0.97110	1.0;0.937;0.672	D	0.93482	0.6828	10	0.87932	D	0	-36.5231	19.2768	0.94034	0.0:1.0:0.0:0.0	.	181;193;181	Q01814-7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	V	181;181;181;181;181;147;68;181	ENSP00000324172:G181V;ENSP00000373311:G181V;ENSP00000380267:G181V;ENSP00000353414:G181V;ENSP00000344677:G181V;ENSP00000414854:G68V	ENSP00000342954:G181V	G	-	2	0	ATP2B2	10418888	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.550000	0.86006	0.467000	0.42956	GGC	.	.		0.592	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	
DAZL	1618	hgsc.bcm.edu	37	3	16639045	16639045	+	Silent	SNP	A	A	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:16639045A>G	ENST00000399444.2	-	4	539	c.246T>C	c.(244-246)taT>taC	p.Y82Y	DAZL_ENST00000250863.8_Silent_p.Y102Y	NM_001351.3	NP_001342.2	Q92904	DAZL_HUMAN	deleted in azoospermia-like	82	Homodimerization. {ECO:0000250}.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				female meiosis II (GO:0007147)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|oocyte maturation (GO:0001556)|positive regulation of meiosis (GO:0045836)|positive regulation of translational initiation (GO:0045948)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|translation activator activity (GO:0008494)		RAF1/DAZL(2)	endometrium(1)|large_intestine(3)|lung(4)|prostate(3)	11						AAACAAATCCATAGCTATAAA	0.289																																					p.Y102Y		Atlas-SNP	.											.	DAZL	23	.	0			c.T306C						.						215.0	175.0	187.0					3																	16639045		1829	4082	5911	SO:0001819	synonymous_variant	1618	exon4			AAATCCATAGCTA	BC027595	CCDS43059.1, CCDS54556.1	3p24	2013-02-12			ENSG00000092345	ENSG00000092345		"""RNA binding motif (RRM) containing"""	2685	protein-coding gene	gene with protein product		601486		DAZLA		8896558	Standard	NM_001351		Approved	DAZH, SPGYLA, MGC26406, DAZL1	uc003cbb.3	Q92904	OTTHUMG00000157050	ENST00000399444.2:c.246T>C	chr3.hg19:g.16639045A>G		112.0	0.0		198.0	68.0	NM_001190811	O15396|Q5HYB4|Q92909	Silent	SNP	ENST00000399444.2	hg19	CCDS43059.1																																																																																			.	.		0.289	DAZL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347261.2	NM_001351	
PBRM1	55193	hgsc.bcm.edu	37	3	52662939	52662939	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:52662939G>A	ENST00000296302.7	-	12	1415	c.1414C>T	c.(1414-1416)Cga>Tga	p.R472*	PBRM1_ENST00000409767.1_Nonsense_Mutation_p.R472*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.R472*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.R472*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.R440*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.R472*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.R472*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.R472*			Q86U86	PB1_HUMAN	polybromo 1	472					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTTAGAACTCGCTTGTAGATG	0.318			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																p.R472X		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.C1414T						.						101.0	95.0	97.0					3																	52662939		2203	4300	6503	SO:0001587	stop_gained	55193	exon13			GAACTCGCTTGTA	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1414C>T	chr3.hg19:g.52662939G>A	ENSP00000296302:p.Arg472*	79.0	0.0		104.0	60.0	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	G	37	6.182101	0.97352	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	5.4	1.45	0.22620	.	0.136047	0.50627	D	0.000116	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-21.0362	11.5495	0.50713	0.0:0.1018:0.3723:0.5259	.	.	.	.	X	440;472;472;472;472;472;472;472;472;416	.	ENSP00000296302:R472X	R	-	1	2	PBRM1	52637979	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	2.206000	0.42779	-0.016000	0.14127	-0.309000	0.09137	CGA	.	.		0.318	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
MCM2	4171	hgsc.bcm.edu	37	3	127323584	127323585	+	Missense_Mutation	DNP	GC	GC	AT			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:127323584_127323585GC>AT	ENST00000265056.7	+	3	614_615	c.370_371GC>AT	c.(370-372)GCt>ATt	p.A124I		NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	124	Interaction with KAT7. {ECO:0000250}.				cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						TGACCGGGAGGCTGGCCGGGGC	0.683																																					p.A124T|p.A124V		Atlas-SNP	.											.	MCM2	79	.	0			c.G370A|c.C371T						.																																			SO:0001583	missense	4171	exon3			CGGGAGGCTGGCC|GGGAGGCTGGCCG	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"""mitotin"""	116945	"""minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)"", ""MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"""	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	Exception_encountered	chr3.hg19:g.127323584_127323585delinsAT	ENSP00000265056:p.Ala124Ile	8.0|6.0	0.0		51.0	20.0|21.0	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Missense_Mutation	SNP	ENST00000265056.7	hg19	CCDS3043.1																																																																																			.	.		0.683	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1		
MCM2	4171	hgsc.bcm.edu	37	3	127323589	127323589	+	Silent	SNP	C	C	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:127323589C>A	ENST00000265056.7	+	3	619	c.375C>A	c.(373-375)ggC>ggA	p.G125G		NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	125	Interaction with KAT7. {ECO:0000250}.				cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						GGGAGGCTGGCCGGGGCCTGG	0.682																																					p.G125G		Atlas-SNP	.											.	MCM2	79	.	0			c.C375A						.						15.0	18.0	17.0					3																	127323589		2196	4293	6489	SO:0001819	synonymous_variant	4171	exon3			GGCTGGCCGGGGC	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"""mitotin"""	116945	"""minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)"", ""MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"""	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.375C>A	chr3.hg19:g.127323589C>A		8.0	0.0		55.0	21.0	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Silent	SNP	ENST00000265056.7	hg19	CCDS3043.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.329669	0.24167	.	.	ENSG00000073111	ENST00000539922	.	.	.	5.29	3.48	0.39840	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.167	0.03840	0.1366:0.4895:0.1999:0.174	.	.	.	.	.	-1	.	.	.	+	.	.	MCM2	128806279	0.993000	0.37304	1.000000	0.80357	0.873000	0.50193	0.310000	0.19356	1.224000	0.43551	0.591000	0.81541	.	.	.		0.682	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1		
COL6A5	256076	hgsc.bcm.edu	37	3	130113755	130113755	+	Silent	SNP	C	C	T	rs541531354		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:130113755C>T	ENST00000432398.2	+	8	3509	c.3015C>T	c.(3013-3015)gaC>gaT	p.D1005D	COL6A5_ENST00000265379.6_Silent_p.D1005D	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1005	Nonhelical region.|VWFA 6. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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						AGGAAGCTGACGTGATTTTCC	0.333																																					p.D1005D		Atlas-SNP	.											.	COL6A5	205	.	0			c.C3015T						.						72.0	58.0	62.0					3																	130113755		692	1591	2283	SO:0001819	synonymous_variant	256076	exon8			AGCTGACGTGATT	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.3015C>T	chr3.hg19:g.130113755C>T		73.0	0.0		124.0	47.0	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	hg19																																																																																				.	.		0.333	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
MRPS22	56945	hgsc.bcm.edu	37	3	139062911	139062911	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:139062911A>T	ENST00000495075.1	+	3	475	c.43A>T	c.(43-45)Agg>Tgg	p.R15W	MRPS22_ENST00000310776.4_Missense_Mutation_p.R15W|MRPS22_ENST00000465056.1_Missense_Mutation_p.R15W|MRPS22_ENST00000478464.1_5'Flank			P82650	RT22_HUMAN	mitochondrial ribosomal protein S22	15						mitochondrial ribosome (GO:0005761)|mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	12						GAGCCTCTTGAGGAGTTCTCC	0.602																																					p.R15W		Atlas-SNP	.											.	MRPS22	40	.	0			c.A43T						.						51.0	51.0	51.0					3																	139062911		2203	4300	6503	SO:0001583	missense	56945	exon1			CTCTTGAGGAGTT	AF226045	CCDS3107.1	3q23	2012-09-13			ENSG00000175110	ENSG00000175110		"""Mitochondrial ribosomal proteins / small subunits"""	14508	protein-coding gene	gene with protein product		605810				11175783	Standard	NM_020191		Approved	MRP-S22, GK002, C3orf5, GIBT	uc003etb.3	P82650	OTTHUMG00000159910	ENST00000495075.1:c.43A>T	chr3.hg19:g.139062911A>T	ENSP00000418008:p.Arg15Trp	26.0	0.0		64.0	18.0	NM_020191	Q9H3I1	Missense_Mutation	SNP	ENST00000495075.1	hg19	CCDS3107.1	.	.	.	.	.	.	.	.	.	.	A	14.19	2.461464	0.43736	.	.	ENSG00000175110	ENST00000495075;ENST00000310776;ENST00000465056;ENST00000465373	D;D;D;T	0.82984	-1.67;-1.67;-1.67;-1.09	4.01	1.49	0.22878	.	3.538940	0.00815	N	0.001535	T	0.70168	0.3193	N	0.14661	0.345	0.09310	N	1	P;P	0.47106	0.89;0.824	B;B	0.40285	0.325;0.173	T	0.63341	-0.6659	10	0.59425	D	0.04	8.1781	2.9878	0.05973	0.6673:0.0:0.1186:0.2141	.	15;15	G5E9V5;P82650	.;RT22_HUMAN	W	15;15;15;11	ENSP00000418008:R15W;ENSP00000310785:R15W;ENSP00000418233:R15W;ENSP00000419920:R11W	ENSP00000310785:R15W	R	+	1	2	MRPS22	140545601	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.067000	0.11579	0.197000	0.20387	0.482000	0.46254	AGG	.	.		0.602	MRPS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358120.1	NM_020191	
EIF4A2	1974	hgsc.bcm.edu	37	3	186504304	186504304	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:186504304C>T	ENST00000323963.5	+	7	705	c.641C>T	c.(640-642)tCt>tTt	p.S214F	EIF4A2_ENST00000440191.2_Missense_Mutation_p.S215F|RP11-573D15.9_ENST00000577781.1_RNA|SNORA63_ENST00000363548.1_RNA|SNORA63_ENST00000363450.1_RNA|EIF4A2_ENST00000356531.5_Missense_Mutation_p.S119F|SNORD2_ENST00000459163.1_RNA|SNORA81_ENST00000408493.2_RNA|SNORA4_ENST00000584302.1_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	214	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)	p.S214C(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1)	28	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		GTGTTGCTTTCTGCCACAATG	0.378			T	BCL6	NHL																																p.S214F		Atlas-SNP	.		Dom	yes		3	3q27.3	1974	"""eukaryotic translation initiation factor 4A, isoform 2"""		L	EIF4A2,NS,carcinoma,0,1	EIF4A2	55	.	1	Substitution - Missense(1)	lung(1)	c.C641T						.						102.0	104.0	103.0					3																	186504304		2203	4299	6502	SO:0001583	missense	1974	exon7			TGCTTTCTGCCAC	D30655	CCDS3282.1	3q28	2012-02-23	2010-02-10		ENSG00000156976	ENSG00000156976	3.6.1.1	"""DEAD-boxes"""	3284	protein-coding gene	gene with protein product		601102	"""eukaryotic translation initiation factor 4A, isoform 2"""	EIF4F		8521730	Standard	NM_001967		Approved	DDX2B, EIF4A, BM-010	uc003fqs.3	Q14240	OTTHUMG00000156564	ENST00000323963.5:c.641C>T	chr3.hg19:g.186504304C>T	ENSP00000326381:p.Ser214Phe	138.0	0.0		405.0	154.0	NM_001967	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Missense_Mutation	SNP	ENST00000323963.5	hg19	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.911871	0.72983	.	.	ENSG00000156976	ENST00000323963;ENST00000440191;ENST00000356531	T;T;T	0.12774	2.65;2.65;2.65	5.13	5.13	0.70059	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.56688	0.2002	H	0.98786	4.33	0.80722	D	1	D;D;D;D	0.76494	0.995;0.999;0.999;0.999	D;D;D;D	0.79108	0.943;0.992;0.946;0.968	T	0.74763	-0.3555	10	0.87932	D	0	-27.6825	16.4642	0.84073	0.0:1.0:0.0:0.0	.	70;119;215;214	B4DJX6;Q9NZE6;Q14240-2;Q14240	.;.;.;IF4A2_HUMAN	F	214;215;119	ENSP00000326381:S214F;ENSP00000398370:S215F;ENSP00000348925:S119F	ENSP00000326381:S214F	S	+	2	0	EIF4A2	187986998	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.075000	0.76798	2.827000	0.97445	0.650000	0.86243	TCT	.	.		0.378	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967	
ATP13A3	79572	hgsc.bcm.edu	37	3	194126804	194126804	+	Silent	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:194126804G>A	ENST00000439040.1	-	33	4316	c.3525C>T	c.(3523-3525)gcC>gcT	p.A1175A	ATP13A3_ENST00000256031.4_Silent_p.A1175A			Q9H7F0	AT133_HUMAN	ATPase type 13A3	1175						integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		TACAGCCCAGGGCCCAGGGTA	0.463																																					p.A1175A		Atlas-SNP	.											.	ATP13A3	94	.	0			c.C3525T						.						122.0	115.0	117.0					3																	194126804		2023	4196	6219	SO:0001819	synonymous_variant	79572	exon32			GCCCAGGGCCCAG	AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657		"""ATPases / P-type"""	24113	protein-coding gene	gene with protein product	"""ATPase family homolog up regulated in senescence cells"""	610232				11867234	Standard	NM_024524		Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.3525C>T	chr3.hg19:g.194126804G>A		96.0	0.0		198.0	79.0	NM_024524	Q8NC11|Q96KS1	Silent	SNP	ENST00000439040.1	hg19	CCDS43187.1	.	.	.	.	.	.	.	.	.	.	G	4.813	0.151232	0.09185	.	.	ENSG00000133657	ENST00000429136	.	.	.	5.79	1.76	0.24704	.	.	.	.	.	T	0.53850	0.1822	.	.	.	0.42295	D	0.992155	.	.	.	.	.	.	T	0.44436	-0.9328	4	.	.	.	-12.1813	6.4084	0.21678	0.0796:0.3519:0.47:0.0985	.	.	.	.	S	111	.	.	P	-	1	0	ATP13A3	195608093	1.000000	0.71417	0.342000	0.25602	0.488000	0.33401	2.473000	0.45145	0.337000	0.23665	0.650000	0.86243	CCT	.	.		0.463	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524	
GPRIN3	285513	hgsc.bcm.edu	37	4	90170546	90170546	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:90170546G>A	ENST00000609438.1	-	2	1234	c.716C>T	c.(715-717)aCt>aTt	p.T239I	GPRIN3_ENST00000333209.4_Missense_Mutation_p.T239I	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	239								p.T239N(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		AGATTCTCTAGTTAGAGGTTT	0.552																																					p.T239I		Atlas-SNP	.											GPRIN3,NS,carcinoma,0,1	GPRIN3	90	.	1	Substitution - Missense(1)	kidney(1)	c.C716T						.						50.0	55.0	53.0					4																	90170546		2203	4300	6503	SO:0001583	missense	285513	exon2			TCTCTAGTTAGAG	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.716C>T	chr4.hg19:g.90170546G>A	ENSP00000476603:p.Thr239Ile	59.0	0.0		101.0	39.0	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	hg19	CCDS34030.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.318807	0.23994	.	.	ENSG00000185477	ENST00000333209	T	0.10860	2.83	4.93	0.83	0.18854	.	0.807286	0.10088	N	0.717539	T	0.04452	0.0122	N	0.14661	0.345	0.09310	N	1	B	0.30824	0.296	B	0.20955	0.032	T	0.40270	-0.9572	10	0.27785	T	0.31	0.635	1.468	0.02410	0.1827:0.1254:0.4522:0.2398	.	239	Q6ZVF9	GRIN3_HUMAN	I	239	ENSP00000328672:T239I	ENSP00000328672:T239I	T	-	2	0	GPRIN3	90389569	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.754000	0.26390	0.311000	0.23014	-0.142000	0.14014	ACT	.	.		0.552	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281	
TBCK	93627	hgsc.bcm.edu	37	4	107092414	107092414	+	Silent	SNP	T	T	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:107092414T>C	ENST00000273980.5	-	24	2520	c.2073A>G	c.(2071-2073)gaA>gaG	p.E691E	TBCK_ENST00000394708.2_Silent_p.E691E|TBCK_ENST00000432496.2_Silent_p.E691E|TBCK_ENST00000361687.4_Silent_p.E628E|TBCK_ENST00000514689.1_5'UTR|TBCK_ENST00000394706.3_Silent_p.E652E					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TCACACAGCGTTCAATGTCAA	0.353																																					p.E691E		Atlas-SNP	.											.	TBCK	89	.	0			c.A2073G						.						116.0	115.0	116.0					4																	107092414		2203	4300	6503	SO:0001819	synonymous_variant	93627	exon23			ACAGCGTTCAATG		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.2073A>G	chr4.hg19:g.107092414T>C		112.0	0.0		255.0	96.0	NM_001163436		Silent	SNP	ENST00000273980.5	hg19	CCDS54788.1																																																																																			.	.		0.353	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115	
DKK2	27123	hgsc.bcm.edu	37	4	107845310	107845310	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:107845310C>T	ENST00000285311.3	-	4	1286	c.581G>A	c.(580-582)tGc>tAc	p.C194Y	DKK2_ENST00000510463.1_Missense_Mutation_p.C148Y|DKK2_ENST00000513208.1_Missense_Mutation_p.C94Y	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	194	DKK-type Cys-2.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)		p.C194F(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		ACGAGCACAGCAAAACCCTTC	0.473																																					p.C194Y		Atlas-SNP	.											DKK2,NS,neuroblastoma,0,1	DKK2	96	.	1	Substitution - Missense(1)	autonomic_ganglia(1)	c.G581A						.						118.0	109.0	112.0					4																	107845310		2203	4300	6503	SO:0001583	missense	27123	exon4			GCACAGCAAAACC	AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"""dickkopf (Xenopus laevis) homolog 2"", ""dickkopf 2 homolog (Xenopus laevis)"""			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.581G>A	chr4.hg19:g.107845310C>T	ENSP00000285311:p.Cys194Tyr	84.0	0.0		179.0	79.0	NM_014421	A0AVE9|B2R6S7|Q9UIU3	Missense_Mutation	SNP	ENST00000285311.3	hg19	CCDS3675.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.610495	0.87258	.	.	ENSG00000155011	ENST00000285311;ENST00000513208;ENST00000510463	D;T;T	0.81821	-1.54;-0.61;-1.14	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.90807	0.7113	M	0.82823	2.61	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	D	0.91523	0.5236	10	0.87932	D	0	-8.7032	19.6876	0.95986	0.0:1.0:0.0:0.0	.	194	Q9UBU2	DKK2_HUMAN	Y	194;94;148	ENSP00000285311:C194Y;ENSP00000421255:C94Y;ENSP00000423797:C148Y	ENSP00000285311:C194Y	C	-	2	0	DKK2	108064759	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	7.487000	0.81328	2.657000	0.90304	0.585000	0.79938	TGC	.	.		0.473	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4		
GYPE	2996	hgsc.bcm.edu	37	4	144801632	144801632	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:144801632G>T	ENST00000358615.4	-	2	119	c.68C>A	c.(67-69)aCt>aAt	p.T23N	GYPE_ENST00000437468.2_Missense_Mutation_p.T23N	NM_198682.2	NP_941391.2	P15421	GLPE_HUMAN	glycophorin E (MNS blood group)	23						integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_hematologic(180;0.158)					TGCCACACCAGTGGTACTTGA	0.378																																					p.T23N		Atlas-SNP	.											.	GYPE	21	.	0			c.C68A						.						214.0	223.0	220.0					4																	144801632		2203	4300	6503	SO:0001583	missense	2996	exon2			ACACCAGTGGTAC		CCDS47138.1	4q31.21	2010-01-19	2010-01-19		ENSG00000197465	ENSG00000197465		"""Blood group antigens"""	4705	protein-coding gene	gene with protein product		138590	"""glycophorin E"""				Standard	NM_198682		Approved	GPE, MNS	uc003ijj.3	P15421	OTTHUMG00000161402	ENST00000358615.4:c.68C>A	chr4.hg19:g.144801632G>T	ENSP00000351430:p.Thr23Asn	188.0	0.0		1165.0	214.0	NM_198682	D3DNZ5	Missense_Mutation	SNP	ENST00000358615.4	hg19	CCDS47138.1	.	.	.	.	.	.	.	.	.	.	G	10.43	1.348990	0.24426	.	.	ENSG00000197465	ENST00000358615;ENST00000437468;ENST00000428604	T;T	0.06371	3.31;3.31	1.75	-1.39	0.08997	.	.	.	.	.	T	0.09024	0.0223	.	.	.	0.09310	N	1	D	0.62365	0.991	P	0.50136	0.632	T	0.19811	-1.0294	8	0.87932	D	0	.	5.159	0.15050	0.5471:0.0:0.4529:0.0	.	23	P15421	GLPE_HUMAN	N	23	ENSP00000351430:T23N;ENSP00000400698:T23N	ENSP00000351430:T23N	T	-	2	0	GYPE	145021082	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.369000	0.07533	-0.448000	0.07128	0.134000	0.15878	ACT	.	.		0.378	GYPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364780.1	NM_002102	
NPY2R	4887	hgsc.bcm.edu	37	4	156135578	156135578	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:156135578C>G	ENST00000329476.3	+	2	976	c.487C>G	c.(487-489)Cga>Gga	p.R163G	NPY2R_ENST00000506608.1_Missense_Mutation_p.R163G	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	163					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	GATCTCCAAGCGAATCAGCTT	0.552																																					p.R163G		Atlas-SNP	.											NPY2R,right_upper_lobe,carcinoma,0,1	NPY2R	87	.	0			c.C487G						.						55.0	51.0	52.0					4																	156135578		2203	4300	6503	SO:0001583	missense	4887	exon2			TCCAAGCGAATCA	U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"""GPCR / Class A : Neuropeptide receptors : Y"""	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		ENST00000329476.3:c.487C>G	chr4.hg19:g.156135578C>G	ENSP00000332591:p.Arg163Gly	14.0	0.0		48.0	19.0	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Missense_Mutation	SNP	ENST00000329476.3	hg19	CCDS3791.1	.	.	.	.	.	.	.	.	.	.	C	8.336	0.827495	0.16749	.	.	ENSG00000185149	ENST00000329476;ENST00000506608	T;T	0.42131	0.98;0.98	5.74	1.05	0.20165	GPCR, rhodopsin-like superfamily (1);	0.627067	0.16311	N	0.220016	T	0.44993	0.1320	M	0.67953	2.075	0.09310	N	1	B	0.22683	0.073	B	0.28553	0.091	T	0.47935	-0.9078	10	0.46703	T	0.11	.	16.4727	0.84115	0.5564:0.4436:0.0:0.0	.	163	P49146	NPY2R_HUMAN	G	163	ENSP00000332591:R163G;ENSP00000426366:R163G	ENSP00000332591:R163G	R	+	1	2	NPY2R	156355028	0.035000	0.19736	0.221000	0.23827	0.744000	0.42396	0.458000	0.21892	0.190000	0.20209	0.643000	0.83706	CGA	.	.		0.552	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910	
SKIV2L2	23517	hgsc.bcm.edu	37	5	54635850	54635850	+	Silent	SNP	A	A	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr5:54635850A>G	ENST00000230640.5	+	6	782	c.528A>G	c.(526-528)gcA>gcG	p.A176A	SKIV2L2_ENST00000545714.1_Silent_p.A75A	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	176	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				ATGCCATTGCATTGGCCTTAA	0.308																																					p.A176A	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.A528G						.						106.0	101.0	103.0					5																	54635850		2203	4300	6503	SO:0001819	synonymous_variant	23517	exon6			CATTGCATTGGCC	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 118"""		"""KIAA0052"""	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.528A>G	chr5.hg19:g.54635850A>G		71.0	0.0		198.0	108.0	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	hg19	CCDS3967.1																																																																																			.	.		0.308	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1		
PAM	5066	hgsc.bcm.edu	37	5	102203011	102203011	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr5:102203011T>A	ENST00000438793.3	+	2	594	c.124T>A	c.(124-126)Tgt>Agt	p.C42S	PAM_ENST00000348126.2_Missense_Mutation_p.C42S|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000346918.2_Missense_Mutation_p.C42S|PAM_ENST00000274392.9_5'UTR|PAM_ENST00000304400.7_Missense_Mutation_p.C42S|PAM_ENST00000455264.2_Missense_Mutation_p.C42S|PAM_ENST00000513648.1_3'UTR	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	42	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	TTCCAATGAATGTCTTGGTAC	0.383																																					p.C42S		Atlas-SNP	.											.	PAM	180	.	0			c.T124A						.						143.0	128.0	133.0					5																	102203011		2203	4300	6503	SO:0001583	missense	5066	exon2			AATGAATGTCTTG	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"""peptidyl-alpha-hydroxyglycine alpha-amidating lyase"", ""peptidylglycine alpha-hydroxylating monooxygenase"""	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.124T>A	chr5.hg19:g.102203011T>A	ENSP00000396493:p.Cys42Ser	78.0	0.0		237.0	66.0	NM_138822	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	hg19	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	T	19.53	3.845756	0.71603	.	.	ENSG00000145730	ENST00000511839;ENST00000511477;ENST00000509832;ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000455264	T;T;T;T;T;T;T	0.71579	-0.56;-0.58;0.93;0.81;0.85;0.93;0.82	5.68	5.68	0.88126	PHM/PNGase F domain (1);	0.000000	0.85682	D	0.000000	T	0.77678	0.4166	L	0.34521	1.04	0.80722	D	1	D;D;D;D;D	0.76494	0.998;0.999;0.999;0.999;0.999	D;D;D;D;D	0.81914	0.988;0.995;0.995;0.995;0.993	T	0.80169	-0.1494	10	0.72032	D	0.01	.	15.9313	0.79663	0.0:0.0:0.0:1.0	.	42;42;42;42;42	P19021;P19021-4;P19021-3;P19021-5;P19021-2	AMD_HUMAN;.;.;.;.	S	42	ENSP00000426448:C42S;ENSP00000423763:C42S;ENSP00000396493:C42S;ENSP00000282992:C42S;ENSP00000314638:C42S;ENSP00000306100:C42S;ENSP00000403461:C42S	ENSP00000306100:C42S	C	+	1	0	PAM	102230910	1.000000	0.71417	1.000000	0.80357	0.443000	0.32047	5.804000	0.69135	2.163000	0.67991	0.402000	0.26972	TGT	.	.		0.383	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919	
FEM1C	56929	hgsc.bcm.edu	37	5	114861063	114861063	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr5:114861063A>C	ENST00000274457.3	-	3	1357	c.796T>G	c.(796-798)Ttg>Gtg	p.L266V		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	266					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		CAGTATTTCAAAGCCCCAAGC	0.398																																					p.L266V		Atlas-SNP	.											.	FEM1C	50	.	0			c.T796G						.						122.0	118.0	119.0					5																	114861063		2202	4300	6502	SO:0001583	missense	56929	exon3			ATTTCAAAGCCCC		CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"""Ankyrin repeat domain containing"""	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.796T>G	chr5.hg19:g.114861063A>C	ENSP00000274457:p.Leu266Val	95.0	0.0		223.0	64.0	NM_020177	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Missense_Mutation	SNP	ENST00000274457.3	hg19	CCDS4118.1	.	.	.	.	.	.	.	.	.	.	A	6.694	0.496617	0.12762	.	.	ENSG00000145780	ENST00000274457	T	0.74947	-0.89	5.76	2.16	0.27623	.	0.000000	0.64402	D	0.000001	T	0.62551	0.2437	L	0.53617	1.68	0.42902	D	0.994231	P	0.39940	0.696	B	0.32022	0.139	T	0.60073	-0.7334	10	0.46703	T	0.11	-11.6108	8.9579	0.35829	0.7232:0.0:0.2768:0.0	.	266	Q96JP0	FEM1C_HUMAN	V	266	ENSP00000274457:L266V	ENSP00000274457:L266V	L	-	1	2	FEM1C	114888962	0.989000	0.36119	0.999000	0.59377	0.519000	0.34347	1.705000	0.37867	0.456000	0.26937	0.528000	0.53228	TTG	.	.		0.398	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250857.3	NM_020177	
PCDHGA12	26025	hgsc.bcm.edu	37	5	140871440	140871440	+	Intron	SNP	A	A	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr5:140871440A>T	ENST00000252085.3	+	2	2566				PCDHGA10_ENST00000398610.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGC5_ENST00000252087.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAGTGGCCGATTAAGGGATG	0.652																																					p.D878V		Atlas-SNP	.											.	PCDHGC5	199	.	0			c.A2633T						.						11.0	15.0	13.0					5																	140871440		1085	2153	3238	SO:0001627	intron_variant	56097	exon1			TGGCCGATTAAGG	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"""Cadherins / Protocadherins : Clustered"""	8699	other	protocadherin	"""fibroblast cadherin FIB3"""	603059	"""cadherin 21"""	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.2425-2934A>T	chr5.hg19:g.140871440A>T		40.0	0.0		141.0	28.0	NM_032407	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	hg19	CCDS4260.1																																																																																			.	.		0.652	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735	
USP49	25862	hgsc.bcm.edu	37	6	41773689	41773689	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr6:41773689T>G	ENST00000394253.3	-	3	1362	c.1033A>C	c.(1033-1035)Atc>Ctc	p.I345L	USP49_ENST00000373009.3_Missense_Mutation_p.I345L|USP49_ENST00000373010.1_Missense_Mutation_p.I345L|USP49_ENST00000297229.2_Missense_Mutation_p.I345L|USP49_ENST00000373006.1_Missense_Mutation_p.I345L			Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	345	USP.				histone H2B conserved C-terminal lysine deubiquitination (GO:0035616)|mRNA splicing, via spliceosome (GO:0000398)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)|skin(2)	23	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TTGTTCTGGATGAGCTCCAGA	0.607																																					p.I345L		Atlas-SNP	.											.	USP49	58	.	0			c.A1033C						.						44.0	46.0	45.0					6																	41773689		2203	4300	6503	SO:0001583	missense	25862	exon4			TCTGGATGAGCTC	AJ586139	CCDS4861.1, CCDS69111.1	6p12.1	2008-02-05	2005-08-08		ENSG00000164663	ENSG00000164663		"""Ubiquitin-specific peptidases"""	20078	protein-coding gene	gene with protein product			"""ubiquitin specific protease 49"""			14715245	Standard	NM_018561		Approved	MGC20741	uc003ori.3	Q70CQ1	OTTHUMG00000014688	ENST00000394253.3:c.1033A>C	chr6.hg19:g.41773689T>G	ENSP00000377797:p.Ile345Leu	15.0	0.0		34.0	13.0	NM_018561	Q5T3D9|Q5T3E0|Q96CK4	Missense_Mutation	SNP	ENST00000394253.3	hg19		.	.	.	.	.	.	.	.	.	.	T	16.64	3.180024	0.57800	.	.	ENSG00000164663	ENST00000394253;ENST00000373010;ENST00000373009;ENST00000373006;ENST00000297229	T;T;T;T;T	0.73575	3.76;3.27;3.76;-0.76;-0.76	5.1	5.1	0.69264	.	0.128325	0.64402	D	0.000007	T	0.50240	0.1604	N	0.26130	0.795	0.35841	D	0.826048	P	0.36330	0.548	B	0.41466	0.358	T	0.53387	-0.8446	10	0.11485	T	0.65	-17.1117	14.8356	0.70180	0.0:0.0:0.0:1.0	.	345	Q70CQ1-2	.	L	345	ENSP00000377797:I345L;ENSP00000362101:I345L;ENSP00000362100:I345L;ENSP00000362097:I345L;ENSP00000297229:I345L	ENSP00000297229:I345L	I	-	1	0	USP49	41881667	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.898000	0.63238	2.039000	0.60335	0.533000	0.62120	ATC	.	.		0.607	USP49-007	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000316513.3	NM_018561	
COL12A1	1303	hgsc.bcm.edu	37	6	75884785	75884785	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr6:75884785G>T	ENST00000322507.8	-	13	2988	c.2679C>A	c.(2677-2679)gaC>gaA	p.D893E	COL12A1_ENST00000416123.2_Missense_Mutation_p.D893E|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Missense_Mutation_p.D893E	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	893	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CAAAGAGGGCGTCTCCAGCCC	0.468																																					p.D893E		Atlas-SNP	.											.	COL12A1	385	.	0			c.C2679A						.						190.0	186.0	187.0					6																	75884785		1983	4159	6142	SO:0001583	missense	1303	exon13			GAGGGCGTCTCCA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2679C>A	chr6.hg19:g.75884785G>T	ENSP00000325146:p.Asp893Glu	75.0	0.0		170.0	69.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	G	0.018	-1.482005	0.01027	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.51817	0.69;0.69;0.69	5.94	-8.61	0.00885	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.463941	0.21967	N	0.066519	T	0.02304	0.0071	N	0.02011	-0.69	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.32771	-0.9894	10	0.05436	T	0.98	.	0.6516	0.00828	0.2097:0.1677:0.2157:0.4069	.	893	Q99715	COCA1_HUMAN	E	893	ENSP00000325146:D893E;ENSP00000412864:D893E;ENSP00000421216:D893E	ENSP00000325146:D893E	D	-	3	2	COL12A1	75941505	0.000000	0.05858	0.397000	0.26308	0.387000	0.30353	-3.514000	0.00445	-1.602000	0.01599	-2.049000	0.00408	GAC	.	.		0.468	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
PHF10	55274	hgsc.bcm.edu	37	6	170105298	170105298	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr6:170105298T>C	ENST00000339209.4	-	11	1465	c.1342A>G	c.(1342-1344)Atg>Gtg	p.M448V	C6orf120_ENST00000332290.2_3'UTR|PHF10_ENST00000366780.4_Missense_Mutation_p.M446V	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	448					nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		CAGAACATCATTTCTTCTTCA	0.373																																					p.M448V		Atlas-SNP	.											.	PHF10	76	.	0			c.A1342G						.						186.0	161.0	169.0					6																	170105298		2203	4300	6503	SO:0001583	missense	55274	exon11			ACATCATTTCTTC	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"""Zinc fingers, PHD-type"""	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.1342A>G	chr6.hg19:g.170105298T>C	ENSP00000341805:p.Met448Val	81.0	0.0		160.0	54.0	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Missense_Mutation	SNP	ENST00000339209.4	hg19	CCDS5308.2	.	.	.	.	.	.	.	.	.	.	T	18.57	3.652033	0.67472	.	.	ENSG00000130024	ENST00000366780;ENST00000339209	D;D	0.88664	-2.41;-2.41	5.91	5.91	0.95273	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.035139	0.85682	D	0.000000	D	0.89996	0.6877	M	0.80332	2.49	0.58432	D	0.999998	P;B	0.46064	0.872;0.392	P;P	0.48304	0.522;0.573	D	0.91696	0.5370	10	0.87932	D	0	-27.6999	15.5248	0.75894	0.0:0.0:0.0:1.0	.	446;448	Q8WUB8-2;Q8WUB8	.;PHF10_HUMAN	V	446;448	ENSP00000355743:M446V;ENSP00000341805:M448V	ENSP00000341805:M448V	M	-	1	0	PHF10	169847223	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.457000	0.80775	2.269000	0.75478	0.533000	0.62120	ATG	.	.		0.373	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288	
Unknown	0	hgsc.bcm.edu	37	7	63680468	63680468	+	IGR	SNP	C	C	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr7:63680468C>A								GUSBP6 (69369 upstream) : ZNF679 (8383 downstream)																							TAAGATAATTCATACTGGAGA	0.408																																					p.H347N		Atlas-SNP	.											.	.	.	.	0			c.C1039A						.						47.0	53.0	51.0					7																	63680468		692	1591	2283	SO:0001628	intergenic_variant	730291	exon4			ATAATTCATACTG																													chr7.hg19:g.63680468C>A		22.0	0.0		31.0	9.0	NM_001159524		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.408								
SSC4D	136853	hgsc.bcm.edu	37	7	76029847	76029847	+	Silent	SNP	G	G	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr7:76029847G>T	ENST00000275560.3	-	4	578	c.231C>A	c.(229-231)ggC>ggA	p.G77G	ZP3_ENST00000336517.4_Intron	NM_080744.1	NP_542782.1														autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(9)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21						TGCCCCAGGAGCCACCGTGCA	0.701																																					p.G77G		Atlas-SNP	.											.	SRCRB4D	47	.	0			c.C231A						.						11.0	9.0	10.0					7																	76029847		2123	4163	6286	SO:0001819	synonymous_variant	136853	exon4			CCAGGAGCCACCG																												ENST00000275560.3:c.231C>A	chr7.hg19:g.76029847G>T		14.0	0.0		45.0	18.0	NM_080744		Silent	SNP	ENST00000275560.3	hg19	CCDS5585.1																																																																																			.	.		0.701	SRCRB4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253001.3		
CCDC146	57639	hgsc.bcm.edu	37	7	76909777	76909777	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr7:76909777A>G	ENST00000285871.4	+	14	1853	c.1726A>G	c.(1726-1728)Aac>Gac	p.N576D	CCDC146_ENST00000431197.1_Missense_Mutation_p.N290D|CCDC146_ENST00000415740.2_3'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	576										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)				GAAACACGCCAACAATGTTAC	0.323																																					p.N576D		Atlas-SNP	.											.	CCDC146	87	.	0			c.A1726G						.						49.0	43.0	45.0					7																	76909777		2203	4300	6503	SO:0001583	missense	57639	exon14			CACGCCAACAATG	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.1726A>G	chr7.hg19:g.76909777A>G	ENSP00000285871:p.Asn576Asp	92.0	0.0		126.0	50.0	NM_020879	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	hg19	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	A	19.43	3.825269	0.71143	.	.	ENSG00000135205	ENST00000285871;ENST00000431197	T;T	0.29655	1.56;1.56	6.17	6.17	0.99709	.	0.043557	0.85682	D	0.000000	T	0.50871	0.1641	M	0.61703	1.905	0.48632	D	0.999688	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.982	T	0.40459	-0.9562	10	0.13108	T	0.6	-22.5428	16.4837	0.84171	1.0:0.0:0.0:0.0	.	290;576	Q8IYE0-2;Q8IYE0	.;CC146_HUMAN	D	576;290	ENSP00000285871:N576D;ENSP00000413885:N290D	ENSP00000285871:N576D	N	+	1	0	AC007000.1	76747713	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.619000	0.61218	2.371000	0.80710	0.533000	0.62120	AAC	.	.		0.323	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
PEG10	23089	hgsc.bcm.edu	37	7	94293700	94293700	+	Missense_Mutation	SNP	C	C	T	rs376581536		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr7:94293700C>T	ENST00000482108.1	+	2	1311	c.832C>T	c.(832-834)Cgc>Tgc	p.R278C	PEG10_ENST00000488574.1_Missense_Mutation_p.R278C	NM_001040152.1|NM_001172438.1|NM_001184962.1	NP_001035242.1|NP_001165909.1|NP_001171891.1	Q86TG7	PEG10_HUMAN	paternally expressed 10	278					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|placenta development (GO:0001890)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(9)|prostate(3)|skin(1)	21	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GGGAGGTGCCCGCATGCGCCT	0.597																																					p.R354C		Atlas-SNP	.											.	PEG10	36	.	0			c.C1060T						.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,3974		0,0,1987	18.0	24.0	22.0		832,1060,1060,934,934,832	4.3	1.0	7		22	1,8303		0,1,4151	no	missense,missense,missense,missense,missense,missense	PEG10	NM_001040152.1,NM_001172437.1,NM_001172438.1,NM_001184961.1,NM_001184962.1,NM_015068.3	180,180,180,180,180,180	0,1,6138	TT,TC,CC		0.012,0.0,0.0081	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	278/326,354/785,354/402,312/743,312/360,278/709	94293700	1,12277	1987	4152	6139	SO:0001583	missense	23089	exon2			GGTGCCCGCATGC	AB049834	CCDS55126.1, CCDS75636.1, CCDS75637.1	7q21	2007-12-07			ENSG00000242265	ENSG00000242265			14005	protein-coding gene	gene with protein product		609810				11318613, 15716091, 16093683	Standard	NM_001172437		Approved	KIAA1051, HB-1, MEF3L, RGAG3, Mar2, Mart2	uc011kie.2	Q86TG7	OTTHUMG00000155578	ENST00000482108.1:c.832C>T	chr7.hg19:g.94293700C>T	ENSP00000417587:p.Arg278Cys	16.0	0.0		50.0	18.0	NM_001172438	Q96A68|Q9UPV1	Missense_Mutation	SNP	ENST00000482108.1	hg19	CCDS55126.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.927626	0.73327	0.0	1.2E-4	ENSG00000242265	ENST00000482108;ENST00000488574	T;T	0.15139	2.45;2.45	4.34	4.34	0.51931	.	.	.	.	.	T	0.29652	0.0740	L	0.34521	1.04	0.40084	D	0.976172	D;D	0.89917	1.0;1.0	D;D	0.69654	0.965;0.948	T	0.03619	-1.1019	9	0.56958	D	0.05	.	14.7868	0.69810	0.0:1.0:0.0:0.0	.	354;278	B4DSP0;Q86TG7	.;PEG10_HUMAN	C	278	ENSP00000417587:R278C;ENSP00000418944:R278C	ENSP00000417587:R278C	R	+	1	0	PEG10	94131636	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.330000	0.43885	2.429000	0.82318	0.555000	0.69702	CGC	.	.		0.597	PEG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340751.1	NM_015068	
ARMC10	83787	hgsc.bcm.edu	37	7	102738867	102738867	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr7:102738867A>G	ENST00000323716.3	+	7	1291	c.899A>G	c.(898-900)cAg>cGg	p.Q300R	ARMC10_ENST00000441711.2_Missense_Mutation_p.Q265R|ARMC10_ENST00000541300.1_Missense_Mutation_p.Q182R|ARMC10_ENST00000454559.1_Missense_Mutation_p.Q206R|ARMC10_ENST00000428183.2_Missense_Mutation_p.Q241R|ARMC10_ENST00000425331.1_Missense_Mutation_p.Q241R	NM_031905.4	NP_114111.2	Q8N2F6	ARM10_HUMAN	armadillo repeat containing 10	300					regulation of growth (GO:0040008)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	11						TTAGCTGTGCAGCCTACTTTC	0.403																																					p.Q300R		Atlas-SNP	.											.	ARMC10	25	.	0			c.A899G						.						77.0	73.0	74.0					7																	102738867		2203	4298	6501	SO:0001583	missense	83787	exon7			CTGTGCAGCCTAC	AY150853	CCDS5728.1, CCDS55145.1, CCDS55146.1, CCDS55147.1, CCDS55148.1, CCDS55149.1	7q22.1	2013-02-14			ENSG00000170632	ENSG00000170632		"""Armadillo repeat containing"""	21706	protein-coding gene	gene with protein product	"""specific Splicing Variant involved in Hepatocarcinogenesis"""	611864				12839973	Standard	NM_031905		Approved	MGC3195, SVH	uc003vaw.2	Q8N2F6	OTTHUMG00000157201	ENST00000323716.3:c.899A>G	chr7.hg19:g.102738867A>G	ENSP00000319412:p.Gln300Arg	175.0	0.0		612.0	166.0	NM_031905	A8K703|B4DWJ8|F5GX65|Q75K91|Q75MG6|Q75ML8|Q8IZC1|Q8IZC2|Q8IZC3|Q9BTM6	Missense_Mutation	SNP	ENST00000323716.3	hg19	CCDS5728.1	.	.	.	.	.	.	.	.	.	.	A	3.673	-0.067130	0.07273	.	.	ENSG00000170632	ENST00000323716;ENST00000428183;ENST00000441711;ENST00000454559;ENST00000425331;ENST00000541300;ENST00000434153;ENST00000431642	T;T;T;T;T;T;T;T	0.53423	1.52;1.52;1.52;1.52;1.52;1.52;0.62;1.52	5.68	-0.724	0.11177	Armadillo-type fold (1);	0.554134	0.21062	N	0.080809	T	0.38427	0.1040	L	0.58669	1.825	0.09310	N	1	B;B;B;B;B;B;B	0.30236	0.004;0.004;0.274;0.116;0.004;0.008;0.008	B;B;B;B;B;B;B	0.27887	0.02;0.006;0.084;0.057;0.008;0.019;0.022	T	0.26155	-1.0111	10	0.30854	T	0.27	1.5325	10.9007	0.47049	0.6685:0.0:0.3315:0.0	.	241;182;206;228;241;265;300	B4DWJ8;F5GX65;Q8N2F6-4;C9J5N7;Q8N2F6-3;Q8N2F6-2;Q8N2F6	.;.;.;.;.;.;ARM10_HUMAN	R	300;241;265;206;241;182;228;142	ENSP00000319412:Q300R;ENSP00000396654:Q241R;ENSP00000413619:Q265R;ENSP00000405612:Q206R;ENSP00000397969:Q241R;ENSP00000440463:Q182R;ENSP00000398201:Q228R;ENSP00000406840:Q142R	ENSP00000319412:Q300R	Q	+	2	0	ARMC10	102526103	0.001000	0.12720	0.000000	0.03702	0.377000	0.30045	0.539000	0.23175	-0.070000	0.12908	0.482000	0.46254	CAG	.	.		0.403	ARMC10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347882.1	NM_031905	
TCEA1	6917	hgsc.bcm.edu	37	8	54912542	54912542	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr8:54912542C>A	ENST00000521604.2	-	3	598	c.195G>T	c.(193-195)ttG>ttT	p.L65F	TCEA1_ENST00000520534.1_Missense_Mutation_p.L65F|TCEA1_ENST00000521086.2_5'UTR|TCEA1_ENST00000396401.3_Missense_Mutation_p.L44F|TCEA1_ENST00000518784.1_Missense_Mutation_p.L65F|TCEA1_ENST00000522635.1_Intron	NM_006756.2	NP_006747.1	P23193	TCEA1_HUMAN	transcription elongation factor A (SII), 1	65	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				DNA repair (GO:0006281)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|regulation of DNA-templated transcription, elongation (GO:0032784)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(1)|lung(1)|skin(1)	4		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)			GAGACTTTGCCAAAGATGTAA	0.323			T	PLAG1	salivary adenoma																																p.L65F		Atlas-SNP	.		Dom	yes		8	8q11.2	6917	"""transcription elongation factor A (SII), 1"""		E	.	TCEA1	30	.	0			c.G195T						.						96.0	88.0	91.0					8																	54912542		1824	4074	5898	SO:0001583	missense	6917	exon3			CTTTGCCAAAGAT	X62585	CCDS47857.1, CCDS47858.1	8q11.2	2011-01-25			ENSG00000187735	ENSG00000187735		"""General transcription factors"""	11612	protein-coding gene	gene with protein product		601425		TCEA, GTF2S		8812434, 8112616	Standard	NM_006756		Approved	SII, TF2S, TFIIS	uc003xru.3	P23193	OTTHUMG00000164262	ENST00000521604.2:c.195G>T	chr8.hg19:g.54912542C>A	ENSP00000428426:p.Leu65Phe	151.0	0.0		392.0	141.0	NM_006756	A6NF25|A8K339|Q15563|Q6FG87	Missense_Mutation	SNP	ENST00000521604.2	hg19	CCDS47858.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.504383	0.44558	.	.	ENSG00000187735	ENST00000396401;ENST00000521604;ENST00000520534;ENST00000518784	.	.	.	5.63	3.28	0.37604	Transcription factor IIS, N-terminal (4);Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type (1);	0.000000	0.64402	D	0.000003	T	0.75968	0.3922	M	0.78049	2.395	0.54753	D	0.999983	D;D	0.89917	1.0;0.997	D;D	0.78314	0.991;0.99	T	0.75216	-0.3396	9	0.72032	D	0.01	-7.9292	9.0457	0.36345	0.0:0.154:0.0:0.846	.	44;65	P23193-2;P23193	.;TCEA1_HUMAN	F	44;65;65;65	.	ENSP00000395483:L44F	L	-	3	2	TCEA1	55075095	1.000000	0.71417	1.000000	0.80357	0.344000	0.29017	0.479000	0.22228	0.433000	0.26313	-0.312000	0.09012	TTG	.	.		0.323	TCEA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377975.2	NM_006756	
KCNB2	9312	hgsc.bcm.edu	37	8	73848335	73848335	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr8:73848335C>G	ENST00000523207.1	+	3	1333	c.745C>G	c.(745-747)Ctt>Gtt	p.L249V		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	249					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)			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)	CATGGAGTACCTTTTGCGATT	0.458																																					p.L249V		Atlas-SNP	.											.	KCNB2	228	.	0			c.C745G						.						195.0	168.0	177.0					8																	73848335		2203	4300	6503	SO:0001583	missense	9312	exon3			GAGTACCTTTTGC	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.745C>G	chr8.hg19:g.73848335C>G	ENSP00000430846:p.Leu249Val	124.0	0.0		294.0	111.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.760784	0.69763	.	.	ENSG00000182674	ENST00000523207	D	0.98419	-4.92	5.93	5.93	0.95920	Ion transport (1);	0.000000	0.40818	N	0.001009	D	0.97654	0.9231	N	0.17631	0.505	0.80722	D	1	P	0.49696	0.927	P	0.61397	0.888	D	0.97710	1.0190	10	0.39692	T	0.17	.	20.3507	0.98813	0.0:1.0:0.0:0.0	.	249	Q92953	KCNB2_HUMAN	V	249	ENSP00000430846:L249V	ENSP00000430846:L249V	L	+	1	0	KCNB2	74010889	1.000000	0.71417	1.000000	0.80357	0.682000	0.39822	7.818000	0.86416	2.808000	0.96608	0.655000	0.94253	CTT	.	.		0.458	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
LRP12	29967	hgsc.bcm.edu	37	8	105510097	105510097	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr8:105510097T>C	ENST00000276654.5	-	5	791	c.683A>G	c.(682-684)aAa>aGa	p.K228R	LRP12_ENST00000424843.2_Missense_Mutation_p.K209R|LRP12_ENST00000518375.1_5'Flank	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	228	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			AGTGTAAACTTTGGTAAAACG	0.453																																					p.K228R		Atlas-SNP	.											.	LRP12	124	.	0			c.A683G						.						141.0	130.0	134.0					8																	105510097		2203	4300	6503	SO:0001583	missense	29967	exon5			TAAACTTTGGTAA	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"""Low density lipoprotein receptors"""	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.683A>G	chr8.hg19:g.105510097T>C	ENSP00000276654:p.Lys228Arg	110.0	0.0		221.0	105.0	NM_013437	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000276654.5	hg19	CCDS6303.1	.	.	.	.	.	.	.	.	.	.	T	9.298	1.052444	0.19907	.	.	ENSG00000147650	ENST00000424843;ENST00000276654	D;D	0.83591	-1.74;-1.67	5.66	5.66	0.87406	.	0.049986	0.85682	D	0.000000	T	0.63721	0.2535	N	0.04508	-0.205	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.62728	-0.6793	10	0.02654	T	1	-29.6762	15.9017	0.79384	0.0:0.0:0.0:1.0	.	209;228	Q9Y561-2;Q9Y561	.;LRP12_HUMAN	R	209;228	ENSP00000399148:K209R;ENSP00000276654:K228R	ENSP00000276654:K228R	K	-	2	0	LRP12	105579273	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.365000	0.59486	2.153000	0.67306	0.460000	0.39030	AAA	.	.		0.453	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437	
IFNA8	3445	hgsc.bcm.edu	37	9	21409564	21409564	+	Missense_Mutation	SNP	T	T	C	rs28383787		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr9:21409564T>C	ENST00000380205.1	+	1	419	c.389T>C	c.(388-390)aTa>aCa	p.I130T		NM_002170.3	NP_002161.2	P32881	IFNA8_HUMAN	interferon, alpha 8	130					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0174)		GTGGGGGTGATAGAGTCTCCC	0.478																																					p.I130T		Atlas-SNP	.											.	IFNA8	19	.	0			c.T389C						.						144.0	142.0	142.0					9																	21409564		2203	4300	6503	SO:0001583	missense	3445	exon1			GGGTGATAGAGTC		CCDS6507.1	9p22	2010-08-24			ENSG00000120242	ENSG00000120242		"""Interferons"""	5429	protein-coding gene	gene with protein product	"""interferon alpha-B''"", ""interferon alpha type 201"""	147568				1385305	Standard	NM_002170		Approved	IFN-alphaB	uc003zpc.1	P32881	OTTHUMG00000019677	ENST00000380205.1:c.389T>C	chr9.hg19:g.21409564T>C	ENSP00000369553:p.Ile130Thr	102.0	0.0		258.0	110.0	NM_002170	P01565|P09236|Q5VWV7|Q5VYQ3	Missense_Mutation	SNP	ENST00000380205.1	hg19	CCDS6507.1	.	.	.	.	.	.	.	.	.	.	T	5.842	0.339510	0.11069	.	.	ENSG00000120242	ENST00000380205	T	0.05081	3.5	3.48	-2.49	0.06403	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	2.002250	0.01939	N	0.041792	T	0.01661	0.0053	N	0.00347	-1.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38436	-0.9661	10	0.40728	T	0.16	.	1.2648	0.02009	0.3469:0.3593:0.1167:0.1771	.	130	P32881	IFNA8_HUMAN	T	130	ENSP00000369553:I130T	ENSP00000369553:I130T	I	+	2	0	IFNA8	21399564	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.378000	0.07446	-0.568000	0.06038	-2.123000	0.00347	ATA	.	.		0.478	IFNA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051906.1	NM_002170	
COL15A1	1306	hgsc.bcm.edu	37	9	101749575	101749575	+	Splice_Site	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr9:101749575G>A	ENST00000375001.3	+	4	1071		c.e4-1			NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1						angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CTTTTCCCCAGGGCTCCCTCC	0.567																																					.		Atlas-SNP	.											.	COL15A1	211	.	0			c.649-1G>A						.						185.0	169.0	174.0					9																	101749575		2203	4300	6503	SO:0001630	splice_region_variant	1306	exon4			TCCCCAGGGCTCC	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.649-1G>A	chr9.hg19:g.101749575G>A		25.0	0.0		65.0	27.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Splice_Site	SNP	ENST00000375001.3	hg19	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.403198	0.83230	.	.	ENSG00000204291	ENST00000375001;ENST00000536083	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3894	0.66968	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL15A1	100789396	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.435000	0.80391	2.524000	0.85096	0.655000	0.94253	.	.	.		0.567	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	Intron
PTPN3	5774	hgsc.bcm.edu	37	9	112200499	112200499	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr9:112200499T>C	ENST00000374541.2	-	8	586	c.482A>G	c.(481-483)tAt>tGt	p.Y161C	PTPN3_ENST00000446349.1_Missense_Mutation_p.Y30C|PTPN3_ENST00000412145.1_Missense_Mutation_p.Y30C|PTPN3_ENST00000262539.3_Missense_Mutation_p.Y52C	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	161	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						GGAAGAATTATAGTCTCCAAA	0.353																																					p.Y161C		Atlas-SNP	.											.	PTPN3	106	.	0			c.A482G						.						71.0	75.0	74.0					9																	112200499		2203	4300	6503	SO:0001583	missense	5774	exon8			GAATTATAGTCTC		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.482A>G	chr9.hg19:g.112200499T>C	ENSP00000363667:p.Tyr161Cys	24.0	0.0		35.0	11.0	NM_001145368	A0AUW9|E7EN99|E9PGU7	Missense_Mutation	SNP	ENST00000374541.2	hg19	CCDS6776.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.038533	0.55003	.	.	ENSG00000070159	ENST00000394831;ENST00000412145;ENST00000446349;ENST00000374541;ENST00000262539	T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9	5.96	4.81	0.61882	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.290359	0.38663	N	0.001618	D	0.84215	0.5423	M	0.78344	2.41	0.80722	D	1	P;D;D	0.59357	0.932;0.985;0.974	P;D;D	0.67103	0.714;0.949;0.925	D	0.85094	0.0953	10	0.87932	D	0	.	10.6503	0.45645	0.1684:0.0:0.0:0.8316	.	52;161;161	B7Z3H5;B7Z9V1;P26045	.;.;PTN3_HUMAN	C	161;30;30;161;52	ENSP00000416654:Y30C;ENSP00000395384:Y30C;ENSP00000363667:Y161C;ENSP00000262539:Y52C	ENSP00000262539:Y52C	Y	-	2	0	PTPN3	111240320	0.952000	0.32445	0.759000	0.31340	0.554000	0.35429	1.687000	0.37680	1.047000	0.40274	0.533000	0.62120	TAT	.	.		0.353	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4		
CACNA1B	774	hgsc.bcm.edu	37	9	140880982	140880982	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr9:140880982G>T	ENST00000371372.1	+	14	2032	c.1887G>T	c.(1885-1887)caG>caT	p.Q629H	CACNA1B_ENST00000277551.2_Missense_Mutation_p.Q629H|CACNA1B_ENST00000371355.4_Missense_Mutation_p.Q630H|CACNA1B_ENST00000371363.1_Missense_Mutation_p.Q629H|CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000371357.1_Missense_Mutation_p.Q630H	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	629					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGGGATGCAGCTGTTTGGGG	0.612																																					p.Q629H		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G1887T						.						47.0	49.0	49.0					9																	140880982		2080	4229	6309	SO:0001583	missense	774	exon14			GATGCAGCTGTTT	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1887G>T	chr9.hg19:g.140880982G>T	ENSP00000360423:p.Gln629His	109.0	0.0		298.0	110.0	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.221756	0.58560	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.98996	-5.31;-5.31;-5.31;-5.31;-5.31	4.35	3.44	0.39384	.	0.000000	0.85682	D	0.000000	D	0.99205	0.9724	M	0.85710	2.77	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	D	0.99486	1.0949	10	0.87932	D	0	.	12.7997	0.57578	0.0816:0.0:0.9184:0.0	.	629;629	B1AQK4;B1AQK6	.;.	H	629;629;629;630;630	ENSP00000360423:Q629H;ENSP00000277551:Q629H;ENSP00000360414:Q629H;ENSP00000360408:Q630H;ENSP00000360406:Q630H	ENSP00000277551:Q629H	Q	+	3	2	CACNA1B	140000803	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.487000	0.60293	0.913000	0.36797	0.462000	0.41574	CAG	.	.		0.612	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
DIP2C	22982	hgsc.bcm.edu	37	10	390969	390969	+	Missense_Mutation	SNP	C	C	A	rs200340134		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr10:390969C>A	ENST00000280886.6	-	27	3400	c.3313G>T	c.(3313-3315)Gtc>Ttc	p.V1105F		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1105						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CACGTCCTGACGTCCACAGCC	0.592																																					p.V1105F		Atlas-SNP	.											.	DIP2C	195	.	0			c.G3313T						.						72.0	59.0	63.0					10																	390969		2203	4300	6503	SO:0001583	missense	22982	exon27			TCCTGACGTCCAC	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.3313G>T	chr10.hg19:g.390969C>A	ENSP00000280886:p.Val1105Phe	29.0	0.0		54.0	23.0	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	C	8.495	0.862866	0.17178	.	.	ENSG00000151240	ENST00000280886;ENST00000535541	T	0.10668	2.85	5.59	4.69	0.59074	AMP-dependent synthetase/ligase (1);	0.188095	0.46145	D	0.000316	T	0.08670	0.0215	N	0.25380	0.74	0.80722	D	1	B	0.13594	0.008	B	0.28305	0.088	T	0.25572	-1.0128	10	0.23891	T	0.37	-31.7464	9.4456	0.38695	0.0:0.7807:0.0:0.2193	.	1105	Q9Y2E4	DIP2C_HUMAN	F	1105;30	ENSP00000280886:V1105F	ENSP00000280886:V1105F	V	-	1	0	DIP2C	380969	0.006000	0.16342	0.885000	0.34714	0.399000	0.30720	0.029000	0.13666	1.368000	0.46115	0.655000	0.94253	GTC	.	C|1.000;T|0.000		0.592	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974	
OGDHL	55753	hgsc.bcm.edu	37	10	50947868	50947868	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr10:50947868C>A	ENST00000374103.4	-	17	2243	c.2158G>T	c.(2158-2160)Gcc>Tcc	p.A720S	OGDHL_ENST00000490844.1_5'Flank|OGDHL_ENST00000432695.1_Missense_Mutation_p.A511S|OGDHL_ENST00000419399.1_Missense_Mutation_p.A663S	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	720					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						CTGGCCATGGCATAGCCCAGC	0.547																																					p.A720S		Atlas-SNP	.											.	OGDHL	149	.	0			c.G2158T						.						65.0	59.0	61.0					10																	50947868		2203	4300	6503	SO:0001583	missense	55753	exon17			CCATGGCATAGCC	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.2158G>T	chr10.hg19:g.50947868C>A	ENSP00000363216:p.Ala720Ser	33.0	0.0		67.0	29.0	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	hg19	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	C	6.641	0.486774	0.12641	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	D;D;D	0.96491	-4.03;-4.03;-4.03	4.61	3.71	0.42584	Transketolase-like, pyrimidine-binding domain (2);	0.057465	0.64402	D	0.000002	D	0.85414	0.5691	N	0.01289	-0.905	0.80722	D	1	B;B;B	0.10296	0.002;0.001;0.003	B;B;B	0.23018	0.025;0.006;0.043	T	0.79825	-0.1640	10	0.02654	T	1	.	12.479	0.55831	0.0:0.9183:0.0:0.0817	.	663;511;720	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	S	720;663;511	ENSP00000363216:A720S;ENSP00000401356:A663S;ENSP00000390240:A511S	ENSP00000363216:A720S	A	-	1	0	OGDHL	50617874	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	7.811000	0.86092	0.950000	0.37743	0.446000	0.29264	GCC	.	.		0.547	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
DGAT2	84649	hgsc.bcm.edu	37	11	75508294	75508294	+	Silent	SNP	T	T	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr11:75508294T>G	ENST00000228027.7	+	6	986	c.726T>G	c.(724-726)gcT>gcG	p.A242A	DGAT2_ENST00000376262.3_Silent_p.A199A	NM_032564.4	NP_115953.2	Q96PD7	DGAT2_HUMAN	diacylglycerol O-acyltransferase 2	242					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|cellular response to oleic acid (GO:0071400)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|diacylglycerol metabolic process (GO:0046339)|fat pad development (GO:0060613)|fatty acid homeostasis (GO:0055089)|glycerol metabolic process (GO:0006071)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)|protein homodimerization activity (GO:0042803)|retinol O-fatty-acyltransferase activity (GO:0050252)			endometrium(3)|large_intestine(5)|lung(5)|prostate(2)|skin(2)	17	Ovarian(111;0.103)					GGGGTGCGGCTGAGTCTCTGA	0.567																																					p.A242A	Melanoma(35;811 1096 8354 24009 39363)	Atlas-SNP	.											.	DGAT2	37	.	0			c.T726G						.						145.0	125.0	132.0					11																	75508294		2200	4293	6493	SO:0001819	synonymous_variant	84649	exon6			TGCGGCTGAGTCT		CCDS31642.1, CCDS58162.1	11q13.3	2010-06-24	2010-06-24		ENSG00000062282	ENSG00000062282			16940	protein-coding gene	gene with protein product		606983	"""diacylglycerol O-acyltransferase homolog 2 (mouse)"""			11481335, 14970677	Standard	NM_032564		Approved		uc001oxa.3	Q96PD7	OTTHUMG00000165338	ENST00000228027.7:c.726T>G	chr11.hg19:g.75508294T>G		40.0	0.0		101.0	36.0	NM_032564	A6ND76|Q5U810|Q68CL3|Q68DJ0|Q8NDB7|Q96BS0|Q9BYE5	Silent	SNP	ENST00000228027.7	hg19	CCDS31642.1																																																																																			.	.		0.567	DGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383506.1	NM_032564	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18534747	18534747	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr12:18534747A>T	ENST00000266497.5	+	12	1843	c.1805A>T	c.(1804-1806)gAg>gTg	p.E602V	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.E602V|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.E643V			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	602	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TTACAGAGTGAGCCTCCCGTA	0.473																																					p.E602V		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.A1805T						.						136.0	129.0	131.0					12																	18534747		1917	4132	6049	SO:0001583	missense	5288	exon13			AGAGTGAGCCTCC	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.1805A>T	chr12.hg19:g.18534747A>T	ENSP00000266497:p.Glu602Val	60.0	0.0		120.0	51.0	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.535389	0.45176	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.71341	-0.56;-0.56;-0.56	4.35	3.17	0.36434	C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (1);	0.871539	0.10193	N	0.704434	T	0.78541	0.4299	M	0.65975	2.015	0.33065	D	0.534569	D;D;D	0.58620	0.983;0.978;0.965	P;P;P	0.62382	0.901;0.84;0.83	T	0.75213	-0.3397	10	0.32370	T	0.25	-12.1363	7.9803	0.30179	0.7924:0.2076:0.0:0.0	.	642;643;602	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	V	602;602;643	ENSP00000404845:E602V;ENSP00000266497:E602V;ENSP00000445381:E643V	ENSP00000266497:E602V	E	+	2	0	PIK3C2G	18426014	0.996000	0.38824	1.000000	0.80357	0.650000	0.38633	1.407000	0.34657	0.957000	0.37930	0.460000	0.39030	GAG	.	.		0.473	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
PTPRQ	374462	hgsc.bcm.edu	37	12	80998958	80998958	+	Splice_Site	SNP	C	C	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr12:80998958C>A	ENST00000266688.5	+	32	4718	c.4718C>A	c.(4717-4719)tCg>tAg	p.S1573*				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	1619	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						GATGTCAAATCGGTAAGGCAT	0.363																																					p.S1405X		Atlas-SNP	.											.	PTPRQ	119	.	0			c.C4214A						.						169.0	131.0	142.0					12																	80998958		692	1590	2282	SO:0001630	splice_region_variant	374462	exon24			TCAAATCGGTAAG	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.4719+1C>A	chr12.hg19:g.80998958C>A		63.0	0.0		102.0	34.0	NM_001145026		Nonsense_Mutation	SNP	ENST00000266688.5	hg19		.	.	.	.	.	.	.	.	.	.	C	44	10.555321	0.99427	.	.	ENSG00000139304	ENST00000266688	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	20.4388	0.99107	0.0:1.0:0.0:0.0	.	.	.	.	X	1573	.	ENSP00000266688:S1573X	S	+	2	0	PTPRQ	79523089	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.276000	0.65580	2.836000	0.97738	0.655000	0.94253	TCG	.	.		0.363	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	Nonsense_Mutation
MED13L	23389	hgsc.bcm.edu	37	12	116429410	116429410	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr12:116429410C>T	ENST00000281928.3	-	17	3555	c.3349G>A	c.(3349-3351)Gat>Aat	p.D1117N		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1117						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		ATCACGGAATCGGAGAGAATC	0.527																																					p.D1117N		Atlas-SNP	.											.	MED13L	193	.	0			c.G3349A						.						61.0	60.0	61.0					12																	116429410		2203	4300	6503	SO:0001583	missense	23389	exon17			CGGAATCGGAGAG	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.3349G>A	chr12.hg19:g.116429410C>T	ENSP00000281928:p.Asp1117Asn	57.0	0.0		128.0	48.0	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.708388	0.68615	.	.	ENSG00000123066	ENST00000281928	D	0.86097	-2.07	5.18	5.18	0.71444	.	0.140018	0.64402	D	0.000006	D	0.83312	0.5227	M	0.64997	1.995	0.80722	D	1	P	0.39551	0.678	B	0.33339	0.162	D	0.86056	0.1529	10	0.87932	D	0	.	18.8897	0.92395	0.0:1.0:0.0:0.0	.	1117	Q71F56	MD13L_HUMAN	N	1117	ENSP00000281928:D1117N	ENSP00000281928:D1117N	D	-	1	0	MED13L	114913793	1.000000	0.71417	0.935000	0.37517	0.843000	0.47879	7.320000	0.79064	2.699000	0.92147	0.460000	0.39030	GAT	.	.		0.527	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
RFXAP	5994	hgsc.bcm.edu	37	13	37399580	37399580	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr13:37399580A>G	ENST00000255476.2	+	2	750	c.616A>G	c.(616-618)Ata>Gta	p.I206V	RFXAP_ENST00000472888.1_3'UTR	NM_000538.3	NP_000529.1	O00287	RFXAP_HUMAN	regulatory factor X-associated protein	206					positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|ovary(1)	4		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)		all cancers(112;3.5e-07)|Epithelial(112;1.27e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.0069)|BRCA - Breast invasive adenocarcinoma(63;0.0116)|GBM - Glioblastoma multiforme(144;0.0405)		TGCAGATAACATACTCTCCAT	0.323																																					p.I206V		Atlas-SNP	.											.	RFXAP	14	.	0			c.A616G						.						96.0	97.0	97.0					13																	37399580		2203	4298	6501	SO:0001583	missense	5994	exon2			GATAACATACTCT	Y12812	CCDS9359.1	13q14	2014-09-17			ENSG00000133111	ENSG00000133111			9988	protein-coding gene	gene with protein product		601861				9118943	Standard	NM_000538		Approved		uc001uvu.1	O00287	OTTHUMG00000016738	ENST00000255476.2:c.616A>G	chr13.hg19:g.37399580A>G	ENSP00000255476:p.Ile206Val	35.0	0.0		72.0	19.0	NM_000538	B2R9T8|Q5VZM6|Q8TC40	Missense_Mutation	SNP	ENST00000255476.2	hg19	CCDS9359.1	.	.	.	.	.	.	.	.	.	.	A	2.616	-0.289716	0.05568	.	.	ENSG00000133111	ENST00000255476	.	.	.	5.92	-1.86	0.07760	.	0.310059	0.35262	N	0.003335	T	0.17746	0.0426	L	0.36672	1.1	0.09310	N	0.999997	B	0.29988	0.264	B	0.28011	0.085	T	0.36286	-0.9754	9	0.02654	T	1	-6.2063	6.5682	0.22523	0.3427:0.1933:0.0:0.464	.	206	O00287	RFXAP_HUMAN	V	206	.	ENSP00000255476:I206V	I	+	1	0	RFXAP	36297580	0.797000	0.28877	0.260000	0.24451	0.993000	0.82548	0.430000	0.21428	-0.108000	0.12066	0.533000	0.62120	ATA	.	.		0.323	RFXAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044521.1	NM_000538	
AKAP11	11215	hgsc.bcm.edu	37	13	42877120	42877120	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr13:42877120C>A	ENST00000025301.2	+	8	4413	c.4238C>A	c.(4237-4239)tCa>tAa	p.S1413*		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1413					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TTAATGTTTTCAAACAAAGAG	0.383																																					p.S1413X		Atlas-SNP	.											.	AKAP11	146	.	0			c.C4238A						.						48.0	51.0	50.0					13																	42877120		2203	4300	6503	SO:0001587	stop_gained	11215	exon8			TGTTTTCAAACAA	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.4238C>A	chr13.hg19:g.42877120C>A	ENSP00000025301:p.Ser1413*	54.0	0.0		56.0	17.0	NM_016248	O75124|Q9NUK7	Nonsense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	C	38	6.961113	0.97964	.	.	ENSG00000023516	ENST00000025301	.	.	.	5.58	4.55	0.56014	.	0.437976	0.20911	N	0.083466	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	3.6947	0.08360	0.0:0.1427:0.2294:0.628	.	.	.	.	X	1413	.	ENSP00000025301:S1413X	S	+	2	0	AKAP11	41775120	0.001000	0.12720	0.159000	0.22649	0.077000	0.17291	0.934000	0.28910	1.138000	0.42230	0.557000	0.71058	TCA	.	.		0.383	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
COG3	83548	hgsc.bcm.edu	37	13	46077404	46077405	+	Missense_Mutation	DNP	AA	AA	TT			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr13:46077404_46077405AA>TT	ENST00000349995.5	+	14	1626_1627	c.1514_1515AA>TT	c.(1513-1515)gAA>gTT	p.E505V	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	505					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		TTGAAAGATGAACAGAAGAAGG	0.361																																					p.E505V|p.E505D	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.A1514T|c.A1515T						.																																			SO:0001583	missense	83548	exon14			AAGATGAACAGAA|AGATGAACAGAAG	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"""Components of oligomeric golgi complex"""	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	Exception_encountered	chr13.hg19:g.46077404_46077405delinsTT	ENSP00000258654:p.Glu505Val	77.0|78.0	0.0		109.0|111.0	15.0|18.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	hg19	CCDS9398.1																																																																																			.	.		0.361	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2		
SLITRK1	114798	hgsc.bcm.edu	37	13	84454266	84454266	+	Silent	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr13:84454266G>A	ENST00000377084.2	-	1	2262	c.1377C>T	c.(1375-1377)atC>atT	p.I459I		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	459					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		GGATGAGCTGGATAGCGTTGT	0.542																																					p.I459I		Atlas-SNP	.											.	SLITRK1	196	.	0			c.C1377T						.						92.0	82.0	86.0					13																	84454266		2203	4300	6503	SO:0001819	synonymous_variant	114798	exon1			GAGCTGGATAGCG	AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"""leucine rich repeat containing 12"""	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1377C>T	chr13.hg19:g.84454266G>A		65.0	0.0		153.0	51.0	NM_052910	Q5U5I6|Q96SF9	Silent	SNP	ENST00000377084.2	hg19	CCDS9464.1																																																																																			.	.		0.542	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910	
DHRS4	10901	hgsc.bcm.edu	37	14	24435604	24435604	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:24435604T>G	ENST00000313250.5	+	6	847	c.644T>G	c.(643-645)aTc>aGc	p.I215S	DHRS4_ENST00000397074.3_Intron|DHRS4_ENST00000559632.1_Intron|DHRS4_ENST00000397075.3_Intron|DHRS4_ENST00000543741.2_Intron|DHRS4_ENST00000397073.2_Intron|DHRS4_ENST00000558581.1_Missense_Mutation_p.I181S|DHRS4_ENST00000558263.1_Intron|DHRS4_ENST00000308178.8_Intron|DHRS4_ENST00000421831.1_Missense_Mutation_p.I163S|DHRS4_ENST00000382761.3_Intron	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	215					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CCTGGACTTATCAAGACTAGC	0.527																																					p.I215S		Atlas-SNP	.											.	DHRS4	22	.	0			c.T644G						.						113.0	96.0	102.0					14																	24435604		2201	4297	6498	SO:0001583	missense	10901	exon6			GACTTATCAAGAC	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.644T>G	chr14.hg19:g.24435604T>G	ENSP00000326219:p.Ile215Ser	182.0	0.0		1253.0	258.0	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	hg19	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.988233	0.53934	.	.	ENSG00000157326	ENST00000313250;ENST00000421831	D;D	0.93307	-3.2;-3.2	3.53	3.53	0.40419	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.96445	0.8840	M	0.86343	2.81	0.80722	D	1	D;D	0.89917	0.997;1.0	P;D	0.97110	0.902;1.0	D	0.96377	0.9278	10	0.87932	D	0	.	10.3596	0.43984	0.0:0.0:0.0:1.0	.	181;215	Q9BTZ2-4;Q9BTZ2	.;DHRS4_HUMAN	S	215;163	ENSP00000326219:I215S;ENSP00000404147:I163S	ENSP00000326219:I215S	I	+	2	0	DHRS4	23505444	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.861000	0.75478	1.379000	0.46325	0.473000	0.43528	ATC	.	.		0.527	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
FOXG1	2290	hgsc.bcm.edu	37	14	29237348	29237348	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:29237348G>A	ENST00000313071.4	+	1	1062	c.863G>A	c.(862-864)cGc>cAc	p.R288H	RP11-966I7.1_ENST00000549487.1_RNA|RP11-966I7.1_ENST00000551395.1_RNA|RP11-966I7.1_ENST00000546560.1_RNA|FOXG1_ENST00000382535.3_Missense_Mutation_p.R288H	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	288				FKRGAR -> AFRWCA (in Ref. 1; CAA52241). {ECO:0000305}.	aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		GCCTTCAAGCGCGGTGCGCGC	0.716																																					p.R288H		Atlas-SNP	.											.	FOXG1	92	.	0			c.G863A						.						32.0	39.0	37.0					14																	29237348		2202	4299	6501	SO:0001583	missense	2290	exon1			TCAAGCGCGGTGC		CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"""Forkhead boxes"""	3811	protein-coding gene	gene with protein product		164874	"""forkhead box G1B"", ""forkhead box G1C"", ""forkhead box G1A"""	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.863G>A	chr14.hg19:g.29237348G>A	ENSP00000339004:p.Arg288His	9.0	0.0		37.0	16.0	NM_005249	A6NFY2|P55315|Q14488|Q86XT7	Missense_Mutation	SNP	ENST00000313071.4	hg19	CCDS9636.1	.	.	.	.	.	.	.	.	.	.	G	32	5.174455	0.94807	.	.	ENSG00000176165	ENST00000382535;ENST00000313071	D;D	0.94687	-3.49;-3.49	4.05	4.05	0.47172	.	0.265561	0.30850	U	0.008757	D	0.95121	0.8419	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.96016	0.9005	10	0.87932	D	0	.	15.7834	0.78281	0.0:0.0:1.0:0.0	.	288	P55316	FOXG1_HUMAN	H	288	ENSP00000371975:R288H;ENSP00000339004:R288H	ENSP00000339004:R288H	R	+	2	0	FOXG1	28307099	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.725000	0.84808	1.777000	0.52277	0.313000	0.20887	CGC	.	.		0.716	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3		
DAAM1	23002	hgsc.bcm.edu	37	14	59820665	59820665	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:59820665T>A	ENST00000395125.1	+	19	2392	c.2369T>A	c.(2368-2370)gTg>gAg	p.V790E	DAAM1_ENST00000351081.1_Missense_Mutation_p.V790E|DAAM1_ENST00000553966.1_Intron|DAAM1_ENST00000360909.3_Missense_Mutation_p.V780E	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	790	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		GTGGCAGAAGTGAAACCTAAA	0.363																																					p.V790E		Atlas-SNP	.											.	DAAM1	95	.	0			c.T2369A						.						98.0	87.0	91.0					14																	59820665		2203	4300	6503	SO:0001583	missense	23002	exon19			CAGAAGTGAAACC	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.2369T>A	chr14.hg19:g.59820665T>A	ENSP00000378557:p.Val790Glu	69.0	0.0		112.0	46.0	NM_014992	Q86U34|Q8N1Z8|Q8TB39	Missense_Mutation	SNP	ENST00000395125.1	hg19	CCDS9737.1	.	.	.	.	.	.	.	.	.	.	t	22.9	4.347348	0.82022	.	.	ENSG00000100592	ENST00000360909;ENST00000351081;ENST00000395125	T;T;T	0.19532	2.14;2.14;2.14	6.03	6.03	0.97812	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.050329	0.85682	D	0.000000	T	0.49949	0.1587	M	0.81802	2.56	0.58432	D	0.999995	D;D	0.69078	0.994;0.997	D;D	0.70227	0.949;0.968	T	0.54166	-0.8334	10	0.87932	D	0	.	16.5808	0.84714	0.0:0.0:0.0:1.0	.	780;790	Q9Y4D1-2;Q9Y4D1	.;DAAM1_HUMAN	E	780;790;790	ENSP00000354162:V780E;ENSP00000247170:V790E;ENSP00000378557:V790E	ENSP00000247170:V790E	V	+	2	0	DAAM1	58890418	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.183000	0.72002	2.317000	0.78254	0.524000	0.50904	GTG	.	.		0.363	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
ZFYVE26	23503	hgsc.bcm.edu	37	14	68274238	68274238	+	Missense_Mutation	SNP	G	G	A	rs267604034		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:68274238G>A	ENST00000347230.4	-	5	901	c.763C>T	c.(763-765)Cgg>Tgg	p.R255W	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.R255W	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	255					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CGCTCCTCCCGCAGGGGACTC	0.627																																					p.R255W		Atlas-SNP	.											ZFYVE26,NS,carcinoma,0,1	ZFYVE26	223	.	0			c.C763T						.						32.0	34.0	33.0					14																	68274238		2203	4300	6503	SO:0001583	missense	23503	exon5			CCTCCCGCAGGGG	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.763C>T	chr14.hg19:g.68274238G>A	ENSP00000251119:p.Arg255Trp	38.0	0.0		64.0	21.0	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.960569	0.53400	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.30714	1.67;1.52	5.43	2.48	0.30137	.	0.598447	0.16810	N	0.198585	T	0.38585	0.1046	L	0.40543	1.245	0.09310	N	1	D;D;D	0.76494	0.999;0.998;0.978	P;P;B	0.53861	0.736;0.736;0.425	T	0.32508	-0.9904	10	0.72032	D	0.01	-0.1957	14.9491	0.71057	0.0:0.0:0.3349:0.6651	.	255;255;255	Q68DK2-4;G3V2D8;Q68DK2	.;.;ZFY26_HUMAN	W	255;234;255	ENSP00000251119:R255W;ENSP00000450603:R255W	ENSP00000251119:R255W	R	-	1	2	ZFYVE26	67343991	0.064000	0.20934	0.177000	0.23020	0.681000	0.39784	1.485000	0.35519	0.215000	0.20761	0.491000	0.48974	CGG	.	.		0.627	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
SIPA1L1	26037	hgsc.bcm.edu	37	14	72190408	72190408	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:72190408G>A	ENST00000555818.1	+	16	4664	c.4316G>A	c.(4315-4317)aGt>aAt	p.S1439N	SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.S1418N|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.S1418N|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.S893N	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1439	Ser-rich.				actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GTTTTCACCAGTGCCCGGAGT	0.537																																					p.S1439N		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.G4316A						.						135.0	111.0	119.0					14																	72190408		2203	4300	6503	SO:0001583	missense	26037	exon16			TCACCAGTGCCCG	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.4316G>A	chr14.hg19:g.72190408G>A	ENSP00000450832:p.Ser1439Asn	68.0	0.0		124.0	41.0	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	hg19	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.674277	0.88445	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;D	0.85484	-1.17;-1.2;-1.17;-1.99	5.54	5.54	0.83059	.	0.170379	0.64402	D	0.000004	D	0.86029	0.5835	N	0.19112	0.55	0.58432	D	0.999999	D;P;D;D;D	0.65815	0.995;0.895;0.989;0.974;0.988	P;B;P;P;P	0.61070	0.836;0.264;0.854;0.796;0.883	D	0.85171	0.0998	10	0.35671	T	0.21	-16.5037	19.8379	0.96666	0.0:0.0:1.0:0.0	.	893;1439;893;1418;1439	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	N	1418;1439;1418;893	ENSP00000370630:S1418N;ENSP00000450832:S1439N;ENSP00000351352:S1418N;ENSP00000440682:S893N	ENSP00000351352:S1439N	S	+	2	0	SIPA1L1	71260161	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.938000	0.70170	2.765000	0.95021	0.655000	0.94253	AGT	.	.		0.537	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	
DPF3	8110	hgsc.bcm.edu	37	14	73159816	73159816	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:73159816G>A	ENST00000556509.1	-	7	709	c.710C>T	c.(709-711)tCc>tTc	p.S237F	DPF3_ENST00000541685.1_Missense_Mutation_p.S237F|DPF3_ENST00000546183.1_Missense_Mutation_p.S247F|DPF3_ENST00000557704.1_5'UTR	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	237					chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GTTGGGTGGGGACCGAGTCTC	0.582																																					p.S237F		Atlas-SNP	.											.	DPF3	117	.	0			c.C710T						.						203.0	204.0	204.0					14																	73159816		2067	4214	6281	SO:0001583	missense	8110	exon7			GGTGGGGACCGAG	U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"""Zinc fingers, PHD-type"""	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.710C>T	chr14.hg19:g.73159816G>A	ENSP00000450518:p.Ser237Phe	159.0	0.0		462.0	175.0	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	hg19		.	.	.	.	.	.	.	.	.	.	G	26.9	4.783260	0.90282	.	.	ENSG00000205683	ENST00000556509;ENST00000398816;ENST00000541685;ENST00000546183	D;T;T	0.90900	-2.75;-0.25;-0.2	5.36	5.36	0.76844	.	.	.	.	.	D	0.92071	0.7487	L	0.47716	1.5	0.80722	D	1	P;D;D	0.61080	0.936;0.978;0.989	P;P;P	0.53912	0.729;0.729;0.737	D	0.92906	0.6343	9	0.87932	D	0	.	19.0841	0.93196	0.0:0.0:1.0:0.0	.	247;237;237	F5H575;Q92784-2;Q92784	.;.;DPF3_HUMAN	F	237;236;237;247	ENSP00000450518:S237F;ENSP00000441640:S237F;ENSP00000444662:S247F	ENSP00000381791:S292F	S	-	2	0	DPF3	72229569	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	9.335000	0.96500	2.504000	0.84457	0.462000	0.41574	TCC	.	.		0.582	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2		
PROX2	283571	hgsc.bcm.edu	37	14	75330524	75330524	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:75330524G>T	ENST00000445876.1	-	1	13	c.14C>A	c.(13-15)tCc>tAc	p.S5Y	PROX2_ENST00000556489.2_Missense_Mutation_p.S5Y|PROX2_ENST00000556084.2_Missense_Mutation_p.S5Y			Q3B8N5	PROX2_HUMAN	prospero homeobox 2	5					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(3)	6			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)		AAGCAAGATGGAGTTTGGATC	0.552																																					p.S5Y		Atlas-SNP	.											PROX2_ENST00000445876,NS,carcinoma,0,2	PROX2	44	.	0			c.C14A						.						66.0	68.0	67.0					14																	75330524		1986	4153	6139	SO:0001583	missense	283571	exon1			AAGATGGAGTTTG		CCDS45136.1, CCDS45136.2, CCDS73663.1	14q24.3	2012-10-02			ENSG00000119608	ENSG00000119608		"""Homeoboxes / PROS class"""	26715	protein-coding gene	gene with protein product		615094					Standard	NM_001080408		Approved	FLJ36749	uc031qpi.1	Q3B8N5	OTTHUMG00000171481	ENST00000445876.1:c.14C>A	chr14.hg19:g.75330524G>T	ENSP00000405932:p.Ser5Tyr	10.0	0.0		21.0	9.0	NM_001080408	C9J5W1|Q8N9Q3	Missense_Mutation	SNP	ENST00000445876.1	hg19	CCDS45136.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.84|17.84	3.488935|3.488935	0.64074|0.64074	.|.	.|.	ENSG00000119608|ENSG00000119608	ENST00000556084|ENST00000556489;ENST00000389664;ENST00000424024;ENST00000445876	.|T;T	.|0.47177	.|0.85;0.85	4.76|4.76	1.83|1.83	0.25207|0.25207	.|.	.|1.400140	.|0.04728	.|N	.|0.420662	T|T	0.32346|0.32346	0.0826|0.0826	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	1|1	.|P	.|0.40398	.|0.716	.|B	.|0.34242	.|0.178	T|T	0.22871|0.22871	-1.0204|-1.0204	5|10	.|0.29301	.|T	.|0.29	-1.0645|-1.0645	2.3974|2.3974	0.04393|0.04393	0.2244:0.1309:0.5105:0.1342|0.2244:0.1309:0.5105:0.1342	.|.	.|5	.|G3V3G0	.|.	T|Y	5|5	.|ENSP00000451223:S5Y;ENSP00000405932:S5Y	.|ENSP00000374315:S5Y	P|S	-|-	1|2	0|0	PROX2|PROX2	74400277|74400277	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.970000|0.970000	0.65996|0.65996	0.616000|0.616000	0.24344|0.24344	0.607000|0.607000	0.29982|0.29982	0.561000|0.561000	0.74099|0.74099	CCA|TCC	.	.		0.552	PROX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
HERC2	8924	hgsc.bcm.edu	37	15	28446674	28446674	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr15:28446674G>C	ENST00000261609.7	-	48	7752	c.7644C>G	c.(7642-7644)agC>agG	p.S2548R		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)		TGTACGTCTGGCTCTCCGTCA	0.368																																					p.S2548R		Atlas-SNP	.											.	HERC2	501	.	0			c.C7644G						.						125.0	114.0	118.0					15																	28446674		2203	4300	6503	SO:0001583	missense	8924	exon48			CGTCTGGCTCTCC	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.7644C>G	chr15.hg19:g.28446674G>C	ENSP00000261609:p.Ser2548Arg	135.0	0.0		378.0	146.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.263445	0.59431	.	.	ENSG00000128731	ENST00000261609	T	0.38887	1.11	5.18	3.3	0.37823	.	0.043831	0.85682	D	0.000000	T	0.55800	0.1943	L	0.56769	1.78	0.80722	D	1	D;D	0.71674	0.998;0.995	D;D	0.75484	0.986;0.979	T	0.49532	-0.8930	10	0.25106	T	0.35	.	11.6869	0.51492	0.1348:0.0:0.8652:0.0	.	15;2548	A8KAQ8;O95714	.;HERC2_HUMAN	R	2548	ENSP00000261609:S2548R	ENSP00000261609:S2548R	S	-	3	2	HERC2	26120269	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.798000	0.38814	0.691000	0.31592	0.561000	0.74099	AGC	.	.		0.368	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
AQR	9716	hgsc.bcm.edu	37	15	35198872	35198872	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr15:35198872G>T	ENST00000156471.5	-	18	1930	c.1705C>A	c.(1705-1707)Ccc>Acc	p.P569T		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	569					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		GGTTTTGTGGGACGTACGGTA	0.388																																					p.P569T		Atlas-SNP	.											.	AQR	139	.	0			c.C1705A						.						126.0	113.0	117.0					15																	35198872		1901	4133	6034	SO:0001583	missense	9716	exon18			TTGTGGGACGTAC	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 164"""	610548	"""aquarius homolog (mouse)"""			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.1705C>A	chr15.hg19:g.35198872G>T	ENSP00000156471:p.Pro569Thr	58.0	0.0		100.0	39.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	hg19	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962361	0.74016	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	D	0.94232	-3.38	5.44	4.51	0.55191	.	0.047946	0.85682	N	0.000000	D	0.96917	0.8993	M	0.93763	3.455	0.48087	D	0.999589	D	0.69078	0.997	P	0.58210	0.835	D	0.97610	1.0129	10	0.72032	D	0.01	-11.5427	15.454	0.75299	0.0:0.0:0.8602:0.1398	.	569	O60306	AQR_HUMAN	T	569	ENSP00000156471:P569T	ENSP00000156471:P569T	P	-	1	0	AQR	32986164	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.416000	0.97383	1.252000	0.44001	0.591000	0.81541	CCC	.	.		0.388	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691	
PEAK1	79834	hgsc.bcm.edu	37	15	77425574	77425574	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr15:77425574C>A	ENST00000560626.2	-	6	4325	c.3850G>T	c.(3850-3852)Gag>Tag	p.E1284*	PEAK1_ENST00000312493.4_Nonsense_Mutation_p.E1284*			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1284					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										ACTACTTCCTCCCGATTCTCA	0.532																																					p.E1284X		Atlas-SNP	.											.	.	.	.	0			c.G3850T						.						147.0	143.0	144.0					15																	77425574		1877	4106	5983	SO:0001587	stop_gained	0	exon7			CTTCCTCCCGATT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.3850G>T	chr15.hg19:g.77425574C>A	ENSP00000452796:p.Glu1284*	103.0	0.0		234.0	85.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Nonsense_Mutation	SNP	ENST00000560626.2	hg19	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	C	46	12.343992	0.99659	.	.	ENSG00000173517	ENST00000312493	.	.	.	5.61	5.61	0.85477	.	0.107611	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-9.2526	12.908	0.58164	0.0:0.9258:0.0:0.0742	.	.	.	.	X	1284	.	ENSP00000309230:E1284X	E	-	1	0	AC087465.1	75212629	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.091000	0.71406	2.642000	0.89623	0.655000	0.94253	GAG	.	.		0.532	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
CREBBP	1387	hgsc.bcm.edu	37	16	3778620	3778620	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr16:3778620T>C	ENST00000262367.5	-	31	7237	c.6428A>G	c.(6427-6429)aAt>aGt	p.N2143S	CREBBP_ENST00000382070.3_Missense_Mutation_p.N2105S	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2143					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)		CTGCATGGCATTCAGGTTCTG	0.682			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.N2143S		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.A6428G						.						56.0	60.0	58.0					16																	3778620		2197	4298	6495	SO:0001583	missense	1387	exon31			ATGGCATTCAGGT	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.6428A>G	chr16.hg19:g.3778620T>C	ENSP00000262367:p.Asn2143Ser	23.0	0.0		63.0	18.0	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	t	4.459	0.084939	0.08583	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.83163	-1.69;-1.58	5.11	3.99	0.46301	.	0.195425	0.44483	N	0.000447	T	0.60117	0.2244	N	0.08118	0	0.33369	D	0.573358	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.57894	-0.7732	10	0.10111	T	0.7	-9.9425	5.7003	0.17879	0.0:0.2769:0.0:0.7231	.	2173;2143	Q4LE28;Q92793	.;CBP_HUMAN	S	2143;2173;2105;678	ENSP00000262367:N2143S;ENSP00000371502:N2105S	ENSP00000262367:N2143S	N	-	2	0	CREBBP	3718621	0.098000	0.21812	0.904000	0.35570	0.512000	0.34134	1.013000	0.29937	1.934000	0.56057	0.533000	0.62120	AAT	.	.		0.682	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
GGA2	23062	hgsc.bcm.edu	37	16	23489767	23489767	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr16:23489767G>A	ENST00000309859.4	-	13	1296	c.1214C>T	c.(1213-1215)cCa>cTa	p.P405L	GGA2_ENST00000567468.1_Intron|GGA2_ENST00000569182.1_5'UTR	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	405	Unstructured hinge.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		ACCACCGCCTGGCAGCGTGCT	0.532																																					p.P405L		Atlas-SNP	.											.	GGA2	49	.	0			c.C1214T						.						110.0	99.0	103.0					16																	23489767		2197	4300	6497	SO:0001583	missense	23062	exon13			CCGCCTGGCAGCG	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.1214C>T	chr16.hg19:g.23489767G>A	ENSP00000311962:p.Pro405Leu	58.0	0.0		101.0	44.0	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	hg19	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	G	9.964	1.223606	0.22457	.	.	ENSG00000103365	ENST00000309859	T	0.14893	2.47	4.11	2.0	0.26442	.	487.764000	0.00166	N	0.000000	T	0.19208	0.0461	L	0.54323	1.7	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19614	-1.0300	10	0.34782	T	0.22	-0.0382	5.4904	0.16773	0.2876:0.0:0.7124:0.0	.	405	Q9UJY4	GGA2_HUMAN	L	405	ENSP00000311962:P405L	ENSP00000311962:P405L	P	-	2	0	GGA2	23397268	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.371000	0.20450	0.403000	0.25479	-0.345000	0.07892	CCA	.	.		0.532	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1		
IL21R	50615	hgsc.bcm.edu	37	16	27460101	27460101	+	Missense_Mutation	SNP	G	G	T	rs36031126		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr16:27460101G>T	ENST00000337929.3	+	9	1587	c.1114G>T	c.(1114-1116)Ggc>Tgc	p.G372C	IL21R_ENST00000395754.4_Missense_Mutation_p.G372C|IL21R_ENST00000564089.1_Missense_Mutation_p.G372C|IL21R_ENST00000395755.1_Missense_Mutation_p.G372C|IL21R-AS1_ENST00000563191.1_RNA	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	372					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						TCGGCCATACGGCCTGGTGTC	0.627			T	BCL6	NHL																																p.G394C		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.G1180T						.						65.0	62.0	63.0					16																	27460101		2197	4300	6497	SO:0001583	missense	50615	exon10			CCATACGGCCTGG	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"""Interleukins and interleukin receptors"", ""CD molecules"""	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1114G>T	chr16.hg19:g.27460101G>T	ENSP00000338010:p.Gly372Cys	19.0	0.0		56.0	19.0	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	hg19	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.337208	0.41398	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.44083	0.93;0.93;0.93	5.19	5.19	0.71726	.	7.212420	0.00166	N	0.000004	T	0.69851	0.3157	M	0.69823	2.125	0.29219	N	0.874075	D	0.89917	1.0	D	0.97110	1.0	T	0.54118	-0.8341	10	0.72032	D	0.01	-25.7504	14.2483	0.66001	0.0:0.0:1.0:0.0	.	372	Q9HBE5	IL21R_HUMAN	C	372	ENSP00000338010:G372C;ENSP00000379104:G372C;ENSP00000379103:G372C	ENSP00000338010:G372C	G	+	1	0	IL21R	27367602	0.997000	0.39634	0.040000	0.18447	0.036000	0.12997	3.922000	0.56462	2.426000	0.82243	0.561000	0.74099	GGC	.	G|0.986;A|0.014		0.627	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078	
CES4A	283848	hgsc.bcm.edu	37	16	67038121	67038121	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr16:67038121G>T	ENST00000326686.5	+	9	1074	c.1074G>T	c.(1072-1074)ttG>ttT	p.L358F	CES4A_ENST00000338718.4_Missense_Mutation_p.L381F|CES4A_ENST00000535696.1_Missense_Mutation_p.L264F|CES4A_ENST00000540947.2_Missense_Mutation_p.L358F|CES4A_ENST00000541479.1_Missense_Mutation_p.L381F|CES4A_ENST00000540579.1_Missense_Mutation_p.L260F|CES4A_ENST00000398354.1_Missense_Mutation_p.L358F			Q5XG92	EST4A_HUMAN	carboxylesterase 4A	358						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			large_intestine(2)|liver(2)|lung(4)|ovary(1)	9						ATTGGCTCTTGCCTTATGTAA	0.517																																					p.L358F		Atlas-SNP	.											.	CES4A	24	.	0			c.G1074T						.						149.0	141.0	144.0					16																	67038121		1981	4172	6153	SO:0001583	missense	283848	exon9			GCTCTTGCCTTAT	AK094783	CCDS42174.1, CCDS42174.2, CCDS54024.1, CCDS54025.1, CCDS42174.3	16q22.1	2011-10-25	2010-10-12	2010-10-12	ENSG00000172824	ENSG00000172824		"""Carboxylesterases"""	26741	protein-coding gene	gene with protein product			"""carboxylesterase 8 (putative)"""	CES8		12975309, 17364878, 20931200	Standard	NM_001190201		Approved	FLJ37464	uc010vix.2	Q5XG92		ENST00000326686.5:c.1074G>T	chr16.hg19:g.67038121G>T	ENSP00000314145:p.Leu358Phe	79.0	0.0		210.0	76.0	NM_173815	A8KAJ6|B7Z349|B7Z3L2|B7Z6R3|Q6UX55|Q8N9F4	Missense_Mutation	SNP	ENST00000326686.5	hg19		.	.	.	.	.	.	.	.	.	.	g	7.020	0.558476	0.13436	.	.	ENSG00000172824	ENST00000540947;ENST00000541479;ENST00000338718;ENST00000398354;ENST00000326686;ENST00000538199;ENST00000540579;ENST00000535696	T;T;T;T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45	4.63	1.3	0.21679	Carboxylesterase, type B (1);	0.000000	0.35772	N	0.002995	T	0.69251	0.3090	L	0.56199	1.76	0.51767	D	0.999931	B;D;B;B	0.59767	0.026;0.986;0.0;0.001	B;P;B;B	0.59221	0.018;0.854;0.021;0.01	T	0.67684	-0.5607	10	0.87932	D	0	.	6.5077	0.22204	0.205:0.1878:0.6072:0.0	.	264;381;358;381	Q5XG92-7;F8WEE9;Q5XG92;F5H5S4	.;.;EST4A_HUMAN;.	F	358;381;381;358;358;321;260;264	ENSP00000444052:L358F;ENSP00000443175:L381F;ENSP00000340714:L381F;ENSP00000381397:L358F;ENSP00000314145:L358F;ENSP00000441103:L321F;ENSP00000441907:L260F;ENSP00000441644:L264F	ENSP00000314145:L358F	L	+	3	2	CES4A	65595622	0.910000	0.30920	0.908000	0.35775	0.142000	0.21351	-0.083000	0.11286	0.372000	0.24591	0.486000	0.48141	TTG	.	.		0.517	CES4A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173815	
ANKRD11	29123	hgsc.bcm.edu	37	16	89349770	89349770	+	Silent	SNP	T	T	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr16:89349770T>C	ENST00000301030.4	-	9	3640	c.3180A>G	c.(3178-3180)aaA>aaG	p.K1060K	ANKRD11_ENST00000378330.2_Silent_p.K1060K	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1060	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		CCTTGGTATCTTTTTTCTCTT	0.378																																					p.K1060K		Atlas-SNP	.											.	ANKRD11	195	.	0			c.A3180G						.						125.0	133.0	131.0					16																	89349770		2198	4300	6498	SO:0001819	synonymous_variant	29123	exon9			GGTATCTTTTTTC	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.3180A>G	chr16.hg19:g.89349770T>C		124.0	0.0		277.0	115.0	NM_001256183	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	hg19	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	T	9.261	1.043111	0.19748	.	.	ENSG00000167522	ENST00000330736	.	.	.	5.39	-2.32	0.06745	.	0.000000	0.85682	D	0.000000	T	0.69672	0.3137	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73056	-0.4103	6	0.87932	D	0	.	13.4948	0.61419	0.0:0.4567:0.0:0.5433	.	.	.	.	R	611	.	ENSP00000330815:K611R	K	-	2	0	ANKRD11	87877271	0.989000	0.36119	0.884000	0.34674	0.989000	0.77384	0.225000	0.17757	-0.377000	0.07930	0.533000	0.62120	AAG	.	.		0.378	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275	
MED13	9969	hgsc.bcm.edu	37	17	60088347	60088347	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr17:60088347T>C	ENST00000397786.2	-	9	1607	c.1531A>G	c.(1531-1533)Atc>Gtc	p.I511V		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	511					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)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TTAGTTCGGATATTTGAAAAT	0.473																																					p.I511V		Atlas-SNP	.											.	MED13	181	.	0			c.A1531G						.						174.0	169.0	171.0					17																	60088347		1998	4172	6170	SO:0001583	missense	9969	exon9			TTCGGATATTTGA	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.1531A>G	chr17.hg19:g.60088347T>C	ENSP00000380888:p.Ile511Val	155.0	0.0		539.0	148.0	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	T	9.364	1.068753	0.20147	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.73469	-0.75	6.16	5.07	0.68467	.	0.182595	0.56097	D	0.000025	T	0.65144	0.2663	L	0.44542	1.39	0.45733	D	0.998636	B;B	0.30193	0.069;0.272	B;B	0.26864	0.068;0.074	T	0.59700	-0.7405	10	0.25751	T	0.34	-6.9427	12.7623	0.57372	0.0:0.0:0.2583:0.7417	.	24;511	Q9P0Q5;Q9UHV7	.;MED13_HUMAN	V	511;510	ENSP00000380888:I511V	ENSP00000262436:I510V	I	-	1	0	MED13	57443129	1.000000	0.71417	0.998000	0.56505	0.943000	0.58893	2.423000	0.44705	1.117000	0.41842	0.528000	0.53228	ATC	.	.		0.473	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
TYMS	7298	hgsc.bcm.edu	37	18	671451	671451	+	Splice_Site	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr18:671451G>A	ENST00000323274.10	+	6	943	c.804G>A	c.(802-804)caG>caA	p.Q268Q	TYMS_ENST00000323250.5_Splice_Site_p.Q185Q|TYMS_ENST00000581920.1_3'UTR|ENOSF1_ENST00000583973.1_5'Flank|TYMS_ENST00000323224.7_Splice_Site_p.Q234Q	NM_001071.2	NP_001062.1	P04818	TYSY_HUMAN	thymidylate synthetase	268					aging (GO:0007568)|cartilage development (GO:0051216)|circadian rhythm (GO:0007623)|deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|developmental growth (GO:0048589)|dTMP biosynthetic process (GO:0006231)|dTTP biosynthetic process (GO:0006235)|dUMP metabolic process (GO:0046078)|G1/S transition of mitotic cell cycle (GO:0000082)|immortalization of host cell by virus (GO:0019088)|intestinal epithelial cell maturation (GO:0060574)|mitotic cell cycle (GO:0000278)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|organ regeneration (GO:0031100)|polysaccharide metabolic process (GO:0005976)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to organophosphorus (GO:0046683)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|response to vitamin A (GO:0033189)|small molecule metabolic process (GO:0044281)|tetrahydrofolate metabolic process (GO:0046653)|uracil metabolic process (GO:0019860)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cofactor binding (GO:0048037)|drug binding (GO:0008144)|folic acid binding (GO:0005542)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|thymidylate synthase activity (GO:0004799)			endometrium(1)|large_intestine(3)|lung(2)|urinary_tract(2)	8					Capecitabine(DB01101)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Leucovorin(DB00650)|Methotrexate(DB00563)|Pemetrexed(DB00642)|Pralatrexate(DB06813)|Raltitrexed(DB00293)|Trifluridine(DB00432)|Trimethoprim(DB00440)	TGAAAATTCAGGTAAGAATTA	0.413																																					p.Q268Q		Atlas-SNP	.											.	TYMS	27	.	0			c.G804A						.						101.0	99.0	100.0					18																	671451		2203	4300	6503	SO:0001630	splice_region_variant	7298	exon6			AATTCAGGTAAGA	X02308	CCDS11821.1	18p11.31-p11.21	2014-09-17			ENSG00000176890	ENSG00000176890	2.1.1.45		12441	protein-coding gene	gene with protein product		188350		TS			Standard	NM_001071		Approved	Tsase, TMS, HsT422	uc010dka.1	P04818	OTTHUMG00000131473	ENST00000323274.10:c.804+1G>A	chr18.hg19:g.671451G>A		72.0	0.0		151.0	57.0	NM_001071	Q8WYK3|Q8WYK4	Silent	SNP	ENST00000323274.10	hg19	CCDS11821.1																																																																																			.	.		0.413	TYMS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254316.1	NM_001071	Silent
VPS4B	9525	hgsc.bcm.edu	37	18	61067824	61067824	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr18:61067824T>C	ENST00000238497.5	-	6	800	c.597A>G	c.(595-597)atA>atG	p.I199M	VPS4B_ENST00000591383.1_5'UTR	NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)	199					ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						CAGAGGAAGATATTGAAAAAA	0.373																																					p.I199M		Atlas-SNP	.											.	VPS4B	33	.	0			c.A597G						.						115.0	115.0	115.0					18																	61067824		2203	4300	6503	SO:0001583	missense	9525	exon6			GGAAGATATTGAA	AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"""ATPases / AAA-type"""	10895	protein-coding gene	gene with protein product		609983	"""suppressor of K+ transport defect 1"", ""vacuolar protein sorting 4B (yeast)"""	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.597A>G	chr18.hg19:g.61067824T>C	ENSP00000238497:p.Ile199Met	99.0	0.0		211.0	88.0	NM_004869	Q69HW4|Q9GZS7	Missense_Mutation	SNP	ENST00000238497.5	hg19	CCDS11983.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.529046	0.64860	.	.	ENSG00000119541	ENST00000238497	D	0.95853	-3.83	6.11	4.95	0.65309	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.173761	0.64402	D	0.000009	D	0.96383	0.8820	M	0.64567	1.98	0.80722	D	1	B;B;P	0.34837	0.295;0.295;0.472	P;P;P	0.51385	0.668;0.668;0.668	D	0.95892	0.8908	10	0.87932	D	0	-15.9957	12.4617	0.55734	0.0:0.0653:0.0:0.9347	.	199;199;199	A8K5D8;A8K4G7;O75351	.;.;VPS4B_HUMAN	M	199	ENSP00000238497:I199M	ENSP00000238497:I199M	I	-	3	3	VPS4B	59218804	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.712000	0.37940	1.119000	0.41883	0.533000	0.62120	ATA	.	.		0.373	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869	
ATCAY	85300	hgsc.bcm.edu	37	19	3910853	3910853	+	Missense_Mutation	SNP	C	C	T	rs376658701		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr19:3910853C>T	ENST00000450849.2	+	8	1299	c.832C>T	c.(832-834)Cgg>Tgg	p.R278W	ATCAY_ENST00000301260.6_Missense_Mutation_p.R278W|ATCAY_ENST00000398448.3_Missense_Mutation_p.R284W|ATCAY_ENST00000600960.1_Missense_Mutation_p.R278W	NM_033064.4	NP_149053.1	Q86WG3	ATCAY_HUMAN	ataxia, cerebellar, Cayman type	278	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Mediates interaction with GLS.				apoptotic process (GO:0006915)|mitochondrion distribution (GO:0048311)|negative regulation of glutamate metabolic process (GO:2000212)|neuron projection development (GO:0031175)|regulation of protein localization (GO:0032880)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|synapse (GO:0045202)	kinesin binding (GO:0019894)	p.R278W(1)		breast(1)|endometrium(2)|kidney(2)|lung(2)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		GTGGTTCATTCGGACTGTGCT	0.592																																					p.R278W		Atlas-SNP	.											ATCAY_ENST00000450849,rectum,carcinoma,0,1	ATCAY	84	.	1	Substitution - Missense(1)	large_intestine(1)	c.C832T						.	C	TRP/ARG	0,4270		0,0,2135	119.0	127.0	124.0		832	4.3	1.0	19		124	1,8483		0,1,4241	no	missense	ATCAY	NM_033064.4	101	0,1,6376	TT,TC,CC		0.0118,0.0,0.0078	probably-damaging	278/372	3910853	1,12753	2135	4242	6377	SO:0001583	missense	85300	exon8			TTCATTCGGACTG		CCDS45923.1	19p13.3	2014-06-24	2008-07-18		ENSG00000167654	ENSG00000167654			779	protein-coding gene	gene with protein product	"""Cayman ataxia"", ""caytaxin"""	608179				8845847, 14556008	Standard	NM_033064		Approved		uc002lyy.4	Q86WG3	OTTHUMG00000181836	ENST00000450849.2:c.832C>T	chr19.hg19:g.3910853C>T	ENSP00000390941:p.Arg278Trp	64.0	0.0		137.0	63.0	NM_033064	Q8NAQ2|Q8TAQ3|Q96HC6|Q96JF5	Missense_Mutation	SNP	ENST00000450849.2	hg19	CCDS45923.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.366995	0.82463	0.0	1.18E-4	ENSG00000167654	ENST00000450849;ENST00000301260;ENST00000357694;ENST00000398448;ENST00000539301	T;T;T	0.67523	-0.27;-0.27;-0.27	4.35	4.35	0.52113	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.063315	0.64402	D	0.000008	D	0.84174	0.5414	M	0.91717	3.235	0.50813	D	0.999898	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.87653	0.2529	10	0.87932	D	0	-2.6229	12.7004	0.57029	0.165:0.835:0.0:0.0	.	284;278;278	B4DS11;Q86WG3-3;Q86WG3	.;.;ATCAY_HUMAN	W	278;278;278;284;256	ENSP00000390941:R278W;ENSP00000301260:R278W;ENSP00000381466:R284W	ENSP00000301260:R278W	R	+	1	2	ATCAY	3861853	0.998000	0.40836	0.999000	0.59377	0.977000	0.68977	3.866000	0.56040	1.970000	0.57323	0.456000	0.33151	CGG	.	.		0.592	ATCAY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457872.2		
ZNF441	126068	hgsc.bcm.edu	37	19	11888443	11888443	+	Silent	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr19:11888443G>A	ENST00000357901.4	+	2	123	c.21G>A	c.(19-21)gaG>gaA	p.E7E	ZNF441_ENST00000454339.2_5'UTR	NM_152355.2	NP_689568.2	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	7	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)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGGCATTTGAGGATGTGGCTA	0.438																																					p.E7E		Atlas-SNP	.											.	ZNF441	123	.	0			c.G21A						.						112.0	94.0	100.0					19																	11888443		692	1591	2283	SO:0001819	synonymous_variant	126068	exon2			ATTTGAGGATGTG	AK095956	CCDS12266.2	19p13.13	2013-01-08			ENSG00000197044	ENSG00000197044		"""Zinc fingers, C2H2-type"", ""-"""	20875	protein-coding gene	gene with protein product							Standard	NM_152355		Approved	FLJ38637	uc010dyj.3	Q8N8Z8	OTTHUMG00000154449	ENST00000357901.4:c.21G>A	chr19.hg19:g.11888443G>A		104.0	0.0		223.0	78.0	NM_152355		Silent	SNP	ENST00000357901.4	hg19	CCDS12266.2																																																																																			.	.		0.438	ZNF441-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335273.3	NM_152355	
FUZ	80199	hgsc.bcm.edu	37	19	50314913	50314913	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr19:50314913A>G	ENST00000313777.4	-	4	525	c.362T>C	c.(361-363)gTg>gCg	p.V121A	AC006942.4_ENST00000600669.1_RNA|FUZ_ENST00000445575.2_Missense_Mutation_p.V121A|FUZ_ENST00000533418.1_Missense_Mutation_p.V71A|FUZ_ENST00000534008.1_5'UTR|FUZ_ENST00000528094.1_Missense_Mutation_p.V85A|FUZ_ENST00000526575.1_3'UTR	NM_025129.4	NP_079405.2	Q9BT04	FUZZY_HUMAN	fuzzy planar cell polarity protein	121					cilium assembly (GO:0042384)|embryonic body morphogenesis (GO:0010172)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of planar polarity (GO:0001736)|hair follicle development (GO:0001942)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)|negative regulation of neural crest formation (GO:0090301)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|positive regulation of cilium assembly (GO:0045724)|protein transport (GO:0015031)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)				endometrium(1)|lung(3)	4		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00793)|GBM - Glioblastoma multiforme(134;0.0116)		CAGTCTCTCCACGTTGCGGAT	0.527																																					p.V121A		Atlas-SNP	.											.	FUZ	18	.	0			c.T362C						.						379.0	343.0	355.0					19																	50314913		2203	4300	6503	SO:0001583	missense	80199	exon4			CTCTCCACGTTGC	BC016793	CCDS12781.1, CCDS54293.1	19q13.33	2013-03-05	2013-03-05			ENSG00000010361			26219	protein-coding gene	gene with protein product		610622	"""fuzzy homolog (Drosophila)"""			21761479	Standard	NM_001171937		Approved	FLJ22688, Fy	uc002ppq.2	Q9BT04		ENST00000313777.4:c.362T>C	chr19.hg19:g.50314913A>G	ENSP00000313309:p.Val121Ala	102.0	0.0		195.0	73.0	NM_025129	B2RD86|B5MDH0|Q6PJY0|Q9H613	Missense_Mutation	SNP	ENST00000313777.4	hg19	CCDS12781.1	.	.	.	.	.	.	.	.	.	.	A	17.40	3.380908	0.61845	.	.	ENSG00000010361	ENST00000528094;ENST00000533418;ENST00000529634;ENST00000313777;ENST00000377092;ENST00000445575;ENST00000529004;ENST00000421740	T;T;T;T;T	0.72942	2.21;2.21;2.21;-0.7;2.21	4.83	4.83	0.62350	.	0.233514	0.33875	N	0.004474	T	0.69305	0.3096	L	0.49350	1.555	0.48341	D	0.999632	P;P;B	0.49961	0.93;0.787;0.202	P;B;B	0.47915	0.561;0.359;0.059	T	0.73360	-0.4007	10	0.87932	D	0	-11.0074	10.7112	0.45984	1.0:0.0:0.0:0.0	.	121;85;121	B4DHF8;Q9BT04-3;Q9BT04	.;.;FUZZY_HUMAN	A	85;71;121;121;21;121;71;121	ENSP00000435177:V85A;ENSP00000431731:V71A;ENSP00000313309:V121A;ENSP00000366296:V21A;ENSP00000408018:V121A	ENSP00000313309:V121A	V	-	2	0	FUZ	55006725	0.713000	0.27926	0.988000	0.46212	0.970000	0.65996	5.556000	0.67307	2.026000	0.59711	0.379000	0.24179	GTG	.	.		0.527	FUZ-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393986.1	NM_025129	
SSC5D	284297	hgsc.bcm.edu	37	19	56029616	56029616	+	Missense_Mutation	SNP	C	C	A	rs35104581|rs150781976	byFrequency	TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr19:56029616C>A	ENST00000389623.6	+	14	3996	c.3973C>A	c.(3973-3975)Ccc>Acc	p.P1325T		NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	1325	Pro-rich.|Thr-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						gacccctcaccccACAACTCC	0.597																																					p.P1325T		Atlas-SNP	.											.	SSC5D	65	.	0			c.C3973A						.						343.0	327.0	332.0					19																	56029616		692	1591	2283	SO:0001583	missense	284297	exon14			CCTCACCCCACAA		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.3973C>A	chr19.hg19:g.56029616C>A	ENSP00000374274:p.Pro1325Thr	29.0	0.0		153.0	8.0	NM_001144950	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Missense_Mutation	SNP	ENST00000389623.6	hg19	CCDS46196.1	.	.	.	.	.	.	.	.	.	.	-	10.40	1.340729	0.24339	.	.	ENSG00000179954	ENST00000389623	T	0.01902	4.57	2.21	2.21	0.28008	.	.	.	.	.	T	0.02119	0.0066	L	0.27053	0.805	0.09310	N	1	B	0.23854	0.092	B	0.14023	0.01	T	0.42361	-0.9456	9	0.72032	D	0.01	.	8.4195	0.32692	0.0:1.0:0.0:0.0	.	1325	A1L4H1	SRCRL_HUMAN	T	1325	ENSP00000374274:P1325T	ENSP00000374274:P1325T	P	+	1	0	SSC5D	60721428	0.006000	0.16342	0.012000	0.15200	0.113000	0.19764	0.520000	0.22878	1.174000	0.42811	0.165000	0.16767	CCC	.	.		0.597	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
ZSCAN1	284312	hgsc.bcm.edu	37	19	58565348	58565348	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr19:58565348G>A	ENST00000282326.1	+	6	1403	c.1156G>A	c.(1156-1158)Ggg>Agg	p.G386R		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	386					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		TAGCGTCTGCGGGAAGGCCTT	0.692																																					p.G386R		Atlas-SNP	.											ZSCAN1,NS,carcinoma,0,1	ZSCAN1	102	.	0			c.G1156A						.						23.0	26.0	25.0					19																	58565348		2201	4298	6499	SO:0001583	missense	284312	exon6			GTCTGCGGGAAGG	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"""-"", ""Zinc fingers, C2H2-type"""	23712	protein-coding gene	gene with protein product			"""zinc finger with SCAN domain 1"""			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.1156G>A	chr19.hg19:g.58565348G>A	ENSP00000282326:p.Gly386Arg	31.0	0.0		43.0	10.0	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	hg19	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.506740	0.64410	.	.	ENSG00000152467	ENST00000282326	T	0.59224	0.28	0.993	0.993	0.19825	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.67239	0.2872	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67309	-0.5703	9	0.87932	D	0	.	7.8299	0.29336	0.0:0.0:1.0:0.0	.	386	Q8NBB4	ZSCA1_HUMAN	R	386	ENSP00000282326:G386R	ENSP00000282326:G386R	G	+	1	0	ZSCAN1	63257160	0.996000	0.38824	0.016000	0.15963	0.376000	0.30014	1.137000	0.31479	0.835000	0.34877	0.313000	0.20887	GGG	.	.		0.692	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572	
SYNGR1	9145	hgsc.bcm.edu	37	22	39777778	39777778	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr22:39777778C>A	ENST00000328933.5	+	4	576	c.561C>A	c.(559-561)gaC>gaA	p.D187E		NM_004711.4	NP_004702.2	O43759	SNG1_HUMAN	synaptogyrin 1	187					protein targeting (GO:0006605)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle membrane (GO:0030672)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	7	Melanoma(58;0.04)					ACTACATGGACCCCAGCCAGG	0.687																																					p.D187E		Atlas-SNP	.											.	SYNGR1	19	.	0			c.C561A						.						49.0	50.0	50.0					22																	39777778		2203	4300	6503	SO:0001583	missense	9145	exon4			CATGGACCCCAGC	AJ002303	CCDS13989.1, CCDS13990.1, CCDS13991.1	22q13	2008-06-10			ENSG00000100321	ENSG00000100321			11498	protein-coding gene	gene with protein product		603925				9760194, 10595519	Standard	NM_004711		Approved			O43759	OTTHUMG00000030978	ENST00000328933.5:c.561C>A	chr22.hg19:g.39777778C>A	ENSP00000332287:p.Asp187Glu	27.0	0.0		97.0	36.0	NM_004711	A6NP69|A8K0E2|O43757|O43758|Q53Y02|Q96J56|Q9UGZ4	Missense_Mutation	SNP	ENST00000328933.5	hg19	CCDS13989.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.155681	0.57259	.	.	ENSG00000100321	ENST00000328933	T	0.65732	-0.17	4.52	-0.00232	0.14030	.	0.047898	0.85682	D	0.000000	T	0.54351	0.1853	M	0.74647	2.275	0.80722	D	1	P	0.48089	0.905	B	0.39152	0.292	T	0.52939	-0.8508	10	0.33141	T	0.24	.	9.3548	0.38159	0.0:0.7044:0.0:0.2956	.	187	O43759	SNG1_HUMAN	E	187	ENSP00000332287:D187E	ENSP00000332287:D187E	D	+	3	2	SYNGR1	38107724	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	2.340000	0.43974	-0.063000	0.13065	0.462000	0.41574	GAC	.	.		0.687	SYNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075866.2	NM_004711	
CNKSR2	22866	hgsc.bcm.edu	37	X	21545015	21545015	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chrX:21545015G>A	ENST00000379510.3	+	10	1024	c.988G>A	c.(988-990)Gtt>Att	p.V330I	CNKSR2_ENST00000279451.4_Missense_Mutation_p.V330I|CNKSR2_ENST00000425654.2_Missense_Mutation_p.V330I|CNKSR2_ENST00000543067.1_Missense_Mutation_p.V281I	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2	330					regulation of signal transduction (GO:0009966)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3)	61						CACAAGCAGCGTTGCCACGCC	0.453													G|||	1	0.000264901	0.0	0.0	3775	,	,		7043	0.0		0.0	False		,,,				2504	0.001				p.V330I		Atlas-SNP	.											.	CNKSR2	158	.	0			c.G988A						.						222.0	211.0	215.0					X																	21545015		2203	4300	6503	SO:0001583	missense	22866	exon10			AGCAGCGTTGCCA	AB020709	CCDS14198.1, CCDS55387.1, CCDS55388.1, CCDS55389.1	Xp22.12	2013-01-10			ENSG00000149970	ENSG00000149970		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	19701	protein-coding gene	gene with protein product		300724					Standard	NM_014927		Approved	KIAA0902, CNK2, KSR2	uc004czx.2	Q8WXI2	OTTHUMG00000021233	ENST00000379510.3:c.988G>A	chrX.hg19:g.21545015G>A	ENSP00000368824:p.Val330Ile	60.0	0.0		177.0	163.0	NM_001168647	B4DGR4|B7ZLJ1|B9EG83|E7ESA4|O94976|Q5JPK4|Q5JPN0|Q8WXI1	Missense_Mutation	SNP	ENST00000379510.3	hg19	CCDS14198.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.384359	0.42308	.	.	ENSG00000149970	ENST00000425654;ENST00000543067;ENST00000279451;ENST00000379510	T;T;T;T	0.18502	2.5;2.25;2.21;2.48	5.58	4.66	0.58398	.	0.196899	0.43416	D	0.000563	T	0.06826	0.0174	N	0.02011	-0.69	0.24045	N	0.996062	B;B;B	0.20988	0.029;0.05;0.007	B;B;B	0.12156	0.007;0.003;0.002	T	0.29852	-0.9998	10	0.17832	T	0.49	-9.6134	14.3431	0.66641	0.0:0.0:0.8514:0.1485	.	330;281;330	B7ZLJ1;B4DGR4;Q8WXI2	.;.;CNKR2_HUMAN	I	330;281;330;330	ENSP00000397906:V330I;ENSP00000444633:V281I;ENSP00000279451:V330I;ENSP00000368824:V330I	ENSP00000279451:V330I	V	+	1	0	CNKSR2	21454936	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.870000	0.63035	2.338000	0.79540	0.544000	0.68410	GTT	.	.		0.453	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	NM_014927	
TAF7L	54457	hgsc.bcm.edu	37	X	100547906	100547906	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chrX:100547906T>A	ENST00000372907.3	-	1	139	c.128A>T	c.(127-129)tAt>tTt	p.Y43F	TAF7L_ENST00000356784.1_5'Flank|TAF7L_ENST00000372905.2_5'UTR	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	43					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						GCTGCTTTCATAGGTGGTTTC	0.527																																					p.Y43F	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.A128T						.						175.0	172.0	173.0					X																	100547906		2203	4300	6503	SO:0001583	missense	54457	exon1			CTTTCATAGGTGG	AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"""cancer/testis antigen 40"""	300314	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"""	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.128A>T	chrX.hg19:g.100547906T>A	ENSP00000361998:p.Tyr43Phe	69.0	0.0		236.0	213.0	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	hg19	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	T	1.946	-0.442518	0.04604	.	.	ENSG00000102387	ENST00000372907	T	0.13901	2.55	3.67	0.913	0.19354	.	1.853500	0.03176	N	0.171455	T	0.06872	0.0175	N	0.08118	0	0.09310	N	0.999998	B	0.14012	0.009	B	0.12156	0.007	T	0.32322	-0.9911	10	0.10111	T	0.7	6.0409	5.3638	0.16103	0.0:0.5947:0.0:0.4053	.	43	Q5H9L4	TAF7L_HUMAN	F	43	ENSP00000361998:Y43F	ENSP00000361998:Y43F	Y	-	2	0	TAF7L	100434562	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-1.444000	0.02403	0.060000	0.16281	-0.183000	0.12914	TAT	.	.		0.527	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2		
MT-ND5	4540	hgsc.bcm.edu	37	M	13344	13344	+	Silent	SNP	A	A	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chrM:13344A>G	ENST00000361567.2	+	1	1008	c.1008A>G	c.(1006-1008)aaA>aaG	p.K336K	MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	336					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						GCCTTCTTCAAAGCCATACTA	0.433																																					p.K336K		Atlas-SNP	.											.	.	.	.	0			c.A1008G						.																																			SO:0001819	synonymous_variant	0	exon1			CTTCAAAGCCATA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1008A>G	chrM.hg19:g.13344A>G		82.0	0.0		302.0	282.0	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.433	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
MT-CYB	4519	hgsc.bcm.edu	37	M	14813	14813	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chrM:14813A>G	ENST00000361789.2	+	1	67	c.67A>G	c.(67-69)Acc>Gcc	p.T23A	MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	23					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						TCGACCTCCCCACCCCATCCA	0.448																																					p.T23A		Atlas-SNP	.											.	.	.	.	0			c.A67G						.																																			SO:0001583	missense	0	exon1			CTCCCCACCCCAT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.67A>G	chrM.hg19:g.14813A>G	ENSP00000354554:p.Thr23Ala	91.0	0.0		296.0	26.0	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	hg19																																																																																				.	.		0.448	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
SIAH1	6477	hgsc.bcm.edu	37	16	48395633	48395644	+	In_Frame_Del	DEL	CAAGTCAATCGT	CAAGTCAATCGT	-	rs112217260	byFrequency	TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	CAAGTCAATCGT	CAAGTCAATCGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr16:48395633_48395644delCAAGTCAATCGT	ENST00000380006.2	-	1	2149_2160	c.696_707delACGATTGACTTG	c.(694-708)cgacgattgacttgg>cgg	p.RLTW233del	LONP2_ENST00000564259.1_3'UTR|SIAH1_ENST00000356721.3_In_Frame_Del_p.RLTW264del|SIAH1_ENST00000394725.2_In_Frame_Del_p.RLTW233del			Q8IUQ4	SIAH1_HUMAN	siah E3 ubiquitin protein ligase 1	233	SBD.				anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell cycle (GO:0007049)|nervous system development (GO:0007399)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein catabolic process (GO:0030163)|protein destabilization (GO:0031648)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	beta-catenin destruction complex (GO:0030877)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|stomach(1)	7		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)				AGTCGCTTCCCAAGTCAATCGTCGCCTATGAC	0.453																																					p.264_267del		Atlas-Indel,Pindel	.											.	SIAH1	33	.	0			c.790_801del						.																																			SO:0001651	inframe_deletion	6477	exon2			.	U76247	CCDS10735.1, CCDS32444.1	16q12.1	2013-06-03	2012-02-23		ENSG00000196470	ENSG00000196470			10857	protein-coding gene	gene with protein product		602212	"""seven in absentia homolog 1 (Drosophila)"""			9403064, 9334332	Standard	NM_001006610		Approved	hSIAH1	uc002efo.1	Q8IUQ4	OTTHUMG00000175417	ENST00000380006.2:c.696_707delACGATTGACTTG	chr16.hg19:g.48395633_48395644delCAAGTCAATCGT	ENSP00000369343:p.Arg233_Trp236del	71.0	0.0		162.0	16.0	NM_001006610	A0FKF3|O43269|Q49A58|Q92880	In_Frame_Del	DEL	ENST00000380006.2	hg19	CCDS10735.1																																																																																			.	.		0.453	SIAH1-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256842.12		
TBC1D10A	83874	hgsc.bcm.edu	37	22	30688449	30688463	+	In_Frame_Del	DEL	GGGGCTGAGTCCTTG	GGGGCTGAGTCCTTG	-	rs530980848|rs36125665		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	GGGGCTGAGTCCTTG	GGGGCTGAGTCCTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr22:30688449_30688463delGGGGCTGAGTCCTTG	ENST00000215790.7	-	9	1592_1606	c.1428_1442delCAAGGACTCAGCCCC	c.(1426-1443)cccaaggactcagcccct>cct	p.476_481PKDSAP>P	TBC1D10A_ENST00000403362.1_In_Frame_Del_p.388_393PKDSAP>P|GATSL3_ENST00000404953.3_5'Flank|GATSL3_ENST00000407689.3_5'Flank|RP1-130H16.18_ENST00000447976.1_Intron|TBC1D10A_ENST00000403477.3_In_Frame_Del_p.483_488PKDSAP>P	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	476					activation of cysteine-type endopeptidase activity (GO:0097202)|positive regulation of proteolysis (GO:0045862)|retrograde transport, endosome to Golgi (GO:0042147)	extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rab GTPase activator activity (GO:0005097)			cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						CAAATCCTGAGGGGCTGAGTCCTTGGGGGCTGAGT	0.628																																					p.484_488del		Atlas-Indel,Pindel	.											.	TBC1D10A	49	.	0			c.1450_1464del						.																																			SO:0001651	inframe_deletion	83874	exon9			.	AF331038	CCDS13874.1, CCDS56227.1	22q12.2	2013-07-09	2005-03-10	2005-03-10	ENSG00000099992	ENSG00000099992			23609	protein-coding gene	gene with protein product	"""EBP50-PDZ interactor of 64 kD"""	610020	"""TBC1 domain family, member 10"""	TBC1D10		11285285, 20404108	Standard	NM_001204240		Approved	EPI64, AC004997.C22.2	uc010gvu.3	Q9BXI6	OTTHUMG00000150924	ENST00000215790.7:c.1428_1442delCAAGGACTCAGCCCC	chr22.hg19:g.30688449_30688463delGGGGCTGAGTCCTTG	ENSP00000215790:p.Pro476_Ala480del	28.0	0.0		81.0	25.0	NM_001204240	B3KXT8|O76053|Q20WK7|Q543A2	In_Frame_Del	DEL	ENST00000215790.7	hg19	CCDS13874.1																																																																																			.	.		0.628	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	NM_031937	
APOB	338	hgsc.bcm.edu	37	2	21245890	21245891	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr2:21245890_21245891insT	ENST00000233242.1	-	18	2755_2756	c.2628_2629insA	c.(2626-2631)aaacccfs	p.P877fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	877			P -> L (in dbSNP:rs12714097).		artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.P877S(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GACACGGAGGGTTTTGCCACCA	0.475																																					p.P877fs		Atlas-Indel,Pindel	.											APOB,NS,malignant_melanoma,0,1	APOB	761	.	1	Substitution - Missense(1)	NS(1)	c.2629_2630insA						.																																			SO:0001589	frameshift_variant	338	exon18			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.2629dupA	chr2.hg19:g.21245894_21245894dupT	ENSP00000233242:p.Pro877fs	79.0	0.0		137.0	51.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.475	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
COG3	83548	hgsc.bcm.edu	37	13	46077408	46077408	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr13:46077408delG	ENST00000349995.5	+	14	1630	c.1518delG	c.(1516-1518)cagfs	p.Q506fs	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	506					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		AAGATGAACAGAAGAAGGTAC	0.373																																					p.Q506fs	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-INDEL	.											.	COG3	52	.	0			c.1517delA						.						108.0	105.0	106.0					13																	46077408		2203	4300	6503	SO:0001589	frameshift_variant	83548	exon14			.	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"""Components of oligomeric golgi complex"""	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1518delG	chr13.hg19:g.46077408delG	ENSP00000258654:p.Gln506fs	80.0	0.0		118.0	18.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Frame_Shift_Del	DEL	ENST00000349995.5	hg19	CCDS9398.1																																																																																			.	.		0.373	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2		
PRR27	401137	hgsc.bcm.edu	37	4	71024317	71024318	+	Frame_Shift_Ins	INS	-	-	T	rs148239542		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:71024317_71024318insT	ENST00000344526.5	+	3	537_538	c.348_349insT	c.(349-351)tttfs	p.F117fs	C4orf40_ENST00000502441.2_3'UTR|C4orf40_ENST00000502294.1_Frame_Shift_Ins_p.F117fs	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		117	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						CTCCTTCAAGGTTTTTTTCAGC	0.55																																					p.R116fs		Atlas-Indel,Pindel	.											.	C4orf40	19	.	0			c.348_349insT						.																																			SO:0001589	frameshift_variant	401137	exon3			.																												ENST00000344526.5:c.355dupT	chr4.hg19:g.71024324_71024324dupT	ENSP00000343172:p.Phe117fs	46.0	0.0		108.0	31.0	NM_214711	A8MXP0|Q6MZR6	Frame_Shift_Ins	INS	ENST00000344526.5	hg19	CCDS3535.1																																																																																			.	.		0.550	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
RPS6KL1	83694	hgsc.bcm.edu	37	14	75376302	75376303	+	Frame_Shift_Ins	INS	-	-	C			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:75376302_75376303insC	ENST00000555647.1	-	8	1500_1501	c.1213_1214insG	c.(1213-1215)gagfs	p.E405fs	RPS6KL1_ENST00000354625.2_Frame_Shift_Ins_p.E374fs|RPS6KL1_ENST00000554900.1_5'Flank|RPS6KL1_ENST00000358328.4_Frame_Shift_Ins_p.E405fs|RPS6KL1_ENST00000557413.1_Frame_Shift_Ins_p.E405fs			Q9Y6S9	RPKL1_HUMAN	ribosomal protein S6 kinase-like 1	405	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					ribosome (GO:0005840)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(234;0.00658)		CACCCCCTGCTCGTGCAGCGCC	0.703																																					p.E405fs		Atlas-Indel,Pindel	.											.	RPS6KL1	35	.	0			c.1214_1215insG						.																																			SO:0001589	frameshift_variant	83694	exon7			.	BC004540	CCDS9834.1, CCDS9834.2	14q24.2	2011-04-05				ENSG00000198208			20222	protein-coding gene	gene with protein product							Standard	NM_031464		Approved	MGC11287	uc010tux.2	Q9Y6S9		ENST00000555647.1:c.1214dupG	chr14.hg19:g.75376303_75376303dupC	ENSP00000452027:p.Glu405fs	35.0	0.0		81.0	36.0	NM_031464	A6NGM9|Q69YT9|Q6ZMQ6|Q96NR9|Q9BSU9	Frame_Shift_Ins	INS	ENST00000555647.1	hg19	CCDS9834.2																																																																																			.	.		0.703	RPS6KL1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413732.1		
NSMCE2	286053	hgsc.bcm.edu	37	8	126114663	126114664	+	Frame_Shift_Ins	INS	-	-	A	rs76206666		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr8:126114663_126114664insA	ENST00000287437.3	+	3	307_308	c.91_92insA	c.(91-93)caafs	p.Q31fs	NSMCE2_ENST00000522563.1_Frame_Shift_Ins_p.Q31fs	NM_173685.2	NP_775956.1	Q96MF7	NSE2_HUMAN	non-SMC element 2, MMS21 homolog (S. cerevisiae)	31					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|protein sumoylation (GO:0016925)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	SUMO ligase activity (GO:0019789)|zinc ion binding (GO:0008270)			breast(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	9	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			GAAAAACTTCCAAGCCTGTATC	0.406																																					p.Q31fs		Atlas-INDEL	.											.	NSMCE2	18	.	0			c.91_92insA						.																																			SO:0001589	frameshift_variant	286053	exon3			.	AK057002	CCDS6356.1	8q24.13	2013-01-28	2006-12-21	2006-07-05	ENSG00000156831	ENSG00000156831		"""Zinc fingers, MIZ-type"""	26513	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 7"""		"""chromosome 8 open reading frame 36"", ""non-SMC element 2 homolog (MMS21, S. cerevisiae)"""	C8orf36		12477932	Standard	NM_173685		Approved	FLJ32440, MMS21, NSE2, ZMIZ7	uc003yrw.2	Q96MF7	OTTHUMG00000164993	ENST00000287437.3:c.93dupA	chr8.hg19:g.126114665_126114665dupA	ENSP00000287437:p.Gln31fs	140.0	0.0		522.0	31.0	NM_173685	Q8N549	Frame_Shift_Ins	INS	ENST00000287437.3	hg19	CCDS6356.1																																																																																			.	.		0.406	NSMCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381378.1	NM_173685	
MMP19	4327	hgsc.bcm.edu	37	12	56231749	56231750	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr12:56231749_56231750delCA	ENST00000322569.4	-	7	1028_1029	c.937_938delTG	c.(937-939)tggfs	p.W313fs	MMP19_ENST00000548629.1_Frame_Shift_Del_p.W290fs|TMEM198B_ENST00000478241.1_RNA|MMP19_ENST00000394182.1_Frame_Shift_Del_p.W27fs|MMP19_ENST00000409200.3_Frame_Shift_Del_p.V266fs	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	313					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	TGATACAGTCCACACATAGTCC	0.545																																					p.313_313del		Atlas-Indel,Pindel	.											.	MMP19	61	.	0			c.938_939del						.																																			SO:0001589	frameshift_variant	4327	exon7			.	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"""matrix metalloproteinase 19"""	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.937_938delTG	chr12.hg19:g.56231753_56231754delCA	ENSP00000313437:p.Trp313fs	53.0	0.0		82.0	33.0	NM_002429	B4E030|O15278|O95606|Q99580	Frame_Shift_Del	DEL	ENST00000322569.4	hg19	CCDS8895.1																																																																																			.	.		0.545	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266093	41266107	+	In_Frame_Del	DEL	CCTGGACTCTGGAAT	CCTGGACTCTGGAAT	-	rs28931589|rs121913396|rs121913416|rs121913417|rs121913399|rs121913400|rs28931588		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	CCTGGACTCTGGAAT	CCTGGACTCTGGAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr3:41266093_41266107delCCTGGACTCTGGAAT	ENST00000349496.5	+	3	370_384	c.90_104delCCTGGACTCTGGAAT	c.(88-105)tacctggactctggaatc>tac	p.LDSGI31del	CTNNB1_ENST00000453024.1_In_Frame_Del_p.LDSGI24del|CTNNB1_ENST00000396183.3_In_Frame_Del_p.LDSGI31del|CTNNB1_ENST00000396185.3_In_Frame_Del_p.LDSGI31del|CTNNB1_ENST00000405570.1_In_Frame_Del_p.LDSGI31del	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	31			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.D32Y(128)|p.S33F(97)|p.G34R(87)|p.D32N(82)|p.G34E(73)|p.G34V(72)|p.D32G(65)|p.S33Y(60)|p.A5_A80del(53)|p.S33P(47)|p.D32H(40)|p.D32V(33)|p.I35S(20)|p.S33A(16)|p.D32A(16)|p.I35T(13)|p.A5_A80>D(7)|p.A5_Q143del(7)|p.WQQQSYLD25?(5)|p.Q28_H134del(5)|p.S33L(4)|p.W25_D32del(4)|p.L31L(4)|p.?(4)|p.W25_I140del(3)|p.V22_G38del(3)|p.T3_A126del(2)|p.S33N(2)|p.M5_N141>D(2)|p.D32_S47del(2)|p.Y30_S33del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5_Y142>D(2)|p.A5fs*7(2)|p.D32E(2)|p.Y30*(2)|p.L10_N141del(2)|p.Q28_Q61del(1)|p.S33T(1)|p.S33S(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S29_H36del(1)|p.H24_L31del(1)|p.Y30_A97del(1)|p.A20_A80del(1)|p.Q28_A43del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.W25_I35del(1)|p.GIHS34?(1)|p.A5_I35del(1)|p.A13_R151del(1)|p.D32del(1)|p.M1_A87del(1)|p.I35_T41del(1)|p.I35K(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.S23_A39del(1)|p.A21_A80del(1)|p.I35_S37>T(1)|p.I35_K170del(1)|p.M14_S45del(1)|p.D32_H36>D(1)|p.S33_G34insGTS(1)|p.P16_K133del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.M8_A80del(1)|p.S33_S37del(1)|p.D32_S33insS(1)|p.Y30_T40del(1)|p.S33_G34insGI(1)|p.A5_Q143>E(1)|p.I35_G38del(1)|p.L31M(1)|p.Q28_D32>H(1)|p.L31Q(1)|p.Y30_A80del(1)|p.L31W(1)|p.D32fs*9(1)|p.Y30Y(1)|p.Q28fs*20(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S23_I35del(1)|p.V22_S71>A(1)|p.V22_Y64del(1)|p.I35N(1)|p.A20_S111del(1)|p.D32_H36del(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)		AACAGTCTTACCTGGACTCTGGAATCCATTCTGGT	0.484	D32N(KE39_STOMACH)|D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)|G34E(AGS_STOMACH)|S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												p.30_35del	Colon(6;3 56 14213 18255)	Atlas-Indel,Pindel	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	CTNNB1,NS,carcinoma,0,1	CTNNB1	4904	.	1197	Substitution - Missense(1031)|Deletion - In frame(126)|Complex - deletion inframe(18)|Unknown(7)|Substitution - coding silent(6)|Insertion - In frame(3)|Deletion - Frameshift(3)|Substitution - Nonsense(2)|Complex - frameshift(1)	liver(384)|central_nervous_system(201)|endometrium(138)|stomach(88)|pancreas(86)|pituitary(59)|large_intestine(58)|skin(44)|ovary(41)|soft_tissue(14)|lung(12)|salivary_gland(12)|prostate(11)|biliary_tract(9)|bone(9)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|NS(4)|breast(4)|adrenal_gland(4)|urinary_tract(3)|parathyroid(2)|small_intestine(2)|thyroid(1)|cervix(1)	c.89_103del						.																																			SO:0001651	inframe_deletion	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	.	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.90_104delCCTGGACTCTGGAAT	chr3.hg19:g.41266093_41266107delCCTGGACTCTGGAAT	ENSP00000344456:p.Leu31_Ile35del	107.0	0.0		193.0	27.0	NM_001098210	A8K1L7|Q8NEW9|Q8NI94|Q9H391	In_Frame_Del	DEL	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	.		0.484	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
AFF2	2334	hgsc.bcm.edu	37	X	148038047	148038048	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chrX:148038047_148038048insA	ENST00000370460.2	+	11	2951_2952	c.2472_2473insA	c.(2473-2475)aagfs	p.K825fs	AFF2_ENST00000286437.5_Frame_Shift_Ins_p.K466fs|AFF2_ENST00000370457.5_Frame_Shift_Ins_p.K792fs|AFF2_ENST00000342251.3_Frame_Shift_Ins_p.K792fs	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	825					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)					CAGCACCTGCCAAGCCAGACCA	0.525																																					p.A824fs		Atlas-INDEL	.											.	AFF2	679	.	0			c.2472_2473insA						.																																			SO:0001589	frameshift_variant	2334	exon11			.	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.2474dupA	chrX.hg19:g.148038049_148038049dupA	ENSP00000359489:p.Lys825fs	27.0	0.0		116.0	11.0	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Frame_Shift_Ins	INS	ENST00000370460.2	hg19	CCDS14684.1																																																																																			.	.		0.525	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	
UGT2B7	7364	hgsc.bcm.edu	37	4	69962823	69962825	+	In_Frame_Del	DEL	TGT	TGT	-			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr4:69962823_69962825delTGT	ENST00000508661.1	+	1	612_614	c.585_587delTGT	c.(583-588)cctgtt>cct	p.V197del	UGT2B7_ENST00000305231.7_In_Frame_Del_p.V197del|UGT2B7_ENST00000509763.1_Intron			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	197					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)	p.V196I(1)		autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CCTACGTACCTGTTGTTATGTCA	0.365																																					p.195_196del		Atlas-Indel,Pindel	.											.	UGT2B7	79	.	1	Substitution - Missense(1)	lung(1)	c.584_586del						.																																			SO:0001651	inframe_deletion	7364	exon1			.	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.585_587delTGT	chr4.hg19:g.69962826_69962828delTGT	ENSP00000427659:p.Val197del	104.0	0.0		304.0	98.0	NM_001074	B2R810|Q6GTW0	In_Frame_Del	DEL	ENST00000508661.1	hg19																																																																																				.	.		0.365	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074	
COG3	83548	hgsc.bcm.edu	37	13	46077399	46077409	+	Frame_Shift_Del	DEL	AGATGAACAGA	AGATGAACAGA	-	rs370937289		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	AGATGAACAGA	AGATGAACAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr13:46077399_46077409delAGATGAACAGA	ENST00000349995.5	+	14	1621_1631	c.1509_1519delAGATGAACAGA	c.(1507-1521)aaagatgaacagaagfs	p.KDEQK503fs	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	503					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		AGAGTTTGAAAGATGAACAGAAGAAGGTACC	0.365																																					p.503_506del	Ovarian(150;1048 1859 18083 21577 42700)	Pindel	.											.	COG3	52	.	0			c.1508_1518del						.																																			SO:0001589	frameshift_variant	83548	exon14			.	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"""Components of oligomeric golgi complex"""	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1509_1519delAGATGAACAGA	chr13.hg19:g.46077399_46077409delAGATGAACAGA	ENSP00000258654:p.Lys503fs	0.0	0.0		113.0	13.0	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Frame_Shift_Del	DEL	ENST00000349995.5	hg19	CCDS9398.1																																																																																			.	.		0.365	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2		
CELA1	1990	hgsc.bcm.edu	37	12	51740405	51740433	+	Start_Codon_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-	rs150350903|rs573952082|rs201074609|rs141305161|rs117443541|rs377599213|rs143199509|rs61761206|rs148235680|rs370927847|rs148270827|rs116944010|rs386762976|rs149358345|rs55827519	byFrequency	TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr12:51740405_51740433delCTGGACCATATCCACTTACCATAAAGGAC	ENST00000293636.1	-	0	30_57					NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1						exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V3fs*21(1)|p.L4P(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						ATATCCACTTACCATAAAGGACCAGCATGTTGCCGATGGAGTAGACCAC	0.524																																					p.3_6del		Pindel	.											.	CELA1	39	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|lung(1)	c.8_16del						.																																			SO:0001582	initiator_codon_variant	1990	exon1			.		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"""elastase 1, pancreatic"""	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523		chr12.hg19:g.51740405_51740433delCTGGACCATATCCACTTACCATAAAGGAC		0.0	0.0		110.0	20.0	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	In_Frame_Del	DEL	ENST00000293636.1	hg19	CCDS8812.1																																																																																			.	-|0.574;CACCAGGAAGCG|0.426		0.524	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	
LTBP2	4053	hgsc.bcm.edu	37	14	74976564	74976565	+	Splice_Site	INS	-	-	GAAATAGGGCATTGCATTCTGTGTG			TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr14:74976564_74976565insGAAATAGGGCATTGCATTCTGTGTG	ENST00000261978.4	-	21	3538		c.e21-2		LTBP2_ENST00000556690.1_Splice_Site	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2						protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CATCCACATCTGAAATAGGGCA	0.624																																					.		Pindel	.											.	LTBP2	158	.	0			c.3152-2->CACACAGAATGCAATGCCCTATTTC						.																																			SO:0001630	splice_region_variant	4053	exon22			.		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"""Latent transforming growth factor, beta binding proteins"""	6715	protein-coding gene	gene with protein product		602091	"""chromosome 14 open reading frame 141"""	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.3152-2->CACACAGAATGCAATGCCCTATTTC	chr14.hg19:g.74976564_74976565insGAAATAGGGCATTGCATTCTGTGTG		0.0	0.0		58.0	11.0	NM_000428	Q99907|Q9NS51	Splice_Site	INS	ENST00000261978.4	hg19	CCDS9831.1																																																																																			.	.		0.624	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428	Intron
CDC27	996	hgsc.bcm.edu	37	17	45234594	45234729	+	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-	rs149474782|rs113608268|rs370849730|rs78395997|rs76624491|rs370261409|rs75353677|rs368304141|rs376818791|rs372212798|rs375653477|rs374472811|rs76359747|rs147617501|rs374614181|rs78108688|rs142987740|rs143453365|rs75990396|rs144985864|rs367644695|rs202182614|rs139751753|rs11570485|rs372926889|rs140171160|rs368750026|rs201098929|rs199899451|rs75175938|rs200340309|rs537990668	byFrequency	TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr17:45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	ENST00000066544.3	-	6	590_724	c.497_631delAGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG	c.(496-633)cagttcttacggaaacaccccaggacacaattgtaagtgtcttatattctagtgttcaaaatattatgaaaactacaaagaatgatctgaactaaataatatattgtgaatgacttggtagaaattttctgtttcaga>cga	p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	CDC27_ENST00000446365.2_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF105fs|CDC27_ENST00000527547.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000531206.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000528748.1_5'UTR	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	166					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.T167T(7)|p.T171T(3)|p.V201I(2)|p.E199E(2)|p.T200T(2)|p.L173S(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACTGTCTCAGGCTGTCTGTGAGATAAACTATGATTAGGTACTTGTGTTGTGCAAGAGTTGGGCAGACAGTTGCTAAAGTTCTGTAAAGATGTGAATTTAAATGTTTGGTCAGGATC	0.342																																					p.201_211del		Pindel	.											.	CDC27	337	.	17	Substitution - coding silent(14)|Substitution - Missense(3)	large_intestine(6)|prostate(6)|kidney(4)|NS(1)	c.601_631del						.																																			SO:0001630	splice_region_variant	996	exon6			.	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.631-104AGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG>-	chr17.hg19:g.45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT		0.0	0.0		173.0	12.0	NM_001114091	G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.342	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Frame_Shift_Del
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33053994	33054040	+	Stop_Codon_Del	DEL	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	-	rs201552902|rs150818884|rs67523850	byFrequency	TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	TTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr6:33053994_33054040delTTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA	ENST00000418931.2	+	0	873_897					NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)	p.R255P(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CTTTCATTTCAGTTCAACGAGGATCTGCATAAACAGGTAATATTCCTGCTTTGATTTCCTTGTGGGG	0.429																																					p.253_259del		Pindel	.											.	HLA-DPB1	28	.	1	Substitution - Missense(1)	cervix(1)	c.758_775del						.																																			SO:0001567	stop_retained_variant	3115	exon5			.		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	Exception_encountered	chr6.hg19:g.33053994_33054040delTTATATAACCTTTCGTCTTTCATTTCAGTTCAACGAGGATCTGCATA		0.0	0.0		278.0	23.0	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	In_Frame_Del	DEL	ENST00000418931.2	hg19	CCDS4765.1																																																																																			.	.		0.429	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
NCAM1	4684	hgsc.bcm.edu	37	11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-DD-A1EA-01A-11D-A12Z-10	TCGA-DD-A1EA-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f2f6ebbe-5e4e-48ff-9782-de22a56fc3c3	ebf27981-4bd7-4636-ad4e-e6153fba6e66	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				RP11-629G13.1_ENST00000532002.1_RNA|RP11-629G13.1_ENST00000500537.2_RNA|NCAM1_ENST00000397957.4_3'UTR	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		0.0	0.0		80.0	24.0	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	
