#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_Confidence	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_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	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_dbSNP_PopFreq	i_dbSNP_Strength	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
AADACL4	343066	hgsc.bcm.edu	37	1	12711237	12711237	+	Silent	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:12711237G>T	ENST00000376221.1	+	2	264	c.264G>T	c.(262-264)gtG>gtT	p.V88V		NM_001013630.1	NP_001013652.1	Q5VUY2	ADCL4_HUMAN	arylacetamide deacetylase-like 4	88						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)	17	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000937)|all_lung(284;0.00122)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.81e-07)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0384)		CTGAACTTGTGGTGACCGACC	0.498																																					p.V88V		Atlas-SNP	.											.	AADACL4	48	.	0			c.G264T						PASS	.						98.0	96.0	97.0					1																	12711237		2203	4300	6503	SO:0001819	synonymous_variant	343066	exon2			ACTTGTGGTGACC		CCDS30590.1	1p36.21	2010-12-14			ENSG00000204518	ENSG00000204518			32038	protein-coding gene	gene with protein product							Standard	XM_006710608		Approved	OTTHUMG00000001889	uc001auf.3	Q5VUY2	OTTHUMG00000001889	ENST00000376221.1:c.264G>T	chr1.hg19:g.12711237G>T		121.0	0.0	.		120.0	66.0	.	NM_001013630		Silent	SNP	ENST00000376221.1	hg19	CCDS30590.1																																																																																			.	.	.	none		0.498	AADACL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005328.1	NM_001013630	
RHD	6007	hgsc.bcm.edu	37	1	25628090	25628090	+	Silent	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:25628090G>A	ENST00000328664.4	+	5	869	c.714G>A	c.(712-714)gtG>gtA	p.V238V	RHD_ENST00000423810.2_Silent_p.V238V|RHD_ENST00000342055.5_Silent_p.V238V|RHD_ENST00000568195.1_Silent_p.V238V|RHD_ENST00000454452.2_Silent_p.V238V|RHD_ENST00000423253.1_3'UTR|RHD_ENST00000417538.2_Silent_p.V238V|RHD_ENST00000357542.4_Silent_p.V238V	NM_001282867.1|NM_016124.3	NP_001269796.1|NP_057208	Q02161	RHD_HUMAN	Rh blood group, D antigen	238			V -> M (in RhDVa(TO) and RhDVa(TT); dbSNP:rs1053360). {ECO:0000269|Ref.9}.			integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)			breast(2)|large_intestine(4)|lung(7)|prostate(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGAATGCCGTGTTCAACACCT	0.562																																					p.V238V		Atlas-SNP	.											.	RHD	38	.	0			c.G714A						PASS	.						199.0	154.0	171.0					1																	25628090		2122	3769	5891	SO:0001819	synonymous_variant	6007	exon5			TGCCGTGTTCAAC	AB012623	CCDS262.1, CCDS53285.1, CCDS60027.1, CCDS60028.1, CCDS60029.1, CCDS60030.1, CCDS60031.1	1p36.11	2014-07-19	2013-10-02		ENSG00000187010	ENSG00000187010		"""CD molecules"", ""Blood group antigens"""	10009	protein-coding gene	gene with protein product		111680	"""Rhesus blood group, D antigen"", ""Rh blood group, D antigen"""	RH		8220426	Standard	NM_016124		Approved	Rh30a, Rh4, RhPI, RhII, DIIIc, CD240D	uc001bjz.3	Q02161	OTTHUMG00000003476	ENST00000328664.4:c.714G>A	chr1.hg19:g.25628090G>A		87.0	0.0	.		134.0	123.0	.	NM_001127691	Q02162|Q07618|Q16147|Q16235|Q16355|Q5VSK0|Q5XLS9|Q5XLT1|Q5XLT2|Q9NPK0|Q9UQ20|Q9UQ21|Q9UQ22|Q9UQ23	Silent	SNP	ENST00000328664.4	hg19	CCDS262.1																																																																																			.	.	.	none		0.562	RHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009660.5	NM_016124	
CSMD2	114784	hgsc.bcm.edu	37	1	34015918	34015918	+	Missense_Mutation	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:34015918G>T	ENST00000373381.4	-	56	8952	c.8776C>A	c.(8776-8778)Cac>Aac	p.H2926N		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2901	Sushi 21. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				ATCTGGGAGTGAGGCGGGGAG	0.572																																					p.H2782N		Atlas-SNP	.											.	CSMD2	946	.	0			c.C8344A						PASS	.						58.0	57.0	57.0					1																	34015918		2203	4300	6503	SO:0001583	missense	114784	exon55			GGGAGTGAGGCGG	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.8776C>A	chr1.hg19:g.34015918G>T	ENSP00000362479:p.His2926Asn	109.0	0.0	.		186.0	106.0	.	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	G	0.673	-0.801317	0.02841	.	.	ENSG00000121904	ENST00000373381	T	0.64618	-0.11	5.71	5.71	0.89125	Complement control module (2);Sushi/SCR/CCP (3);	0.060404	0.64402	D	0.000002	T	0.27241	0.0668	N	0.00661	-1.28	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.14023	0.01;0.01	T	0.43294	-0.9400	10	0.02654	T	1	.	13.8354	0.63406	0.0:0.0:0.8474:0.1526	.	2782;2926	Q7Z408;E7EUA6	CSMD2_HUMAN;.	N	2926	ENSP00000362479:H2926N	ENSP00000241312:H2782N	H	-	1	0	CSMD2	33788505	1.000000	0.71417	0.982000	0.44146	0.320000	0.28249	3.614000	0.54160	2.720000	0.93068	0.650000	0.86243	CAC	.	.	.	none		0.572	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
MACF1	23499	hgsc.bcm.edu	37	1	39853737	39853737	+	Missense_Mutation	SNP	G	G	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:39853737G>C	ENST00000372915.3	+	57	15325	c.15238G>C	c.(15238-15240)Ggt>Cgt	p.G5080R	MACF1_ENST00000361689.2_Missense_Mutation_p.G3013R|MACF1_ENST00000289893.4_Missense_Mutation_p.G3515R|MACF1_ENST00000564288.1_Missense_Mutation_p.G5075R|MACF1_ENST00000539005.1_Missense_Mutation_p.G2992R|MACF1_ENST00000317713.7_Missense_Mutation_p.G3013R|MACF1_ENST00000567887.1_Missense_Mutation_p.G5112R|MACF1_ENST00000545844.1_Missense_Mutation_p.G3013R			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	5080					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CTTTACTCAGGGTCTGGTAGA	0.502																																					p.G3013R		Atlas-SNP	.											.	MACF1	909	.	0			c.G9037C						PASS	.						51.0	52.0	52.0					1																	39853737		2203	4300	6503	SO:0001583	missense	23499	exon54			ACTCAGGGTCTGG	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.15238G>C	chr1.hg19:g.39853737G>C	ENSP00000362006:p.Gly5080Arg	139.0	0.0	.		138.0	42.0	.	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.13|17.13	3.311133|3.311133	0.60414|0.60414	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	.|T;T;T;T;T;T	.|0.32272	.|1.46;1.46;1.46;1.46;1.46;1.46	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000005|0.000005	T|T	0.55273|0.55273	0.1910|0.1910	L|L	0.58101|0.58101	1.795|1.795	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.99;0.991	.|D;D;D	.|0.97110	.|1.0;0.952;0.962	T|T	0.43475|0.43475	-0.9389|-0.9389	6|10	.|0.44086	.|T	.|0.13	.|.	20.5568|20.5568	0.99304|0.99304	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|5080;3013;2957	.|Q9UPN3;F8W8Q1;Q9UPN3-3	.|MACF1_HUMAN;.;.	A|R	2125|3013;5080;3013;3013;2992;3515	.|ENSP00000439537:G3013R;ENSP00000362006:G5080R;ENSP00000354573:G3013R;ENSP00000313438:G3013R;ENSP00000444364:G2992R;ENSP00000289893:G3515R	.|ENSP00000289893:G3515R	G|G	+|+	2|1	0|0	MACF1|MACF1	39626324|39626324	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.947000|0.947000	0.59692|0.59692	9.869000|9.869000	0.99810|0.99810	2.861000|2.861000	0.98227|0.98227	0.655000|0.655000	0.94253|0.94253	GGG|GGT	.	.	.	none		0.502	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
ITGB3BP	23421	hgsc.bcm.edu	37	1	63974218	63974218	+	Missense_Mutation	SNP	T	T	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:63974218T>G	ENST00000271002.10	-	2	110	c.29A>C	c.(28-30)gAt>gCt	p.D10A	ITGB3BP_ENST00000371092.3_Missense_Mutation_p.D49A|ITGB3BP_ENST00000283568.8_Missense_Mutation_p.D10A	NM_014288.4	NP_055103.3	Q13352	CENPR_HUMAN	integrin beta 3 binding protein (beta3-endonexin)	10					apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)	p.D10G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	9						TAACAGACCATCCAACTTCAG	0.259																																					p.D49A		Atlas-SNP	.											ITGB3BP,larynx,carcinoma,0,1	ITGB3BP	20	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.A146C						PASS	.						28.0	28.0	28.0					1																	63974218		2149	4215	6364	SO:0001583	missense	23421	exon3			AGACCATCCAACT	U37139	CCDS30736.1, CCDS55603.1	1p31.3	2013-11-05			ENSG00000142856	ENSG00000142856			6157	protein-coding gene	gene with protein product	"""centromere protein R"""	605494				7593198, 10490654	Standard	NM_014288		Approved	NRIF3, HSU37139, TAP20, CENPR	uc001dbb.2	Q13352	OTTHUMG00000013364	ENST00000271002.10:c.29A>C	chr1.hg19:g.63974218T>G	ENSP00000271002:p.Asp10Ala	292.0	2.0	.		201.0	53.0	.	NM_001206739	B2R7D8|Q13353|Q5RJ42|Q5RJ44|Q5RJ45|Q7KYX2|Q96CD5|Q9UKB6	Missense_Mutation	SNP	ENST00000271002.10	hg19	CCDS30736.1	.	.	.	.	.	.	.	.	.	.	T	3.341	-0.134587	0.06711	.	.	ENSG00000142856	ENST00000271002;ENST00000371092;ENST00000283568	T;T;T	0.67698	-0.27;0.25;-0.28	4.91	3.79	0.43588	.	0.260117	0.25997	N	0.026964	T	0.46073	0.1374	N	0.19112	0.55	0.38496	D	0.948093	P;P;P	0.51537	0.944;0.946;0.78	P;P;B	0.50825	0.651;0.592;0.265	T	0.53947	-0.8366	10	0.66056	D	0.02	-2.1447	10.3835	0.44125	0.0:0.0772:0.0:0.9228	.	10;49;10	Q13352-2;Q13352-5;Q13352	.;.;CENPR_HUMAN	A	10;49;10	ENSP00000271002:D10A;ENSP00000360133:D49A;ENSP00000283568:D10A	ENSP00000271002:D10A	D	-	2	0	ITGB3BP	63746806	1.000000	0.71417	0.469000	0.27204	0.029000	0.11900	5.252000	0.65445	0.732000	0.32470	-0.256000	0.11100	GAT	.	.	.	none		0.259	ITGB3BP-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000037242.2	NM_014288	
GNG12	55970	hgsc.bcm.edu	37	1	68171150	68171150	+	Missense_Mutation	SNP	G	G	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:68171150G>C	ENST00000370982.3	-	4	402	c.203C>G	c.(202-204)aCt>aGt	p.T68S		NM_018841.5	NP_061329.3	Q9UBI6	GBG12_HUMAN	guanine nucleotide binding protein (G protein), gamma 12	68					cellular response to glucagon stimulus (GO:0071377)|cerebral cortex development (GO:0021987)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|phosphate ion binding (GO:0042301)|signal transducer activity (GO:0004871)			lung(3)	3						GATGATGCAAGTTTTTTTATC	0.433																																					p.T68S		Atlas-SNP	.											.,1	GNG12	11	.	0			c.C203G						PASS	.						173.0	163.0	167.0					1																	68171150		2203	4300	6503	SO:0001583	missense	55970	exon4			ATGCAAGTTTTTT	AF119663	CCDS30749.1	1p31.2	2008-02-05			ENSG00000172380	ENSG00000172380			19663	protein-coding gene	gene with protein product		615405				10819326	Standard	NM_018841		Approved		uc001dea.2	Q9UBI6	OTTHUMG00000009545	ENST00000370982.3:c.203C>G	chr1.hg19:g.68171150G>C	ENSP00000360021:p.Thr68Ser	73.0	0.0	.		89.0	43.0	.	NM_018841	Q69YP5|Q9BRV5	Missense_Mutation	SNP	ENST00000370982.3	hg19	CCDS30749.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.282741	0.59867	.	.	ENSG00000172380	ENST00000370982	T	0.20200	2.09	5.79	5.79	0.91817	G-protein gamma domain (3);	0.054877	0.85682	D	0.000000	T	0.05502	0.0145	.	.	.	0.41685	D	0.98931	B	0.27625	0.183	B	0.31495	0.131	T	0.08146	-1.0736	9	0.02654	T	1	-5.209	18.8047	0.92032	0.0:0.0:1.0:0.0	.	68	Q9UBI6	GBG12_HUMAN	S	68	ENSP00000360021:T68S	ENSP00000360021:T68S	T	-	2	0	GNG12	67943738	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	7.072000	0.76777	2.749000	0.94314	0.491000	0.48974	ACT	.	.	.	none		0.433	GNG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026355.2		
ZBTB7B	51043	hgsc.bcm.edu	37	1	154987232	154987232	+	Missense_Mutation	SNP	C	C	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:154987232C>G	ENST00000368426.3	+	3	233	c.96C>G	c.(94-96)caC>caG	p.H32Q	ZBTB7B_ENST00000535420.1_Missense_Mutation_p.H32Q|ZBTB7B_ENST00000417934.2_Missense_Mutation_p.H66Q|ZBTB7B_ENST00000487542.1_3'UTR|ZBTB7B_ENST00000292176.2_Missense_Mutation_p.H32Q	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	32					cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)	29	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			AGCTGGGCCACCTATGTGACC	0.587																																					p.H66Q		Atlas-SNP	.											.	ZBTB7B	69	.	0			c.C198G						PASS	.						68.0	69.0	69.0					1																	154987232		2203	4300	6503	SO:0001583	missense	51043	exon4			GGGCCACCTATGT	AF007833	CCDS1081.1, CCDS58030.1	1q21.2	2013-01-08		2005-04-07	ENSG00000160685	ENSG00000160685		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	18668	protein-coding gene	gene with protein product	"""zinc finger and BTB domain containing 15"""	607646	"""zinc finger protein 67 homolog (mouse)"""	ZFP67		9370309, 7937772	Standard	NR_045515		Approved	ZBTB15, c-Krox, hcKrox, ZNF857B	uc010peq.3	O15156	OTTHUMG00000037414	ENST00000368426.3:c.96C>G	chr1.hg19:g.154987232C>G	ENSP00000357411:p.His32Gln	77.0	0.0	.		80.0	26.0	.	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Missense_Mutation	SNP	ENST00000368426.3	hg19	CCDS1081.1	.	.	.	.	.	.	.	.	.	.	C	10.76	1.439712	0.25900	.	.	ENSG00000160685	ENST00000535420;ENST00000368426;ENST00000417934;ENST00000292176	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	3.59	-1.19	0.09585	BTB/POZ (1);BTB/POZ fold (2);	0.413847	0.21695	N	0.070510	T	0.12561	0.0305	N	0.02539	-0.55	0.27857	N	0.940546	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.08055	0.003;0.002;0.003	T	0.21075	-1.0256	10	0.66056	D	0.02	.	5.0228	0.14370	0.0:0.4765:0.1713:0.3521	.	32;32;66	A8K6F4;O15156;B4E3K5	.;ZBT7B_HUMAN;.	Q	32;32;66;32	ENSP00000438647:H32Q;ENSP00000357411:H32Q;ENSP00000406286:H66Q;ENSP00000292176:H32Q	ENSP00000292176:H32Q	H	+	3	2	ZBTB7B	153253856	0.762000	0.28451	0.963000	0.40424	0.981000	0.71138	-0.185000	0.09684	-0.072000	0.12864	-0.379000	0.06801	CAC	.	.	.	none		0.587	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872	
RCOR3	55758	hgsc.bcm.edu	37	1	211462545	211462545	+	Missense_Mutation	SNP	C	C	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:211462545C>A	ENST00000367005.4	+	7	713	c.572C>A	c.(571-573)aCt>aAt	p.T191N	RCOR3_ENST00000419091.2_Missense_Mutation_p.T249N|RCOR3_ENST00000367006.4_Missense_Mutation_p.T249N|RCOR3_ENST00000452621.2_Missense_Mutation_p.T249N	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	191					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		CCTGTCCAAACTAGCAAGATT	0.378																																					p.T249N		Atlas-SNP	.											RCOR3,caecum,carcinoma,0,1	RCOR3	51	.	0			c.C746A						PASS	.						127.0	113.0	118.0					1																	211462545		2203	4300	6503	SO:0001583	missense	55758	exon8			TCCAAACTAGCAA	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.572C>A	chr1.hg19:g.211462545C>A	ENSP00000355972:p.Thr191Asn	181.0	0.0	.		244.0	26.0	.	NM_001136223	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Missense_Mutation	SNP	ENST00000367005.4	hg19	CCDS31016.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.33|13.33	2.205841|2.205841	0.39003|0.39003	.|.	.|.	ENSG00000117625|ENSG00000117625	ENST00000534460|ENST00000367006;ENST00000452621;ENST00000419091;ENST00000367005;ENST00000529763	.|T;T;T;T	.|0.28454	.|1.61;1.61;1.61;1.61	5.62|5.62	4.7|4.7	0.59300|0.59300	.|.	.|0.488580	.|0.25119	.|N	.|0.032996	T|T	0.17874|0.17874	0.0429|0.0429	N|N	0.11201|0.11201	0.11|0.11	0.38814|0.38814	D|D	0.955493|0.955493	.|B;B;B;B	.|0.17268	.|0.002;0.0;0.021;0.018	.|B;B;B;B	.|0.15052	.|0.003;0.001;0.006;0.012	T|T	0.06250|0.06250	-1.0837|-1.0837	5|10	.|0.14252	.|T	.|0.57	-7.2822|-7.2822	16.1088|16.1088	0.81244|0.81244	0.0:0.8548:0.1452:0.0|0.0:0.8548:0.1452:0.0	.|.	.|249;191;249;249	.|Q9P2K3-3;Q9P2K3;Q9P2K3-2;Q9P2K3-4	.|.;RCOR3_HUMAN;.;.	K|N	35|249;249;249;191;9	.|ENSP00000355973:T249N;ENSP00000398558:T249N;ENSP00000413929:T249N;ENSP00000355972:T191N	.|ENSP00000355972:T191N	N|T	+|+	3|2	2|0	RCOR3|RCOR3	209529168|209529168	0.981000|0.981000	0.34729|0.34729	0.995000|0.995000	0.50966|0.50966	0.997000|0.997000	0.91878|0.91878	2.148000|2.148000	0.42235|0.42235	1.335000|1.335000	0.45486|0.45486	0.655000|0.655000	0.94253|0.94253	AAC|ACT	.	.	.	none		0.378	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254	
AKT3	10000	hgsc.bcm.edu	37	1	243800913	243800913	+	Splice_Site	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:243800913C>T	ENST00000366539.1	-	6	761	c.561G>A	c.(559-561)aaG>aaA	p.K187K	AKT3_ENST00000263826.5_Splice_Site_p.K187K|AKT3_ENST00000366540.1_Splice_Site_p.K187K|AKT3_ENST00000336199.5_Splice_Site_p.K187K			Q9Y243	AKT3_HUMAN	v-akt murine thymoma viral oncogene homolog 3	187	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitochondrial genome maintenance (GO:0000002)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|skin(3)|stomach(1)	26	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)			AATCAGTTACCTTTGCAATAA	0.328																																					p.K187K		Atlas-SNP	.											.	AKT3	177	.	0			c.G561A						PASS	.						81.0	81.0	81.0					1																	243800913		2202	4295	6497	SO:0001630	splice_region_variant	10000	exon6			AGTTACCTTTGCA	AF124141	CCDS31076.1, CCDS31077.1	1q44	2013-07-09	2013-07-09		ENSG00000117020	ENSG00000117020	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	393	protein-coding gene	gene with protein product	"""protein kinase B, gamma"""	611223				10092583, 10208883	Standard	NM_005465		Approved	PKBG, RAC-gamma, PRKBG	uc001iab.2	Q9Y243	OTTHUMG00000039994	ENST00000366539.1:c.561+1G>A	chr1.hg19:g.243800913C>T		75.0	0.0	.		42.0	6.0	.	NM_001206729	Q0VAA6|Q5VTI1|Q5VTI2|Q96QV3|Q9UFP5	Silent	SNP	ENST00000366539.1	hg19	CCDS31077.1																																																																																			.	.	.	none		0.328	AKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096479.1	NM_181690	Silent
KCNS3	3790	hgsc.bcm.edu	37	2	18113163	18113163	+	Missense_Mutation	SNP	G	G	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:18113163G>C	ENST00000403915.1	+	3	1339	c.888G>C	c.(886-888)agG>agC	p.R296S	KCNS3_ENST00000465292.1_Intron|KCNS3_ENST00000304101.4_Missense_Mutation_p.R296S	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	296					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GGCTTATGAGGATTTTCCGAA	0.502																																					p.R296S		Atlas-SNP	.											.	KCNS3	85	.	0			c.G888C						PASS	.						109.0	107.0	108.0					2																	18113163		2203	4300	6503	SO:0001583	missense	3790	exon3			TATGAGGATTTTC	AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.888G>C	chr2.hg19:g.18113163G>C	ENSP00000385968:p.Arg296Ser	161.0	0.0	.		220.0	83.0	.	NM_002252	D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	ENST00000403915.1	hg19	CCDS1692.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.808968	0.50421	.	.	ENSG00000170745	ENST00000403915;ENST00000304101	D;D	0.99594	-6.25;-6.25	5.86	1.98	0.26296	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99638	0.9867	H	0.96301	3.8	0.52099	D	0.999942	D	0.76494	0.999	D	0.85130	0.997	D	0.99194	1.0871	10	0.87932	D	0	.	6.5286	0.22314	0.2607:0.1183:0.621:0.0	.	296	Q9BQ31	KCNS3_HUMAN	S	296	ENSP00000385968:R296S;ENSP00000305824:R296S	ENSP00000305824:R296S	R	+	3	2	KCNS3	17976644	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.263000	0.33004	0.374000	0.24650	0.655000	0.94253	AGG	.	.	.	none		0.502	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252	
KHK	3795	hgsc.bcm.edu	37	2	27315218	27315218	+	Missense_Mutation	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:27315218G>T	ENST00000260599.6	+	2	624	c.111G>T	c.(109-111)tgG>tgT	p.W37C	KHK_ENST00000260598.5_Missense_Mutation_p.W37C|KHK_ENST00000490823.1_3'UTR	NM_000221.2	NP_000212.1	P50053	KHK_HUMAN	ketohexokinase (fructokinase)	37					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose catabolic process (GO:0006001)|regulation of glycogen metabolic process (GO:0070873)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ketohexokinase activity (GO:0004454)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCAGAGATGGCAGCGCGGAG	0.607																																					p.W37C		Atlas-SNP	.											.	KHK	60	.	0			c.G111T						PASS	.						91.0	80.0	84.0					2																	27315218		2203	4300	6503	SO:0001583	missense	3795	exon2			GAGATGGCAGCGC		CCDS1734.1, CCDS1735.1	2p23.3-p23.2	2008-02-05			ENSG00000138030	ENSG00000138030	2.7.1.3		6315	protein-coding gene	gene with protein product		614058				7833921	Standard	NM_000221		Approved		uc002rim.2	P50053	OTTHUMG00000097077	ENST00000260599.6:c.111G>T	chr2.hg19:g.27315218G>T	ENSP00000260599:p.Trp37Cys	32.0	0.0	.		65.0	31.0	.	NM_006488	Q6IBK2|Q99532|Q9BRJ3|Q9UMN1	Missense_Mutation	SNP	ENST00000260599.6	hg19	CCDS1734.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.750913	0.49257	.	.	ENSG00000138030	ENST00000260599;ENST00000260598;ENST00000429697	T;T;T	0.75938	-0.98;-0.98;-0.98	5.5	5.5	0.81552	Carbohydrate/purine kinase (1);	0.000000	0.85682	D	0.000000	D	0.88377	0.6420	M	0.90082	3.085	0.80722	D	1	D;P;D	0.76494	0.999;0.495;0.999	D;B;D	0.75020	0.985;0.122;0.985	D	0.89208	0.3562	10	0.46703	T	0.11	-18.2402	16.8828	0.86067	0.0:0.0:1.0:0.0	.	37;37;37	Q6IBK2;P50053-2;P50053	.;.;KHK_HUMAN	C	37	ENSP00000260599:W37C;ENSP00000260598:W37C;ENSP00000404741:W37C	ENSP00000260598:W37C	W	+	3	0	KHK	27168722	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	8.964000	0.93389	2.595000	0.87683	0.462000	0.41574	TGG	.	.	.	none		0.607	KHK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214196.1		
ERLEC1	27248	hgsc.bcm.edu	37	2	54028861	54028861	+	Missense_Mutation	SNP	C	C	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:54028861C>A	ENST00000185150.4	+	8	892	c.761C>A	c.(760-762)tCt>tAt	p.S254Y	ERLEC1_ENST00000378239.5_Missense_Mutation_p.S254Y|ERLEC1_ENST00000405123.3_Missense_Mutation_p.S254Y|GPR75-ASB3_ENST00000352846.3_Intron|ASB3_ENST00000498475.2_Intron|ASB3_ENST00000406625.2_Intron	NM_015701.4	NP_056516.2	Q96DZ1	ERLEC_HUMAN	endoplasmic reticulum lectin 1	254					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	glycoprotein binding (GO:0001948)			endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|stomach(1)|urinary_tract(1)	18						TTCAGAGCATCTCCTGTGAAT	0.418																																					p.S254Y		Atlas-SNP	.											.	ERLEC1	32	.	0			c.C761A						PASS	.						102.0	92.0	96.0					2																	54028861		2203	4300	6503	SO:0001583	missense	27248	exon8			GAGCATCTCCTGT	AF131849	CCDS1848.1, CCDS46283.1, CCDS46284.1	2p16	2010-03-19	2009-08-26	2009-08-26	ENSG00000068912	ENSG00000068912			25222	protein-coding gene	gene with protein product	"""erlectin 1"""	611229	"""chromosome 2 open reading frame 30"""	C2orf30		9110174, 8619474, 16531414, 18264092	Standard	NM_015701		Approved	CL25084, XTP3TPB, XTP3-B, ERLECTIN	uc002rxl.3	Q96DZ1	OTTHUMG00000129281	ENST00000185150.4:c.761C>A	chr2.hg19:g.54028861C>A	ENSP00000185150:p.Ser254Tyr	122.0	0.0	.		128.0	61.0	.	NM_015701	B2RDB4|B5MC72|O95901|Q6UWN7|Q9NUY7|Q9UQL4	Missense_Mutation	SNP	ENST00000185150.4	hg19	CCDS1848.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.909863	0.92107	.	.	ENSG00000068912	ENST00000405123;ENST00000185150;ENST00000378239	T;T	0.47528	0.84;0.84	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.71350	0.3329	.	.	.	0.80722	D	1	D;P;D	0.71674	0.997;0.756;0.998	D;B;D	0.69479	0.964;0.283;0.931	T	0.72567	-0.4254	9	0.72032	D	0.01	-13.4706	20.4024	0.99000	0.0:1.0:0.0:0.0	.	254;254;254	Q96DZ1-2;B5MC72;Q96DZ1	.;.;ERLEC_HUMAN	Y	254	ENSP00000385629:S254Y;ENSP00000185150:S254Y	ENSP00000185150:S254Y	S	+	2	0	ERLEC1	53882365	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.827000	0.97445	0.650000	0.86243	TCT	.	.	.	none		0.418	ERLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251404.1	NM_015701	
NAGK	55577	hgsc.bcm.edu	37	2	71304704	71304704	+	Missense_Mutation	SNP	A	A	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:71304704A>G	ENST00000244204.6	+	9	844	c.782A>G	c.(781-783)aAg>aGg	p.K261R	NAGK_ENST00000443872.2_Missense_Mutation_p.K113R|NAGK_ENST00000455662.2_Missense_Mutation_p.K307R|NAGK_ENST00000443938.2_Missense_Mutation_p.K257R|NAGK_ENST00000418807.3_Missense_Mutation_p.K210R			Q9UJ70	NAGK_HUMAN	N-acetylglucosamine kinase	261					carbohydrate phosphorylation (GO:0046835)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|N-acetylglucosamine kinase activity (GO:0045127)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|urinary_tract(1)	18					N-Acetyl-D-glucosamine(DB00141)	TTCCAGGGCAAGATTGGACTC	0.602																																					p.K307R		Atlas-SNP	.											.	NAGK	34	.	0			c.A920G						PASS	.						66.0	53.0	57.0					2																	71304704		2203	4300	6503	SO:0001583	missense	55577	exon9			AGGGCAAGATTGG	AJ242910	CCDS33220.1, CCDS33220.2	2p24.3-p24.1	2008-02-05			ENSG00000124357	ENSG00000124357	2.7.1.59		17174	protein-coding gene	gene with protein product		606828				10824116	Standard	NM_017567		Approved	GNK	uc002shp.4	Q9UJ70	OTTHUMG00000153239	ENST00000244204.6:c.782A>G	chr2.hg19:g.71304704A>G	ENSP00000244204:p.Lys261Arg	59.0	0.0	.		99.0	38.0	.	NM_017567	B4DLZ5|Q53HD5|Q6IA84|Q9BS29|Q9BVP0|Q9NV37	Missense_Mutation	SNP	ENST00000244204.6	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.73|11.73	1.724892|1.724892	0.30593|0.30593	.|.	.|.	ENSG00000124357|ENSG00000124357	ENST00000244204;ENST00000455662;ENST00000418807|ENST00000443938	T;T;T|.	0.44083|.	1.52;1.49;0.93|.	5.63|5.63	1.85|1.85	0.25348|0.25348	ATPase, BadF/BadG/BcrA/BcrD type (1);|.	0.811995|.	0.11191|.	N|.	0.589950|.	T|T	0.17619|0.17619	0.0423|0.0423	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.18398|0.18398	-1.0338|-1.0338	10|5	0.18276|.	T|.	0.48|.	-17.2471|-17.2471	2.0065|2.0065	0.03478|0.03478	0.4877:0.2795:0.0916:0.1411|0.4877:0.2795:0.0916:0.1411	.|.	261|.	Q9UJ70|.	NAGK_HUMAN|.	R|G	261;307;210|279	ENSP00000244204:K261R;ENSP00000389087:K307R;ENSP00000396070:K210R|.	ENSP00000244204:K261R|.	K|R	+|+	2|1	0|2	NAGK|NAGK	71158212|71158212	0.037000|0.037000	0.19845|0.19845	0.003000|0.003000	0.11579|0.11579	0.043000|0.043000	0.13939|0.13939	1.412000|1.412000	0.34714|0.34714	0.937000|0.937000	0.37394|0.37394	-0.336000|-0.336000	0.08194|0.08194	AAG|AGA	.	.	.	none		0.602	NAGK-032	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471889.1		
UGGT1	56886	hgsc.bcm.edu	37	2	128941262	128941262	+	Missense_Mutation	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:128941262G>T	ENST00000259253.6	+	38	4305	c.4258G>T	c.(4258-4260)Gtg>Ttg	p.V1420L	UGGT1_ENST00000375990.3_Missense_Mutation_p.V1396L	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1420	Glucosyltransferase. {ECO:0000250}.				'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						ACTATATGTTGTGGATCTGAA	0.438																																					p.V1420L		Atlas-SNP	.											.	UGGT1	126	.	0			c.G4258T						PASS	.						107.0	102.0	104.0					2																	128941262		2203	4300	6503	SO:0001583	missense	56886	exon38			TATGTTGTGGATC	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"""UDP-glucose ceramide glucosyltransferase-like 1"""	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.4258G>T	chr2.hg19:g.128941262G>T	ENSP00000259253:p.Val1420Leu	140.0	0.0	.		141.0	59.0	.	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	hg19	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.733269	0.89482	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.37411	1.2;1.2	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.71978	0.3404	H	0.96175	3.78	0.80722	D	1	D	0.71674	0.998	D	0.69307	0.963	T	0.82600	-0.0377	9	.	.	.	.	18.0955	0.89488	0.0:0.0:1.0:0.0	.	1420	Q9NYU2	UGGG1_HUMAN	L	1396;1420	ENSP00000365158:V1396L;ENSP00000259253:V1420L	.	V	+	1	0	UGGT1	128657732	1.000000	0.71417	0.994000	0.49952	0.844000	0.47949	9.090000	0.94144	2.577000	0.86979	0.563000	0.77884	GTG	.	.	.	none		0.438	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
MAP3K19	80122	hgsc.bcm.edu	37	2	135744072	135744072	+	Missense_Mutation	SNP	C	C	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:135744072C>G	ENST00000375845.3	-	7	2400	c.2370G>C	c.(2368-2370)caG>caC	p.Q790H	MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.Q807H|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.Q677H	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	790							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										GCTCAGGTGTCTGAGCCAAGT	0.398																																					p.Q790H		Atlas-SNP	.											.	.	.	.	0			c.G2370C						PASS	.						65.0	65.0	65.0					2																	135744072		2203	4300	6503	SO:0001583	missense	80122	exon7			AGGTGTCTGAGCC	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	26249	protein-coding gene	gene with protein product			"""Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"""	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.2370G>C	chr2.hg19:g.135744072C>G	ENSP00000365005:p.Gln790His	80.0	0.0	.		112.0	40.0	.	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	hg19	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	C	0.926	-0.714163	0.03206	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915;ENST00000437365	T;T;T;T	0.72615	-0.53;-0.53;1.83;-0.67	4.61	0.257	0.15574	.	0.519636	0.16240	N	0.223204	T	0.48607	0.1509	N	0.17082	0.46	0.09310	N	0.999998	B;B;B	0.23854	0.023;0.092;0.014	B;B;B	0.22880	0.028;0.042;0.013	T	0.31971	-0.9924	10	0.35671	T	0.21	.	6.5935	0.22659	0.0:0.5532:0.2308:0.2159	.	677;807;790	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	H	790;677;807;180	ENSP00000365005:Q790H;ENSP00000351140:Q677H;ENSP00000376647:Q807H;ENSP00000392827:Q180H	ENSP00000351140:Q677H	Q	-	3	2	YSK4	135460542	0.000000	0.05858	0.005000	0.12908	0.148000	0.21650	-0.294000	0.08309	0.133000	0.18654	0.407000	0.27541	CAG	.	.	.	none		0.398	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052	
GCA	25801	hgsc.bcm.edu	37	2	163208899	163208899	+	Missense_Mutation	SNP	A	A	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:163208899A>C	ENST00000437150.2	+	3	405	c.244A>C	c.(244-246)Att>Ctt	p.I82L	GCA_ENST00000233612.4_Missense_Mutation_p.I63L|GCA_ENST00000473240.1_3'UTR|GCA_ENST00000429691.2_Missense_Mutation_p.I63L	NM_012198.3	NP_036330.1	P28676	GRAN_HUMAN	grancalcin, EF-hand calcium binding protein	82	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				membrane fusion (GO:0061025)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|lung(4)|ovary(1)	9						ACAGTCTGGAATTAATGGAAC	0.308																																					p.I82L		Atlas-SNP	.											.	GCA	15	.	0			c.A244C						PASS	.						175.0	175.0	175.0					2																	163208899		2203	4300	6503	SO:0001583	missense	25801	exon3			TCTGGAATTAATG	M81637	CCDS2218.1	2q24.2	2013-01-10	2001-11-28		ENSG00000115271	ENSG00000115271		"""EF-hand domain containing"""	15990	protein-coding gene	gene with protein product		607030	"""grancalcin, EF-hand calcium-binding protein"""			1737748, 1530588, 12804766	Standard	NM_012198		Approved	GCL	uc002ucg.3	P28676	OTTHUMG00000132057	ENST00000437150.2:c.244A>C	chr2.hg19:g.163208899A>C	ENSP00000394842:p.Ile82Leu	111.0	0.0	.		119.0	58.0	.	NM_012198	B2R5X3|Q53TB5|Q59EP3	Missense_Mutation	SNP	ENST00000437150.2	hg19	CCDS2218.1	.	.	.	.	.	.	.	.	.	.	A	15.48	2.845886	0.51164	.	.	ENSG00000115271	ENST00000446271;ENST00000429691;ENST00000437150;ENST00000453113;ENST00000233612	T;T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92;-0.92	5.19	5.19	0.71726	EF-hand-like domain (1);	0.726139	0.12958	N	0.425264	T	0.77471	0.4135	M	0.72118	2.19	0.52501	D	0.999952	B	0.33940	0.433	B	0.43536	0.423	T	0.69892	-0.5022	10	0.09843	T	0.71	.	14.0628	0.64810	1.0:0.0:0.0:0.0	.	82	P28676	GRAN_HUMAN	L	108;63;82;63;63	ENSP00000393218:I108L;ENSP00000412899:I63L;ENSP00000394842:I82L;ENSP00000403805:I63L;ENSP00000233612:I63L	ENSP00000233612:I63L	I	+	1	0	GCA	162917145	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	6.473000	0.73572	1.951000	0.56629	0.528000	0.53228	ATT	.	.	.	none		0.308	GCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255080.3	NM_012198	
SPC25	57405	hgsc.bcm.edu	37	2	169746011	169746011	+	Missense_Mutation	SNP	C	C	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:169746011C>G	ENST00000282074.2	-	2	160	c.19G>C	c.(19-21)Gca>Cca	p.A7P	SPC25_ENST00000472216.2_5'UTR	NM_020675.3	NP_065726.1	Q9HBM1	SPC25_HUMAN	SPC25, NDC80 kinetochore complex component	7	Interaction with the N-terminus of SPBC24.|Interaction with the NDC80-NUF2 subcomplex.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)	condensed chromosome kinetochore (GO:0000777)|cytosol (GO:0005829)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1)	9						TCGAAAAGTGCCAGTTCGTCC	0.368																																					p.A7P		Atlas-SNP	.											SPC25,NS,carcinoma,0,1	SPC25	21	.	0			c.G19C						PASS	.						59.0	55.0	57.0					2																	169746011		2203	4300	6503	SO:0001583	missense	57405	exon2			AAAGTGCCAGTTC	AF225416	CCDS2229.1	2q31.1	2013-06-05	2013-06-05	2007-03-02	ENSG00000152253	ENSG00000152253			24031	protein-coding gene	gene with protein product		609395	"""spindle pole body component 25 homolog (S. cerevisiae)"", ""SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)"""	SPBC25		12477932	Standard	NM_020675		Approved	MGC22228, AD024	uc002uel.3	Q9HBM1	OTTHUMG00000132181	ENST00000282074.2:c.19G>C	chr2.hg19:g.169746011C>G	ENSP00000282074:p.Ala7Pro	59.0	0.0	.		44.0	18.0	.	NM_020675	A8K4X8|D3DPC0	Missense_Mutation	SNP	ENST00000282074.2	hg19	CCDS2229.1	.	.	.	.	.	.	.	.	.	.	C	8.902	0.956561	0.18507	.	.	ENSG00000152253	ENST00000282074;ENST00000451987	.	.	.	6.16	3.38	0.38709	.	0.449522	0.26963	N	0.021614	T	0.18257	0.0438	L	0.27053	0.805	0.26399	N	0.976457	P	0.43169	0.8	B	0.37943	0.261	T	0.08330	-1.0727	9	0.46703	T	0.11	0.0356	6.4946	0.22136	0.0:0.693:0.1487:0.1583	.	7	Q9HBM1	SPC25_HUMAN	P	7	.	ENSP00000282074:A7P	A	-	1	0	SPC25	169454257	0.107000	0.21998	0.161000	0.22692	0.012000	0.07955	0.142000	0.16096	0.469000	0.27268	-0.142000	0.14014	GCA	.	.	.	none		0.368	SPC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255233.2	NM_020675	
METTL5	29081	hgsc.bcm.edu	37	2	170677784	170677784	+	Splice_Site	SNP	C	C	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:170677784C>A	ENST00000260953.5	-	3	541		c.e3-1		METTL5_ENST00000410097.1_Splice_Site|METTL5_ENST00000409837.1_Splice_Site|METTL5_ENST00000409965.1_Splice_Site|METTL5_ENST00000308099.3_Splice_Site|METTL5_ENST00000409340.1_Intron|METTL5_ENST00000392640.2_Splice_Site	NM_014168.2	NP_054887.2	Q9NRN9	METL5_HUMAN	methyltransferase like 5								methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|large_intestine(5)|lung(1)|prostate(1)	10						AACACACAACCTATAAATACA	0.299																																					.		Atlas-SNP	.											.	METTL5	24	.	0			c.225-1G>T						PASS	.						75.0	75.0	75.0					2																	170677784		2203	4298	6501	SO:0001630	splice_region_variant	29081	exon4			CACAACCTATAAA	AF201938	CCDS33320.1	2q31.1	2011-01-28			ENSG00000138382	ENSG00000138382			25006	protein-coding gene	gene with protein product						11042152	Standard	XM_005246478		Approved	HSPC133	uc002ufn.3	Q9NRN9	OTTHUMG00000154117	ENST00000260953.5:c.225-1G>T	chr2.hg19:g.170677784C>A		82.0	0.0	.		114.0	39.0	.	NM_014168	D3DPC9|Q9NVX1	Splice_Site	SNP	ENST00000260953.5	hg19	CCDS33320.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065087	0.76187	.	.	ENSG00000138382	ENST00000409837;ENST00000540464;ENST00000260953;ENST00000409965;ENST00000392640;ENST00000308099;ENST00000410097	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7542	0.91826	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	METTL5	170386030	1.000000	0.71417	0.932000	0.37286	0.983000	0.72400	7.590000	0.82653	2.490000	0.84030	0.655000	0.94253	.	.	.	.	none		0.299	METTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333957.1	NM_014168	Intron
NHEJ1	79840	hgsc.bcm.edu	37	2	220022946	220022946	+	Missense_Mutation	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:220022946C>T	ENST00000356853.5	-	2	272	c.139G>A	c.(139-141)Gaa>Aaa	p.E47K	NHEJ1_ENST00000409720.1_Missense_Mutation_p.E47K	NM_024782.2	NP_079058.1	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1	47	Globular head.				B cell differentiation (GO:0030183)|central nervous system development (GO:0007417)|DNA recombination (GO:0006310)|double-strand break repair via nonhomologous end joining (GO:0006303)|positive regulation of ligase activity (GO:0051351)|response to ionizing radiation (GO:0010212)|T cell differentiation (GO:0030217)	nonhomologous end joining complex (GO:0070419)|nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	12		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)		TCCACCTGTTCATGCCACACC	0.527								Non-homologous end-joining																													p.E47K		Atlas-SNP	.											.	NHEJ1	26	.	0			c.G139A						PASS	.						158.0	135.0	143.0					2																	220022946		2203	4300	6503	SO:0001583	missense	79840	exon2			CCTGTTCATGCCA	AJ972687	CCDS2432.1	2q35	2014-09-17			ENSG00000187736	ENSG00000187736			25737	protein-coding gene	gene with protein product		611290				16439204, 16439205	Standard	NM_024782		Approved	Cernunnos, XLF, FLJ12610	uc002vjp.4	Q9H9Q4	OTTHUMG00000133127	ENST00000356853.5:c.139G>A	chr2.hg19:g.220022946C>T	ENSP00000349313:p.Glu47Lys	76.0	0.0	.		112.0	47.0	.	NM_024782	B8ZZA4|Q4ZFW7|Q6IA64|Q96JS9	Missense_Mutation	SNP	ENST00000356853.5	hg19	CCDS2432.1	.	.	.	.	.	.	.	.	.	.	C	34	5.320702	0.95682	.	.	ENSG00000187736	ENST00000409720;ENST00000356853;ENST00000457600	T;T;T	0.71698	-0.59;-0.59;-0.59	5.7	5.7	0.88788	DNA double-strand break repair and VJ recombination XRCC4, N-terminal (1);	0.000000	0.85682	U	0.000000	D	0.85414	0.5691	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86392	0.1736	10	0.87932	D	0	0.2919	19.8022	0.96513	0.0:1.0:0.0:0.0	.	47	Q9H9Q4	NHEJ1_HUMAN	K	47	ENSP00000387290:E47K;ENSP00000349313:E47K;ENSP00000407201:E47K	ENSP00000349313:E47K	E	-	1	0	NHEJ1	219731190	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	4.959000	0.63666	2.683000	0.91414	0.655000	0.94253	GAA	.	.	.	none		0.527	NHEJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256817.2	NM_024782	
SETD5	55209	hgsc.bcm.edu	37	3	9475587	9475587	+	Missense_Mutation	SNP	A	A	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:9475587A>G	ENST00000406341.1	+	3	320	c.130A>G	c.(130-132)Aat>Gat	p.N44D	SETD5_ENST00000402466.1_5'UTR|SETD5_ENST00000407969.1_Missense_Mutation_p.N44D|SETD5_ENST00000402198.1_Missense_Mutation_p.N44D|SETD5_ENST00000302463.6_5'UTR			Q9C0A6	SETD5_HUMAN	SET domain containing 5	44										NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		TTCCACTCATAATTATGGGAC	0.468																																					p.N44D		Atlas-SNP	.											.	SETD5	210	.	0			c.A130G						PASS	.						204.0	200.0	201.0					3																	9475587		2010	4171	6181	SO:0001583	missense	55209	exon4			ACTCATAATTATG	BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.130A>G	chr3.hg19:g.9475587A>G	ENSP00000383939:p.Asn44Asp	168.0	0.0	.		155.0	41.0	.	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	ENST00000406341.1	hg19	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.537828	0.27475	.	.	ENSG00000168137	ENST00000450326;ENST00000402198;ENST00000406341;ENST00000407969	T;D;D;D	0.90261	1.45;-2.64;-2.64;-2.59	6.07	6.07	0.98685	.	.	.	.	.	D	0.82986	0.5156	L	0.47716	1.5	0.80722	D	1	P	0.38922	0.651	B	0.30401	0.115	T	0.79579	-0.1745	9	0.11485	T	0.65	-13.9018	9.0586	0.36421	0.8937:0.0:0.1063:0.0	.	44	Q9C0A6	SETD5_HUMAN	D	44	ENSP00000413786:N44D;ENSP00000385852:N44D;ENSP00000383939:N44D;ENSP00000384114:N44D	ENSP00000385852:N44D	N	+	1	0	SETD5	9450587	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.856000	0.75450	2.330000	0.79161	0.477000	0.44152	AAT	.	.	.	none		0.468	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614	
DNAH1	25981	hgsc.bcm.edu	37	3	52428521	52428521	+	Missense_Mutation	SNP	T	T	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:52428521T>C	ENST00000420323.2	+	67	10928	c.10667T>C	c.(10666-10668)aTc>aCc	p.I3556T		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3621					cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TCCATCTCGATCATGACTGAG	0.622																																					p.I3556T		Atlas-SNP	.											.	DNAH1	534	.	0			c.T10667C						PASS	.						72.0	79.0	77.0					3																	52428521		2065	4195	6260	SO:0001583	missense	25981	exon67			TCTCGATCATGAC	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.10667T>C	chr3.hg19:g.52428521T>C	ENSP00000401514:p.Ile3556Thr	109.0	0.0	.		115.0	58.0	.	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	1.598	-0.527373	0.04141	.	.	ENSG00000114841	ENST00000420323;ENST00000273600	D	0.87103	-2.21	5.27	-5.01	0.02991	.	1.697270	0.03317	N	0.191372	T	0.70996	0.3288	N	0.12569	0.235	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.56721	-0.7932	10	0.33141	T	0.24	.	2.3064	0.04175	0.1418:0.4088:0.1794:0.27	.	3556;3621	C9JXH6;Q9P2D7-2	.;.	T	3556;309	ENSP00000401514:I3556T	ENSP00000273600:I309T	I	+	2	0	DNAH1	52403561	0.000000	0.05858	0.000000	0.03702	0.215000	0.24574	-0.451000	0.06795	-0.554000	0.06150	-0.274000	0.10170	ATC	.	.	.	none		0.622	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
ABHD6	57406	hgsc.bcm.edu	37	3	58242370	58242370	+	Silent	SNP	A	A	T	rs11544005		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:58242370A>T	ENST00000478253.1	+	3	558	c.57A>T	c.(55-57)ccA>ccT	p.P19P	ABHD6_ENST00000295962.4_Silent_p.P19P			Q9BV23	ABHD6_HUMAN	abhydrolase domain containing 6	19					long term synaptic depression (GO:0060292)|negative regulation of cell migration (GO:0030336)|regulation of endocannabinoid signaling pathway (GO:2000124)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acylglycerol lipase activity (GO:0047372)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	16				BRCA - Breast invasive adenocarcinoma(55;0.000225)|KIRC - Kidney renal clear cell carcinoma(284;0.0471)|Kidney(284;0.0589)|OV - Ovarian serous cystadenocarcinoma(275;0.209)		TGGCCATCCCAATCCTGGCAT	0.463																																					p.P19P		Atlas-SNP	.											.	ABHD6	28	.	0			c.A57T						PASS	.						174.0	165.0	168.0					3																	58242370		2203	4300	6503	SO:0001819	synonymous_variant	57406	exon2			CATCCCAATCCTG	AF225418	CCDS2887.1	3p21.2	2006-03-10			ENSG00000163686	ENSG00000163686		"""Abhydrolase domain containing"""	21398	protein-coding gene	gene with protein product							Standard	NM_020676		Approved		uc003djs.4	Q9BV23	OTTHUMG00000159150	ENST00000478253.1:c.57A>T	chr3.hg19:g.58242370A>T		106.0	0.0	.		103.0	23.0	.	NM_020676	B2R7Y9|Q6ZMF7	Silent	SNP	ENST00000478253.1	hg19	CCDS2887.1																																																																																			.	.	.	alt		0.463	ABHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353511.1	NM_020676	
CBLB	868	hgsc.bcm.edu	37	3	105572285	105572285	+	Missense_Mutation	SNP	C	C	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:105572285C>A	ENST00000264122.4	-	3	713	c.392G>T	c.(391-393)aGa>aTa	p.R131I	CBLB_ENST00000394027.3_Missense_Mutation_p.R153I|CBLB_ENST00000403724.1_Missense_Mutation_p.R131I|CBLB_ENST00000405772.1_Missense_Mutation_p.R131I|CBLB_ENST00000545639.1_Missense_Mutation_p.R153I	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	131	4H.|Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						TTCATACATTCTCTCCTTGCC	0.343			Mis S		AML																																p.R131I	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.G392T						PASS	.						240.0	242.0	241.0					3																	105572285		2203	4300	6503	SO:0001583	missense	868	exon3			TACATTCTCTCCT	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"""RING-type (C3HC4) zinc fingers"""	1542	protein-coding gene	gene with protein product		604491	"""Cas-Br-M (murine) ectropic retroviral transforming sequence b"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence b"""			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.392G>T	chr3.hg19:g.105572285C>A	ENSP00000264122:p.Arg131Ile	145.0	0.0	.		135.0	33.0	.	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Missense_Mutation	SNP	ENST00000264122.4	hg19	CCDS2948.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280158	0.95489	.	.	ENSG00000114423	ENST00000264122;ENST00000394027;ENST00000403724;ENST00000405772;ENST00000545639;ENST00000438603;ENST00000447441;ENST00000443752	T;T;T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	5.69	5.69	0.88448	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.000000	0.85682	D	0.000000	D	0.85991	0.5826	L	0.50333	1.59	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.74348	0.983;0.972;0.937	D	0.86563	0.1842	10	0.87932	D	0	-13.8454	19.8034	0.96518	0.0:1.0:0.0:0.0	.	153;131;131	E7ENW2;Q13191-3;Q13191	.;.;CBLB_HUMAN	I	131;153;131;131;153;153;131;131	ENSP00000264122:R131I;ENSP00000377595:R153I;ENSP00000384816:R131I;ENSP00000384938:R131I;ENSP00000446116:R153I;ENSP00000409750:R153I;ENSP00000400949:R131I;ENSP00000393906:R131I	ENSP00000264122:R131I	R	-	2	0	CBLB	107054975	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.603000	0.82811	2.669000	0.90835	0.655000	0.94253	AGA	.	.	.	none		0.343	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662	
EAF2	55840	hgsc.bcm.edu	37	3	121554190	121554190	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:121554190G>A	ENST00000273668.2	+	1	129	c.58G>A	c.(58-60)Ggg>Agg	p.G20R	EAF2_ENST00000465664.1_3'UTR|EAF2_ENST00000451944.2_Missense_Mutation_p.G20R|IQCB1_ENST00000310864.6_5'Flank|IQCB1_ENST00000349820.6_5'Flank	NM_018456.4	NP_060926.2	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	20	Necessary for interaction with ELL.				apoptotic process (GO:0006915)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	ELL-EAF complex (GO:0032783)|transcription elongation factor complex (GO:0008023)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)	9				GBM - Glioblastoma multiforme(114;0.0972)		TCTCAAGTTAGGGGAGAGTTT	0.592																																					p.G20R	Esophageal Squamous(194;1942 2097 24663 29345 31866)	Atlas-SNP	.											.	EAF2	26	.	0			c.G58A						PASS	.						60.0	57.0	58.0					3																	121554190		2203	4300	6503	SO:0001583	missense	55840	exon1			AAGTTAGGGGAGA	AF517829	CCDS3006.1	3q21.1	2007-08-01			ENSG00000145088	ENSG00000145088			23115	protein-coding gene	gene with protein product		607659				12446457, 12907652	Standard	NM_018456		Approved	BM040, TRAITS, U19	uc003een.3	Q96CJ1	OTTHUMG00000159424	ENST00000273668.2:c.58G>A	chr3.hg19:g.121554190G>A	ENSP00000273668:p.Gly20Arg	75.0	0.0	.		97.0	9.0	.	NM_018456	Q9NZ82	Missense_Mutation	SNP	ENST00000273668.2	hg19	CCDS3006.1	.	.	.	.	.	.	.	.	.	.	G	36	5.612769	0.96637	.	.	ENSG00000145088	ENST00000273668;ENST00000451944	.	.	.	5.95	5.95	0.96441	Transcription elognation factor  Eaf, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84238	0.5428	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.85853	0.1405	9	0.87932	D	0	-12.3041	17.8686	0.88804	0.0:0.0:1.0:0.0	.	20	Q96CJ1	EAF2_HUMAN	R	20	.	ENSP00000273668:G20R	G	+	1	0	EAF2	123036880	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.606000	0.82863	2.817000	0.96982	0.563000	0.77884	GGG	.	.	.	none		0.592	EAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355247.1	NM_018456	
PARP14	54625	hgsc.bcm.edu	37	3	122436993	122436993	+	Nonsense_Mutation	SNP	C	C	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:122436993C>G	ENST00000474629.2	+	13	4342	c.4076C>G	c.(4075-4077)tCa>tGa	p.S1359*		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1359	Macro 3. {ECO:0000255|PROSITE- ProRule:PRU00490}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CAGAAAGGATCAGCCCAGTCT	0.388																																					p.S1359X		Atlas-SNP	.											.	PARP14	242	.	0			c.C4076G						PASS	.						88.0	82.0	84.0					3																	122436993		1860	4108	5968	SO:0001587	stop_gained	54625	exon13			AAGGATCAGCCCA	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4076C>G	chr3.hg19:g.122436993C>G	ENSP00000418194:p.Ser1359*	165.0	0.0	.		185.0	102.0	.	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Nonsense_Mutation	SNP	ENST00000474629.2	hg19	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	C	40	8.082615	0.98646	.	.	ENSG00000173193	ENST00000474629;ENST00000398162;ENST00000398157	.	.	.	5.28	-1.14	0.09741	.	1.436610	0.04490	N	0.379296	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	5.3252	0.15903	0.1259:0.4927:0.0:0.3814	.	.	.	.	X	1359;1278;355	.	ENSP00000381224:S355X	S	+	2	0	PARP14	123919683	0.000000	0.05858	0.000000	0.03702	0.971000	0.66376	0.777000	0.26718	-0.442000	0.07190	0.650000	0.86243	TCA	.	.	.	none		0.388	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
RBP2	5948	hgsc.bcm.edu	37	3	139195286	139195286	+	Missense_Mutation	SNP	T	T	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:139195286T>A	ENST00000232217.2	-	1	72	c.16A>T	c.(16-18)Aat>Tat	p.N6Y	RP11-319G6.1_ENST00000515247.1_RNA	NM_004164.2	NP_004155.2	P50120	RET2_HUMAN	retinol binding protein 2, cellular	6					epidermis development (GO:0008544)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|vitamin A metabolic process (GO:0006776)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	12					Vitamin A(DB00162)	CAGGTTCCATTCTGGTCCCTT	0.537																																					p.N6Y		Atlas-SNP	.											.	RBP2	21	.	0			c.A16T						PASS	.						154.0	132.0	139.0					3																	139195286		2203	4300	6503	SO:0001583	missense	5948	exon1			TTCCATTCTGGTC	U13831	CCDS3109.1	3q23	2013-03-01	2001-11-28		ENSG00000114113	ENSG00000114113		"""Fatty acid binding protein family"""	9920	protein-coding gene	gene with protein product		180280	"""retinol-binding protein 2, cellular"""			7657783, 10072590	Standard	NM_004164		Approved	CRBP2, RBPC2, CRBPII, CRABP-II	uc003eth.3	P50120	OTTHUMG00000159956	ENST00000232217.2:c.16A>T	chr3.hg19:g.139195286T>A	ENSP00000232217:p.Asn6Tyr	76.0	0.0	.		74.0	11.0	.	NM_004164	A8K7G3|Q6ISQ9|Q6ISS7	Missense_Mutation	SNP	ENST00000232217.2	hg19	CCDS3109.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.138577	0.77775	.	.	ENSG00000114113	ENST00000232217;ENST00000511956;ENST00000506825	T;T	0.08102	3.13;3.13	5.44	5.44	0.79542	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.550372	0.21049	N	0.081028	T	0.17023	0.0409	L	0.29908	0.895	0.54753	D	0.999987	D	0.76494	0.999	D	0.68039	0.955	T	0.01666	-1.1300	10	0.44086	T	0.13	.	13.5403	0.61671	0.0:0.0:0.0:1.0	.	6	P50120	RET2_HUMAN	Y	6	ENSP00000232217:N6Y;ENSP00000424333:N6Y	ENSP00000232217:N6Y	N	-	1	0	RBP2	140677976	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	3.604000	0.54081	2.194000	0.70268	0.460000	0.39030	AAT	.	.	.	none		0.537	RBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358490.1	NM_004164	
PLD1	5337	hgsc.bcm.edu	37	3	171395429	171395429	+	Silent	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:171395429G>A	ENST00000351298.4	-	17	2049	c.1923C>T	c.(1921-1923)acC>acT	p.T641T	PLD1_ENST00000356327.5_Silent_p.T603T|PLD1_ENST00000340989.4_Silent_p.T641T|PLD1_ENST00000342215.6_Missense_Mutation_p.P532L	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	641	Catalytic.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	GCCAGAATCTGGTTTCCCCAT	0.498																																					p.T641T	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											.	PLD1	134	.	0			c.C1923T						PASS	.						169.0	150.0	157.0					3																	171395429		2203	4300	6503	SO:0001819	synonymous_variant	5337	exon17			GAATCTGGTTTCC	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"""Pleckstrin homology (PH) domain containing"""	9067	protein-coding gene	gene with protein product	"""choline phosphatase 1"""	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.1923C>T	chr3.hg19:g.171395429G>A		141.0	0.0	.		118.0	31.0	.	NM_002662		Silent	SNP	ENST00000351298.4	hg19	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.196234	0.38806	.	.	ENSG00000075651	ENST00000342215	T	0.34072	1.38	6.16	0.406	0.16366	.	.	.	.	.	T	0.25827	0.0629	.	.	.	0.30550	N	0.765587	.	.	.	.	.	.	T	0.31110	-0.9955	6	0.27785	T	0.31	-24.3912	4.8638	0.13598	0.1371:0.3306:0.4295:0.1029	.	.	.	.	L	532	ENSP00000339936:P532L	ENSP00000339936:P532L	P	-	2	0	PLD1	172878123	0.948000	0.32251	0.748000	0.31131	0.981000	0.71138	0.123000	0.15708	0.117000	0.18138	0.650000	0.86243	CCA	.	.	.	none		0.498	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	
RFC4	5984	hgsc.bcm.edu	37	3	186508173	186508173	+	Missense_Mutation	SNP	T	T	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:186508173T>A	ENST00000392481.2	-	9	1105	c.824A>T	c.(823-825)gAt>gTt	p.D275V	RFC4_ENST00000296273.2_Missense_Mutation_p.D275V|RFC4_ENST00000433496.1_Intron|SNORA63_ENST00000363450.1_RNA|SNORA4_ENST00000584302.1_RNA	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	275					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.D275G(1)		breast(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		AAATACTCCATCAATTTTCTC	0.428																																					p.D275V		Atlas-SNP	.											RFC4,NS,carcinoma,0,1	RFC4	54	.	1	Substitution - Missense(1)	kidney(1)	c.A824T						PASS	.						112.0	112.0	112.0					3																	186508173		2203	4300	6503	SO:0001583	missense	5984	exon9			ACTCCATCAATTT		CCDS3283.1	3q27	2010-04-21	2002-08-29		ENSG00000163918	ENSG00000163918		"""ATPases / AAA-type"""	9972	protein-coding gene	gene with protein product	"""A1 37 kDa subunit"", ""activator 1 37 kDa subunit"", ""RFC 37 kDa subunit"""	102577	"""replication factor C (activator 1) 4 (37kD)"""			7774928	Standard	NM_181573		Approved	A1, RFC37	uc003fqz.3	P35249	OTTHUMG00000156515	ENST00000392481.2:c.824A>T	chr3.hg19:g.186508173T>A	ENSP00000376272:p.Asp275Val	182.0	0.0	.		144.0	36.0	.	NM_181573	B4DM41|D3DNV2|Q6FHX7	Missense_Mutation	SNP	ENST00000392481.2	hg19	CCDS3283.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.670832	0.29693	.	.	ENSG00000163918	ENST00000392481;ENST00000296273;ENST00000417876	T;T;T	0.44083	0.93;0.93;0.93	5.32	2.79	0.32731	Replication factor C (1);DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal (1);	0.428568	0.30538	N	0.009405	T	0.44808	0.1311	M	0.84326	2.69	0.80722	D	1	B	0.18013	0.025	B	0.27887	0.084	T	0.46373	-0.9196	10	0.54805	T	0.06	.	6.9715	0.24652	0.0:0.0842:0.1493:0.7664	.	275	P35249	RFC4_HUMAN	V	275;275;50	ENSP00000376272:D275V;ENSP00000296273:D275V;ENSP00000401429:D50V	ENSP00000296273:D275V	D	-	2	0	RFC4	187990867	0.999000	0.42202	0.697000	0.30258	0.437000	0.31866	2.471000	0.45127	0.970000	0.38263	0.459000	0.35465	GAT	.	.	.	none		0.428	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916	
HTT	3064	hgsc.bcm.edu	37	4	3162057	3162057	+	Missense_Mutation	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:3162057C>T	ENST00000355072.5	+	29	3947	c.3802C>T	c.(3802-3804)Cgc>Tgc	p.R1268C		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1268					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AGGGTTTCTCCGCTCAGCCTT	0.512																																					p.R1268C		Atlas-SNP	.											.	HTT	221	.	0			c.C3802T						PASS	.																																			SO:0001583	missense	3064	exon29			TTTCTCCGCTCAG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.3802C>T	chr4.hg19:g.3162057C>T	ENSP00000347184:p.Arg1268Cys	173.0	0.0	.		181.0	67.0	.	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.674542	0.29693	.	.	ENSG00000197386	ENST00000355072	T	0.65916	-0.18	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.57740	0.2074	L	0.52364	1.645	0.80722	D	1	B	0.18166	0.026	B	0.11329	0.006	T	0.57946	-0.7723	10	0.44086	T	0.13	.	16.6252	0.84968	0.0:1.0:0.0:0.0	.	1268	P42858	HD_HUMAN	C	1268	ENSP00000347184:R1268C	ENSP00000347184:R1268C	R	+	1	0	HTT	3131855	1.000000	0.71417	1.000000	0.80357	0.221000	0.24807	4.125000	0.57931	2.069000	0.61940	0.563000	0.77884	CGC	.	.	.	none		0.512	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
PI4K2B	55300	hgsc.bcm.edu	37	4	25235821	25235821	+	Silent	SNP	C	C	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:25235821C>A	ENST00000264864.6	+	1	225	c.36C>A	c.(34-36)tcC>tcA	p.S12S	PI4K2B_ENST00000512921.1_Intron	NM_018323.3	NP_060793.2	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	12					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|skin(3)	15		Breast(46;0.173)				GGTTGGCGTCCGCGGACGGCG	0.731																																					p.S12S		Atlas-SNP	.											.	PI4K2B	42	.	0			c.C36A						PASS	.						3.0	3.0	3.0					4																	25235821		1446	3354	4800	SO:0001819	synonymous_variant	55300	exon1			GGCGTCCGCGGAC	AK001967	CCDS3433.1	4p15.31	2009-05-07			ENSG00000038210	ENSG00000038210			18215	protein-coding gene	gene with protein product		612101				11923287	Standard	NM_018323		Approved	PI4KIIB, FLJ11105, PIK42B	uc003grk.2	Q8TCG2	OTTHUMG00000128564	ENST00000264864.6:c.36C>A	chr4.hg19:g.25235821C>A		7.0	0.0	.		44.0	13.0	.	NM_018323	Q9NUW2	Silent	SNP	ENST00000264864.6	hg19	CCDS3433.1																																																																																			.	.	.	none		0.731	PI4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250415.1	NM_018323	
ARAP2	116984	hgsc.bcm.edu	37	4	36152575	36152575	+	Silent	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:36152575G>T	ENST00000303965.4	-	16	3333	c.2844C>A	c.(2842-2844)atC>atA	p.I948I		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	948	PH 3. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						TAACTTCATTGATATTAATGG	0.343																																					p.I948I		Atlas-SNP	.											ARAP2,NS,carcinoma,0,1	ARAP2	210	.	0			c.C2844A						PASS	.						169.0	174.0	172.0					4																	36152575		2203	4298	6501	SO:0001819	synonymous_variant	116984	exon16			TTCATTGATATTA	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16924	protein-coding gene	gene with protein product		606645	"""centaurin, delta 1"""	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.2844C>A	chr4.hg19:g.36152575G>T		121.0	1.0	.		115.0	36.0	.	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Silent	SNP	ENST00000303965.4	hg19	CCDS3441.1																																																																																			.	.	.	none		0.343	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230	
SYNPO2	171024	hgsc.bcm.edu	37	4	119952707	119952707	+	Missense_Mutation	SNP	A	A	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:119952707A>T	ENST00000429713.2	+	4	2959	c.2777A>T	c.(2776-2778)aAt>aTt	p.N926I	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000434046.2_Missense_Mutation_p.N926I|SYNPO2_ENST00000307142.4_Missense_Mutation_p.N926I	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	926						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GTGGCCTATAATCCTATCCAC	0.572																																					p.N926I		Atlas-SNP	.											.	SYNPO2	353	.	0			c.A2777T						PASS	.						87.0	83.0	84.0					4																	119952707		2203	4300	6503	SO:0001583	missense	171024	exon4			CCTATAATCCTAT	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.2777A>T	chr4.hg19:g.119952707A>T	ENSP00000395143:p.Asn926Ile	58.0	0.0	.		78.0	11.0	.	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	hg19	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.9|20.9	4.067512|4.067512	0.76301|0.76301	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.14893|.	2.47;2.58;2.47|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|.	0.77239|.	0.4101|.	M|M	0.80982|0.80982	2.52|2.52	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;0.999;0.997|.	D;D;D;D|.	0.91635|.	0.998;0.999;0.997;0.972|.	T|.	0.78874|.	-0.2032|.	9|.	.|.	.|.	.|.	-24.3416|-24.3416	15.8861|15.8861	0.79251|0.79251	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	926;926;926;926|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	I|Y	926|877	ENSP00000306015:N926I;ENSP00000395143:N926I;ENSP00000390965:N926I|.	.|.	N|X	+|+	2|3	0|2	SYNPO2|SYNPO2	120172155|120172155	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.914000|0.914000	0.54420|0.54420	9.339000|9.339000	0.96797|0.96797	2.156000|2.156000	0.67533|0.67533	0.533000|0.533000	0.62120|0.62120	AAT|TAA	.	.	.	none		0.572	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
SMAD1	4086	hgsc.bcm.edu	37	4	146463798	146463798	+	Silent	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:146463798G>A	ENST00000515385.1	+	4	1265	c.723G>A	c.(721-723)ccG>ccA	p.P241P	SMAD1_ENST00000302085.4_Silent_p.P241P|SMAD1_ENST00000394092.2_Silent_p.P241P			Q15797	SMAD1_HUMAN	SMAD family member 1	241					BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cardiac muscle cell proliferation (GO:0060038)|cartilage development (GO:0051216)|cellular response to BMP stimulus (GO:0071773)|embryonic pattern specification (GO:0009880)|gamete generation (GO:0007276)|hindbrain development (GO:0030902)|homeostatic process (GO:0042592)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|mesodermal cell fate commitment (GO:0001710)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|osteoblast fate commitment (GO:0002051)|positive regulation of cartilage development (GO:0061036)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of gene expression (GO:0010628)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|primary miRNA processing (GO:0031053)|protein phosphorylation (GO:0006468)|response to drug (GO:0042493)|response to organonitrogen compound (GO:0010243)|signal transduction (GO:0007165)|SMAD protein complex assembly (GO:0007183)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	co-SMAD binding (GO:0070410)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)			endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	17	all_hematologic(180;0.151)					GCTCTCAGCCGATGGACACAA	0.473																																					p.P241P	Pancreas(182;1287 2092 10326 35158 50562)	Atlas-SNP	.											.	SMAD1	48	.	0			c.G723A						PASS	.						65.0	68.0	67.0					4																	146463798		2203	4300	6503	SO:0001819	synonymous_variant	4086	exon4			TCAGCCGATGGAC	U59423	CCDS3765.1	4q31.21	2013-10-22	2006-11-06	2004-05-26	ENSG00000170365	ENSG00000170365		"""SMADs"""	6767	protein-coding gene	gene with protein product		601595	"""MAD, mothers against decapentaplegic homolog 1 (Drosophila)"", ""SMAD, mothers against DPP homolog 1 (Drosophila)"""	MADH1		8653785, 8673135	Standard	NM_005900		Approved	MADR1, JV4-1	uc003ikc.3	Q15797	OTTHUMG00000161592	ENST00000515385.1:c.723G>A	chr4.hg19:g.146463798G>A		89.0	0.0	.		88.0	4.0	.	NM_005900	A8KAJ0|D3DNZ9|Q16636|Q9UFT8	Silent	SNP	ENST00000515385.1	hg19	CCDS3765.1																																																																																			.	.	.	none		0.473	SMAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365467.1	NM_005900	
IQGAP2	10788	hgsc.bcm.edu	37	5	75888702	75888702	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:75888702G>A	ENST00000274364.6	+	9	1156	c.859G>A	c.(859-861)Gaa>Aaa	p.E287K	IQGAP2_ENST00000379730.3_5'UTR	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	287					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		TGCTTATGAAGAACTGCTGAC	0.323																																					p.E287K		Atlas-SNP	.											.	IQGAP2	186	.	0			c.G859A						PASS	.						138.0	145.0	142.0					5																	75888702		2203	4300	6503	SO:0001583	missense	10788	exon9			TATGAAGAACTGC	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.859G>A	chr5.hg19:g.75888702G>A	ENSP00000274364:p.Glu287Lys	316.0	0.0	.		466.0	78.0	.	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	hg19	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	G	32	5.141279	0.94560	.	.	ENSG00000145703	ENST00000274364;ENST00000514350;ENST00000505766	T;T;T	0.39787	4.12;1.06;4.13	5.83	5.83	0.93111	.	0.100666	0.64402	D	0.000002	T	0.54287	0.1849	M	0.80616	2.505	0.80722	D	1	P	0.42483	0.781	P	0.44732	0.459	T	0.50988	-0.8762	10	0.21540	T	0.41	-17.3562	20.1863	0.98216	0.0:0.0:1.0:0.0	.	287	Q13576	IQGA2_HUMAN	K	287;260;237	ENSP00000274364:E287K;ENSP00000423672:E260K;ENSP00000421097:E237K	ENSP00000274364:E287K	E	+	1	0	IQGAP2	75924458	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	9.798000	0.99111	2.781000	0.95711	0.650000	0.86243	GAA	.	.	.	none		0.323	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
IQGAP2	10788	hgsc.bcm.edu	37	5	75888710	75888710	+	Silent	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:75888710G>A	ENST00000274364.6	+	9	1164	c.867G>A	c.(865-867)ctG>ctA	p.L289L	IQGAP2_ENST00000379730.3_5'UTR	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	289					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AAGAACTGCTGACACAAGCAG	0.333																																					p.L289L		Atlas-SNP	.											.	IQGAP2	186	.	0			c.G867A						PASS	.						145.0	152.0	149.0					5																	75888710		2203	4300	6503	SO:0001819	synonymous_variant	10788	exon9			ACTGCTGACACAA	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.867G>A	chr5.hg19:g.75888710G>A		344.0	0.0	.		484.0	78.0	.	NM_006633	A8K4V1|B7Z8A4|J3KR91	Silent	SNP	ENST00000274364.6	hg19	CCDS34188.1																																																																																			.	.	.	none		0.333	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
IQGAP2	10788	hgsc.bcm.edu	37	5	75973147	75973147	+	Missense_Mutation	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:75973147C>T	ENST00000274364.6	+	28	3929	c.3632C>T	c.(3631-3633)tCa>tTa	p.S1211L	IQGAP2_ENST00000502745.1_Missense_Mutation_p.S707L|IQGAP2_ENST00000396234.3_Missense_Mutation_p.S707L|IQGAP2_ENST00000379730.3_Missense_Mutation_p.S713L	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1211					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		ATTTATATTTCAATTGAAGAA	0.393																																					p.S1211L		Atlas-SNP	.											.	IQGAP2	186	.	0			c.C3632T						PASS	.						65.0	66.0	65.0					5																	75973147		2203	4300	6503	SO:0001583	missense	10788	exon28			ATATTTCAATTGA	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.3632C>T	chr5.hg19:g.75973147C>T	ENSP00000274364:p.Ser1211Leu	88.0	0.0	.		95.0	11.0	.	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	hg19	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	C	32	5.108409	0.94292	.	.	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000505766;ENST00000396234;ENST00000502745	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	4.98	4.98	0.66077	Rho GTPase activation protein (1);Ras GTPase-activating protein (1);	0.329934	0.33144	N	0.005221	T	0.73094	0.3543	M	0.84326	2.69	0.80722	D	1	D;D;P	0.65815	0.995;0.995;0.792	P;P;B	0.60609	0.877;0.877;0.322	T	0.77910	-0.2411	10	0.72032	D	0.01	-12.9253	18.4229	0.90597	0.0:1.0:0.0:0.0	.	713;707;1211	F5H7S7;Q13576-2;Q13576	.;.;IQGA2_HUMAN	L	1211;713;1161;707;707	ENSP00000274364:S1211L;ENSP00000442313:S713L;ENSP00000421097:S1161L;ENSP00000379535:S707L;ENSP00000426027:S707L	ENSP00000274364:S1211L	S	+	2	0	IQGAP2	76008903	1.000000	0.71417	0.991000	0.47740	0.986000	0.74619	7.557000	0.82243	2.597000	0.87782	0.591000	0.81541	TCA	.	.	.	none		0.393	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
FNIP1	96459	hgsc.bcm.edu	37	5	131007961	131007961	+	Missense_Mutation	SNP	C	C	T	rs367969091		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:131007961C>T	ENST00000510461.1	-	14	2271	c.2176G>A	c.(2176-2178)Gga>Aga	p.G726R	FNIP1_ENST00000307954.8_Missense_Mutation_p.G681R|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307968.7_Missense_Mutation_p.G698R	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	726					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		ACAACCATTCCTGTGGATCTC	0.448																																					p.G726R		Atlas-SNP	.											.	FNIP1	104	.	0			c.G2176A						PASS	.	C	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	218.0	207.0	211.0		2092,2176	4.9	1.0	5		211	0,8600		0,0,4300	no	missense,missense	FNIP1	NM_001008738.2,NM_133372.2	125,125	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	698/1139,726/1167	131007961	1,13005	2203	4300	6503	SO:0001583	missense	96459	exon14			CCATTCCTGTGGA	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.2176G>A	chr5.hg19:g.131007961C>T	ENSP00000421985:p.Gly726Arg	82.0	0.0	.		109.0	63.0	.	NM_133372	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	hg19	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.212357	0.58452	2.27E-4	0.0	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461	T;T;T	0.42131	0.98;0.98;0.98	5.76	4.89	0.63831	.	.	.	.	.	T	0.45538	0.1347	L	0.43152	1.355	0.80722	D	1	P;P;P	0.46512	0.879;0.879;0.773	P;P;B	0.50708	0.648;0.494;0.414	T	0.31420	-0.9944	9	0.49607	T	0.09	-8.8964	12.306	0.54902	0.0:0.8667:0.0:0.1333	.	726;698;726	A8K8V8;Q8TF40-3;Q8TF40	.;.;FNIP1_HUMAN	R	698;681;478;726	ENSP00000309266:G698R;ENSP00000310453:G681R;ENSP00000421985:G726R	ENSP00000310453:G681R	G	-	1	0	FNIP1	131035860	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.191000	0.58372	2.726000	0.93360	0.655000	0.94253	GGA	.	.	.	weak		0.448	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372	
NSD1	64324	hgsc.bcm.edu	37	5	176721020	176721020	+	Missense_Mutation	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:176721020G>T	ENST00000439151.2	+	23	6696	c.6651G>T	c.(6649-6651)gaG>gaT	p.E2217D	NSD1_ENST00000354179.4_Missense_Mutation_p.E1948D|NSD1_ENST00000361032.4_Missense_Mutation_p.E2114D|NSD1_ENST00000347982.4_Missense_Mutation_p.E1948D	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2217	Pro-rich.				gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		AACCTGGGGAGATCCGTGAGT	0.562			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.E2217D		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G6651T						PASS	.						81.0	80.0	81.0					5																	176721020		2203	4300	6503	SO:0001583	missense	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TGGGGAGATCCGT	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.6651G>T	chr5.hg19:g.176721020G>T	ENSP00000395929:p.Glu2217Asp	91.0	0.0	.		120.0	46.0	.	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	hg19	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.840800	0.71488	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000002	D	0.84419	0.5468	L	0.27053	0.805	0.53688	D	0.999975	D;D	0.76494	0.999;0.999	D;D	0.71870	0.975;0.933	D	0.84097	0.0393	10	0.51188	T	0.08	.	11.9775	0.53100	0.1325:0.0:0.8675:0.0	.	1948;2217	Q96L73-2;Q96L73	.;NSD1_HUMAN	D	1948;2217;1948;2114	ENSP00000346111:E1948D;ENSP00000395929:E2217D;ENSP00000343209:E1948D;ENSP00000354310:E2114D	ENSP00000343209:E1948D	E	+	3	2	NSD1	176653626	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.583000	0.53928	2.941000	0.99782	0.655000	0.94253	GAG	.	.	.	none		0.562	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
CLK4	57396	hgsc.bcm.edu	37	5	178050363	178050363	+	Nonsense_Mutation	SNP	C	C	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:178050363C>A	ENST00000316308.4	-	2	223	c.55G>T	c.(55-57)Gga>Tga	p.G19*	CLK4_ENST00000520957.1_Nonsense_Mutation_p.G19*	NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	19					protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		CTTTCATGTCCCCAGCTTTCT	0.438																																					p.G19X		Atlas-SNP	.											.	CLK4	103	.	0			c.G55T						PASS	.						207.0	181.0	190.0					5																	178050363		2203	4300	6503	SO:0001587	stop_gained	57396	exon2			CATGTCCCCAGCT	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"""CDC-like kinases"""	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.55G>T	chr5.hg19:g.178050363C>A	ENSP00000316948:p.Gly19*	83.0	0.0	.		135.0	60.0	.	NM_020666		Nonsense_Mutation	SNP	ENST00000316308.4	hg19	CCDS4437.1	.	.	.	.	.	.	.	.	.	.	C	38	7.083910	0.98051	.	.	ENSG00000113240	ENST00000316308;ENST00000536763;ENST00000520957	.	.	.	5.83	4.97	0.65823	.	0.325167	0.32548	N	0.005960	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	10.8916	0.46998	0.0:0.9136:0.0:0.0864	.	.	.	.	X	19	.	ENSP00000316948:G19X	G	-	1	0	CLK4	177982969	0.989000	0.36119	0.999000	0.59377	0.962000	0.63368	2.363000	0.44178	1.477000	0.48234	0.491000	0.48974	GGA	.	.	.	none		0.438	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2		
ZSCAN23	222696	hgsc.bcm.edu	37	6	28402345	28402345	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:28402345G>A	ENST00000289788.4	-	4	1212	c.1067C>T	c.(1066-1068)aCt>aTt	p.T356I	ZSCAN23_ENST00000486481.1_5'Flank	NM_001012455.1	NP_001012458.1	Q3MJ62	ZSC23_HUMAN	zinc finger and SCAN domain containing 23	356					transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|prostate(1)|stomach(2)	4						TCTCTCTCCAGTGTGAATTCT	0.448																																					p.T356I		Atlas-SNP	.											.	ZSCAN23	18	.	0			c.C1067T						PASS	.						158.0	136.0	142.0					6																	28402345		692	1591	2283	SO:0001583	missense	222696	exon4			TCTCCAGTGTGAA	AK092117	CCDS47393.1	6p21.33	2013-01-08	2007-02-20	2007-02-20	ENSG00000187987	ENSG00000187987		"""-"", ""Zinc fingers, C2H2-type"""	21193	protein-coding gene	gene with protein product			"""zinc finger protein 453"", ""zinc finger protein 390"""	ZNF453, ZNF390			Standard	NM_001012455		Approved	dJ29K1.3.1	uc003nli.4	Q3MJ62	OTTHUMG00000016346	ENST00000289788.4:c.1067C>T	chr6.hg19:g.28402345G>A	ENSP00000289788:p.Thr356Ile	99.0	0.0	.		110.0	61.0	.	NM_001012455	Q96KV9	Missense_Mutation	SNP	ENST00000289788.4	hg19	CCDS47393.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245900	0.80024	.	.	ENSG00000187987	ENST00000289788	T	0.25749	1.78	3.93	3.93	0.45458	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39909	N	0.001229	T	0.36386	0.0965	M	0.80183	2.485	0.34741	D	0.730734	D	0.55385	0.971	P	0.56788	0.806	T	0.46541	-0.9184	10	0.87932	D	0	.	13.4765	0.61312	0.0:0.0:1.0:0.0	.	356	Q3MJ62	ZSC23_HUMAN	I	356	ENSP00000289788:T356I	ENSP00000289788:T356I	T	-	2	0	ZSCAN23	28510324	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.856000	0.69518	2.007000	0.58848	0.650000	0.86243	ACT	.	.	.	none		0.448	ZSCAN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043751.2	XM_167147	
DPCR1	135656	hgsc.bcm.edu	37	6	30918494	30918494	+	Missense_Mutation	SNP	C	C	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:30918494C>G	ENST00000462446.1	+	2	2281	c.2253C>G	c.(2251-2253)aaC>aaG	p.N751K	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	315						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CCAATGAGAACACCACACCAT	0.483																																					p.N751K		Atlas-SNP	.											.	DPCR1	99	.	0			c.C2253G						PASS	.						47.0	48.0	48.0					6																	30918494		692	1591	2283	SO:0001583	missense	135656	exon2			TGAGAACACCACA	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2253C>G	chr6.hg19:g.30918494C>G	ENSP00000417182:p.Asn751Lys	117.0	0.0	.		113.0	5.0	.	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	hg19	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	-	0.005	-2.134125	0.00338	.	.	ENSG00000168631	ENST00000462446	T	0.42900	0.96	1.63	-3.25	0.05079	.	.	.	.	.	T	0.04770	0.0129	N	0.14661	0.345	0.20196	N	0.999924	B	0.10296	0.003	B	0.04013	0.001	T	0.35375	-0.9791	9	0.05833	T	0.94	.	4.4043	0.11402	0.0:0.2495:0.2493:0.5011	.	751	E9PEI6	.	K	751	ENSP00000417182:N751K	ENSP00000417182:N751K	N	+	3	2	DPCR1	31026473	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-0.332000	0.07904	-0.774000	0.04590	0.282000	0.19409	AAC	.	.	.	none		0.483	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
TNXB	7148	hgsc.bcm.edu	37	6	32016288	32016288	+	Silent	SNP	C	C	T	rs373655652		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:32016288C>T	ENST00000375244.3	-	29	10098	c.9897G>A	c.(9895-9897)gcG>gcA	p.A3299A	TNXB_ENST00000451343.1_5'Flank|TNXB_ENST00000375247.2_Silent_p.A3297A			P22105	TENX_HUMAN	tenascin XB	3344	Fibronectin type-III 24. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GCTGCCCCTGCGCGTCCCTGT	0.687																																					p.A3297A		Atlas-SNP	.											.	TNXB	553	.	0			c.G9891A						PASS	.	C		0,3902		0,0,1951	17.0	21.0	19.0		9891	-7.3	0.0	6		19	3,8267		0,3,4132	no	coding-synonymous	TNXB	NM_019105.6		0,3,6083	TT,TC,CC		0.0363,0.0,0.0246		3297/4243	32016288	3,12169	1951	4135	6086	SO:0001819	synonymous_variant	7148	exon29			CCCCTGCGCGTCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.9897G>A	chr6.hg19:g.32016288C>T		97.0	0.0	.		173.0	105.0	.	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	hg19																																																																																				.	.	.	weak		0.687	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
TNXB	7148	hgsc.bcm.edu	37	6	32063589	32063589	+	Missense_Mutation	SNP	C	C	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:32063589C>G	ENST00000479795.1	-	3	2181	c.2041G>C	c.(2041-2043)Gaa>Caa	p.E681Q	TNXB_ENST00000375244.3_Missense_Mutation_p.E681Q|TNXB_ENST00000375247.2_Missense_Mutation_p.E681Q			P22105	TENX_HUMAN	tenascin XB	681					actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GGAGGCTCTTCCTGCCCGCAG	0.701																																					p.E681Q		Atlas-SNP	.											.	TNXB	553	.	0			c.G2041C						PASS	.						16.0	20.0	18.0					6																	32063589		2114	4231	6345	SO:0001583	missense	7148	exon3			GCTCTTCCTGCCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000479795.1:c.2041G>C	chr6.hg19:g.32063589C>G	ENSP00000418248:p.Glu681Gln	109.0	0.0	.		291.0	13.0	.	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000479795.1	hg19		.	.	.	.	.	.	.	.	.	.	C	20.2	3.955354	0.73902	.	.	ENSG00000168477	ENST00000375244;ENST00000375247;ENST00000479795	T;T;T	0.08546	3.08;3.08;3.08	4.78	4.78	0.61160	.	0.000000	0.45126	D	0.000397	T	0.08088	0.0202	L	0.37750	1.13	0.26200	N	0.979459	D	0.65815	0.995	P	0.61477	0.889	T	0.19549	-1.0302	10	0.30078	T	0.28	.	13.3295	0.60479	0.0:1.0:0.0:0.0	.	681	P22105-3	.	Q	681	ENSP00000364393:E681Q;ENSP00000364396:E681Q;ENSP00000418248:E681Q	ENSP00000364393:E681Q	E	-	1	0	TNXB	32171567	0.970000	0.33590	0.850000	0.33497	0.919000	0.55068	0.746000	0.26275	2.198000	0.70561	0.563000	0.77884	GAA	.	.	.	none		0.701	TNXB-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000357059.1	NM_019105	
CUL9	23113	hgsc.bcm.edu	37	6	43155541	43155541	+	Missense_Mutation	SNP	A	A	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:43155541A>G	ENST00000252050.4	+	7	1756	c.1672A>G	c.(1672-1674)Agc>Ggc	p.S558G	CUL9_ENST00000372647.2_Missense_Mutation_p.S558G|CUL9_ENST00000354495.3_Missense_Mutation_p.S448G	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	558					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						ATTTGAGGGCAGCACTCTCAA	0.517																																					p.S558G		Atlas-SNP	.											.	CUL9	248	.	0			c.A1672G						PASS	.						122.0	121.0	121.0					6																	43155541		2203	4300	6503	SO:0001583	missense	23113	exon7			GAGGGCAGCACTC	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.1672A>G	chr6.hg19:g.43155541A>G	ENSP00000252050:p.Ser558Gly	84.0	0.0	.		84.0	19.0	.	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	A	13.47	2.245727	0.39697	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.77489	-1.1;-0.91;-1.0	5.5	4.35	0.52113	.	0.665930	0.17251	N	0.181151	T	0.50343	0.1610	L	0.43152	1.355	0.27626	N	0.948198	B;B;B	0.16603	0.018;0.018;0.003	B;B;B	0.16722	0.016;0.016;0.002	T	0.40794	-0.9544	10	0.48119	T	0.1	-13.3974	4.4793	0.11759	0.702:0.0:0.1464:0.1516	.	558;558;558	E9PEZ1;Q8IWT3;Q05C85	.;CUL9_HUMAN;.	G	558;448;558	ENSP00000252050:S558G;ENSP00000346490:S448G;ENSP00000361730:S558G	ENSP00000252050:S558G	S	+	1	0	CUL9	43263519	0.994000	0.37717	1.000000	0.80357	0.943000	0.58893	1.801000	0.38843	2.090000	0.63153	0.383000	0.25322	AGC	.	.	.	none		0.517	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
PKHD1	5314	hgsc.bcm.edu	37	6	51586795	51586795	+	Intron	SNP	T	T	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:51586795T>G	ENST00000371117.3	-	60	10432				PKHD1_ENST00000340994.4_Missense_Mutation_p.I3394L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)						cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TATTCTGAAATCTTCAAAGCC	0.448																																					p.I3394L		Atlas-SNP	.											.	PKHD1	927	.	0			c.A10180C						PASS	.						71.0	70.0	70.0					6																	51586795		2203	4300	6503	SO:0001627	intron_variant	5314	exon61			CTGAAATCTTCAA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.10156+22387A>C	chr6.hg19:g.51586795T>G		92.0	0.0	.		76.0	32.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.692382	0.30052	.	.	ENSG00000170927	ENST00000340994	D	0.86627	-2.15	3.72	-0.352	0.12598	.	.	.	.	.	T	0.61949	0.2388	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.54275	-0.8318	8	0.54805	T	0.06	.	4.5853	0.12279	0.0:0.1103:0.3908:0.4988	.	3394	P08F94-2	.	L	3394	ENSP00000341097:I3394L	ENSP00000341097:I3394L	I	-	1	0	PKHD1	51694754	0.000000	0.05858	0.000000	0.03702	0.220000	0.24768	0.004000	0.13106	-0.046000	0.13446	0.379000	0.24179	ATT	.	.	.	none		0.448	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
COL21A1	81578	hgsc.bcm.edu	37	6	55933890	55933890	+	Missense_Mutation	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:55933890G>T	ENST00000244728.5	-	22	2442	c.2045C>A	c.(2044-2046)cCa>cAa	p.P682Q	COL21A1_ENST00000535941.1_Missense_Mutation_p.P682Q|COL21A1_ENST00000370808.2_Missense_Mutation_p.P82Q|COL21A1_ENST00000370819.1_Missense_Mutation_p.P679Q|COL21A1_ENST00000467045.1_5'UTR	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	682	Collagen-like 4.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			TGGTTCTCCTGGGGAACCCGT	0.423																																					p.P682Q		Atlas-SNP	.											.	COL21A1	201	.	0			c.C2045A						PASS	.						62.0	62.0	62.0					6																	55933890		1831	4076	5907	SO:0001583	missense	81578	exon22			TCTCCTGGGGAAC	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"""Collagens"""	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.2045C>A	chr6.hg19:g.55933890G>T	ENSP00000244728:p.Pro682Gln	84.0	0.0	.		95.0	5.0	.	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	hg19	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.143568	0.37825	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370808	D;D;D;D	0.97752	-4.52;-4.52;-4.52;-4.52	4.38	3.48	0.39840	.	0.000000	0.49305	U	0.000144	D	0.95968	0.8687	L	0.28192	0.835	0.47407	D	0.999413	P;P;D	0.89917	0.886;0.77;1.0	B;P;D	0.97110	0.381;0.515;1.0	D	0.94500	0.7709	10	0.27785	T	0.31	.	12.3453	0.55118	0.0:0.0:0.8294:0.1705	.	82;682;682	Q96P44-2;B7ZLK3;Q96P44	.;.;COLA1_HUMAN	Q	682;679;682;679;82	ENSP00000244728:P682Q;ENSP00000359855:P679Q;ENSP00000444384:P682Q;ENSP00000359844:P82Q	ENSP00000244728:P682Q	P	-	2	0	COL21A1	56041849	1.000000	0.71417	0.163000	0.22734	0.829000	0.46940	4.396000	0.59684	0.905000	0.36596	0.557000	0.71058	CCA	.	.	.	none		0.423	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2		
UBE3D	90025	hgsc.bcm.edu	37	6	83767555	83767555	+	Missense_Mutation	SNP	T	T	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:83767555T>G	ENST00000369747.3	-	2	386	c.264A>C	c.(262-264)aaA>aaC	p.K88N		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	88					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)										TTGTGCCTAATTTTGCTTGCG	0.443											OREG0017549	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K88N		Atlas-SNP	.											.	.	.	.	0			c.A264C						PASS	.						67.0	68.0	68.0					6																	83767555		2203	4300	6503	SO:0001583	missense	90025	exon2			GCCTAATTTTGCT	AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"""UBCH10 binding protein with a hect-like domain"""	612495	"""chromosome 6 open reading frame 157"", ""ubiquitin-conjugating enzyme E2C binding protein"""	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.264A>C	chr6.hg19:g.83767555T>G	ENSP00000358762:p.Lys88Asn	83.0	0.0	.	1224	78.0	39.0	.	NM_198920	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Missense_Mutation	SNP	ENST00000369747.3	hg19	CCDS34491.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490288	0.26686	.	.	ENSG00000118420	ENST00000369747	T	0.30714	1.52	5.27	-10.5	0.00291	.	0.631105	0.16070	N	0.231043	T	0.02767	0.0083	N	0.08118	0	0.09310	N	0.999998	B;B	0.20164	0.042;0.002	B;B	0.18871	0.023;0.002	T	0.20009	-1.0288	10	0.33141	T	0.24	-18.3097	5.2116	0.15320	0.1807:0.4793:0.1961:0.1438	.	88;88	D6RD24;Q7Z6J8	.;UB2CB_HUMAN	N	88	ENSP00000358762:K88N	ENSP00000358762:K88N	K	-	3	2	UBE2CBP	83824274	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.412000	0.02476	-2.085000	0.00864	-0.911000	0.02809	AAA	.	.	.	none		0.443	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920	
COQ3	51805	hgsc.bcm.edu	37	6	99823846	99823846	+	Silent	SNP	T	T	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:99823846T>A	ENST00000254759.3	-	5	723	c.699A>T	c.(697-699)acA>acT	p.T233T	COQ3_ENST00000369240.1_Intron|COQ3_ENST00000479163.1_5'Flank|COQ3_ENST00000369242.1_Intron	NM_017421.3	NP_059117.3	Q9NZJ6	COQ3_HUMAN	coenzyme Q3 methyltransferase	233					glycerol metabolic process (GO:0006071)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity (GO:0008425)|3-demethylubiquinone-9 3-O-methyltransferase activity (GO:0008689)|hexaprenyldihydroxybenzoate methyltransferase activity (GO:0004395)|O-methyltransferase activity (GO:0008171)			cervix(1)|lung(5)|upper_aerodigestive_tract(2)	8		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)		ACTGTAAAAATGTTTCTAGAT	0.368																																					p.T233T		Atlas-SNP	.											.	COQ3	19	.	0			c.A699T						PASS	.						154.0	149.0	151.0					6																	99823846		2203	4300	6503	SO:0001819	synonymous_variant	51805	exon5			TAAAAATGTTTCT	AF193016	CCDS5042.1	6q21	2013-05-01	2013-05-01		ENSG00000132423	ENSG00000132423	2.1.1.114		18175	protein-coding gene	gene with protein product	"""polyprenyldihydroxybenzoate methyltransferase"""	605196	"""coenzyme Q3 homolog, methyltransferase (yeast)"", ""coenzyme Q3 homolog, methyltransferase (S. cerevisiae)"""			10777520	Standard	NM_017421		Approved	bA9819.1	uc003ppk.3	Q9NZJ6	OTTHUMG00000015264	ENST00000254759.3:c.699A>T	chr6.hg19:g.99823846T>A		114.0	0.0	.		79.0	26.0	.	NM_017421	B3KPX0|Q5T061|Q6P4F0|Q8IXG6|Q96BG1|Q9H0N1	Silent	SNP	ENST00000254759.3	hg19	CCDS5042.1																																																																																			.	.	.	none		0.368	COQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041602.1	NM_017421	
LATS1	9113	hgsc.bcm.edu	37	6	149997827	149997827	+	Silent	SNP	C	C	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:149997827C>G	ENST00000543571.1	-	6	3187	c.2640G>C	c.(2638-2640)ggG>ggC	p.G880G	LATS1_ENST00000253339.5_Silent_p.G880G|LATS1_ENST00000542747.1_5'UTR	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		TTGAGGGATCCCCCCATTCAT	0.473																																					p.G880G		Atlas-SNP	.											.	LATS1	241	.	0			c.G2640C						PASS	.						73.0	63.0	66.0					6																	149997827		2203	4300	6503	SO:0001819	synonymous_variant	9113	exon6			GGGATCCCCCCAT	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"""LATS (large tumor suppressor, Drosophila) homolog 1"", ""LATS, large tumor suppressor, homolog 1 (Drosophila)"""			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2640G>C	chr6.hg19:g.149997827C>G		59.0	0.0	.		71.0	20.0	.	NM_004690		Silent	SNP	ENST00000543571.1	hg19	CCDS34551.1																																																																																			.	.	.	none		0.473	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690	
RNF216	54476	hgsc.bcm.edu	37	7	5781127	5781127	+	Nonsense_Mutation	SNP	G	G	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:5781127G>C	ENST00000425013.2	-	4	574	c.350C>G	c.(349-351)tCa>tGa	p.S117*	RNF216_ENST00000389902.3_Nonsense_Mutation_p.S174*	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	117					apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		TTTCTGCTCTGATCTGGGGTT	0.463																																					p.S174X		Atlas-SNP	.											.	RNF216	71	.	0			c.C521G						PASS	.						267.0	250.0	256.0					7																	5781127		2203	4300	6503	SO:0001587	stop_gained	54476	exon4			TGCTCTGATCTGG	AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"""RING-type (C3HC4) zinc fingers"""	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.350C>G	chr7.hg19:g.5781127G>C	ENSP00000404602:p.Ser117*	139.0	0.0	.		147.0	74.0	.	NM_207111	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Nonsense_Mutation	SNP	ENST00000425013.2	hg19	CCDS34595.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.567910	0.65651	.	.	ENSG00000011275	ENST00000425013;ENST00000389902	.	.	.	5.97	3.93	0.45458	.	0.519284	0.17997	N	0.155007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-4.5609	7.8068	0.29206	0.2458:0.0:0.7542:0.0	.	.	.	.	X	117;174	.	ENSP00000374550:S117X	S	-	2	0	RNF216	5747653	0.000000	0.05858	0.995000	0.50966	0.994000	0.84299	0.252000	0.18278	1.509000	0.48786	0.561000	0.74099	TCA	.	.	.	none		0.463	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111	
ZNF655	79027	hgsc.bcm.edu	37	7	99158261	99158261	+	Silent	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:99158261C>T	ENST00000394163.2	+	2	262	c.79C>T	c.(79-81)Ctg>Ttg	p.L27L	GS1-259H13.10_ENST00000455905.1_Silent_p.L27L|GS1-259H13.10_ENST00000486324.1_3'UTR|ZNF655_ENST00000449244.1_Silent_p.L27L|ZNF655_ENST00000440391.1_Silent_p.L27L|ZNF655_ENST00000424881.1_Silent_p.L27L|ZNF655_ENST00000493277.1_Silent_p.L27L|ZNF655_ENST00000252713.4_Silent_p.L27L|ZNF655_ENST00000320583.5_Silent_p.L27L|ZNF655_ENST00000454654.1_Silent_p.L27L|ZNF655_ENST00000425063.1_Silent_p.L27L|ZNF655_ENST00000357864.2_Silent_p.L27L	NM_001009960.1|NM_138494.2	NP_001009960.1|NP_612503.1	Q8N720	ZN655_HUMAN	zinc finger protein 655	27					negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	16	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)					GTCTGAGTGTCTGTCCCCAGA	0.567																																					p.L27L		Atlas-SNP	.											.	ZNF655	75	.	0			c.C79T						PASS	.						118.0	113.0	114.0					7																	99158261		2203	4300	6503	SO:0001819	synonymous_variant	79027	exon2			GAGTGTCTGTCCC	AY099353	CCDS5669.1, CCDS5670.1, CCDS34695.1, CCDS47655.1	7q22.1	2013-01-08			ENSG00000197343	ENSG00000197343		"""Zinc fingers, C2H2-type"", ""-"""	30899	protein-coding gene	gene with protein product						11179890, 15558030	Standard	NM_001083956		Approved	VIK-1, VIK	uc010lgc.3	Q8N720	OTTHUMG00000156637	ENST00000394163.2:c.79C>T	chr7.hg19:g.99158261C>T		69.0	0.0	.		79.0	21.0	.	NM_024061	A4D291|A6NGD3|B4E3M4|B7Z9Q9|D6W5T4|Q8IV00|Q8TA89|Q96EZ3|Q9BQ85	Silent	SNP	ENST00000394163.2	hg19	CCDS5669.1																																																																																			.	.	.	none		0.567	ZNF655-009	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000344929.1	NM_138494	
SSMEM1	136263	hgsc.bcm.edu	37	7	129856036	129856036	+	Missense_Mutation	SNP	A	A	T	rs144099660		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:129856036A>T	ENST00000297819.3	+	3	512	c.461A>T	c.(460-462)gAg>gTg	p.E154V		NM_145268.3	NP_660311.1	Q8WWF3	SSMM1_HUMAN	serine-rich single-pass membrane protein 1	154						integral component of membrane (GO:0016021)											GGCAGTGAAGAGTCTAACTCA	0.478																																					p.E154V		Atlas-SNP	.											.	.	.	.	0			c.A461T						PASS	.						98.0	99.0	99.0					7																	129856036		2203	4300	6503	SO:0001583	missense	0	exon3			GTGAAGAGTCTAA	AK097635	CCDS5816.1	7q32.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000165120	ENSG00000165120			29580	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 45"""	C7orf45		12477932	Standard	NM_145268		Approved	FLJ40316	uc003vpp.3	Q8WWF3	OTTHUMG00000157844	ENST00000297819.3:c.461A>T	chr7.hg19:g.129856036A>T	ENSP00000297819:p.Glu154Val	171.0	0.0	.		185.0	48.0	.	NM_145268		Missense_Mutation	SNP	ENST00000297819.3	hg19	CCDS5816.1	.	.	.	.	.	.	.	.	.	.	A	15.74	2.921732	0.52653	.	.	ENSG00000165120	ENST00000297819	T	0.55052	0.54	5.56	3.09	0.35607	.	0.365080	0.26103	N	0.026340	T	0.48589	0.1508	M	0.63428	1.95	0.32923	D	0.516117	B	0.20671	0.047	B	0.24541	0.054	T	0.56044	-0.8044	10	0.87932	D	0	-6.405	8.8929	0.35446	0.702:0.0:0.0:0.2979	.	154	Q8WWF3	CG045_HUMAN	V	154	ENSP00000297819:E154V	ENSP00000297819:E154V	E	+	2	0	C7orf45	129643272	0.962000	0.33011	0.961000	0.40146	0.396000	0.30629	2.242000	0.43106	0.352000	0.24053	0.402000	0.26972	GAG	.	A|1.000;C|0.000	.	alt		0.478	SSMEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349768.1	NM_145268	
HIPK2	28996	hgsc.bcm.edu	37	7	139258060	139258060	+	Silent	SNP	C	C	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:139258060C>A	ENST00000406875.3	-	15	3304	c.3210G>T	c.(3208-3210)ccG>ccT	p.P1070P	HIPK2_ENST00000428878.2_Silent_p.P1043P	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	1070	Autoinhibitory domain (AID).				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					GGAAGGAGTACGGAGCCTGGG	0.682																																					p.P1070P		Atlas-SNP	.											.	HIPK2	192	.	0			c.G3210T						PASS	.						84.0	104.0	97.0					7																	139258060		2181	4276	6457	SO:0001819	synonymous_variant	28996	exon15			GGAGTACGGAGCC	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"""homeodomain-interacting protein kinase 2"""			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.3210G>T	chr7.hg19:g.139258060C>A		12.0	0.0	.		37.0	12.0	.	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Silent	SNP	ENST00000406875.3	hg19																																																																																				.	.	.	none		0.682	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740	
LRRCC1	85444	hgsc.bcm.edu	37	8	86057651	86057651	+	Nonsense_Mutation	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr8:86057651G>T	ENST00000360375.3	+	19	3153	c.3004G>T	c.(3004-3006)Gaa>Taa	p.E1002*	LRRCC1_ENST00000414626.2_Nonsense_Mutation_p.E982*	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	1002					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						AGAAATGCGTGAACTTTTGGA	0.269																																					p.E1002X		Atlas-SNP	.											.	LRRCC1	212	.	0			c.G3004T						PASS	.						49.0	45.0	46.0					8																	86057651		1795	4056	5851	SO:0001587	stop_gained	85444	exon19			ATGCGTGAACTTT	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.3004G>T	chr8.hg19:g.86057651G>T	ENSP00000353538:p.Glu1002*	335.0	0.0	.		275.0	71.0	.	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Nonsense_Mutation	SNP	ENST00000360375.3	hg19	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	G	38	6.807978	0.97853	.	.	ENSG00000133739	ENST00000360375;ENST00000414626	.	.	.	4.97	4.06	0.47325	.	0.467007	0.15962	N	0.236193	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	-1.6865	14.481	0.67582	0.0:0.2766:0.7234:0.0	.	.	.	.	X	1002;982	.	ENSP00000353538:E1002X	E	+	1	0	LRRCC1	86244903	1.000000	0.71417	0.956000	0.39512	0.626000	0.37791	3.387000	0.52501	2.567000	0.86603	0.491000	0.48974	GAA	.	.	.	none		0.269	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	
CSMD3	114788	hgsc.bcm.edu	37	8	113678545	113678545	+	Missense_Mutation	SNP	T	T	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr8:113678545T>G	ENST00000297405.5	-	17	3021	c.2777A>C	c.(2776-2778)gAa>gCa	p.E926A	CSMD3_ENST00000352409.3_Missense_Mutation_p.E926A|CSMD3_ENST00000343508.3_Missense_Mutation_p.E886A|CSMD3_ENST00000455883.2_Missense_Mutation_p.E822A	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	926	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AGGTTCAGCTTCAATCACCCA	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.E926A		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A2777C						PASS	.						66.0	64.0	65.0					8																	113678545		2203	4300	6503	SO:0001583	missense	114788	exon17			TCAGCTTCAATCA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.2777A>C	chr8.hg19:g.113678545T>G	ENSP00000297405:p.Glu926Ala	145.0	0.0	.		141.0	90.0	.	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.621461	0.87460	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21	5.97	5.97	0.96955	CUB (5);	0.000000	0.64402	D	0.000001	T	0.38214	0.1032	L	0.58428	1.81	0.46028	D	0.998827	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.997;0.998;0.999	T	0.03374	-1.1043	10	0.25751	T	0.34	.	16.4523	0.83996	0.0:0.0:0.0:1.0	.	822;926;886	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	A	886;926;266;822;926	ENSP00000345799:E886A;ENSP00000297405:E926A;ENSP00000341558:E266A;ENSP00000412263:E822A;ENSP00000343124:E926A	ENSP00000297405:E926A	E	-	2	0	CSMD3	113747721	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.286000	0.76751	0.455000	0.32223	GAA	.	.	.	none		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
PLAA	9373	hgsc.bcm.edu	37	9	26925951	26925951	+	Silent	SNP	C	C	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:26925951C>A	ENST00000397292.3	-	6	1158	c.741G>T	c.(739-741)gtG>gtT	p.V247V	PLAA_ENST00000520884.1_Silent_p.V247V	NM_001031689.2	NP_001026859.1	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	247					inflammatory response (GO:0006954)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	phospholipase A2 activator activity (GO:0016005)			breast(1)|endometrium(7)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)	17		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)		CTGCTGTTGTCACAAAGTCTA	0.373																																					p.V247V	Melanoma(175;2670 2735 14091 35526)	Atlas-SNP	.											.	PLAA	48	.	0			c.G741T						PASS	.						90.0	80.0	83.0					9																	26925951		2203	4300	6503	SO:0001819	synonymous_variant	9373	exon6			TGTTGTCACAAAG	AF083395	CCDS35000.1	9p21	2013-01-10			ENSG00000137055	ENSG00000137055		"""WD repeat domain containing"""	9043	protein-coding gene	gene with protein product	"""DOA1 homolog (S. cerevisiae)"""	603873				9931468, 10644453	Standard	NM_001031689		Approved	PLAP, PLA2P, FLJ11281, FLJ12699, DOA1	uc003zqd.3	Q9Y263	OTTHUMG00000019708	ENST00000397292.3:c.741G>T	chr9.hg19:g.26925951C>A		92.0	0.0	.		81.0	48.0	.	NM_001031689	Q53EU5|Q5VY33|Q9NUL8|Q9NVE9|Q9UF53|Q9Y5L1	Silent	SNP	ENST00000397292.3	hg19	CCDS35000.1	.	.	.	.	.	.	.	.	.	.	C	6.836	0.523440	0.13066	.	.	ENSG00000137055	ENST00000523212	.	.	.	4.07	3.16	0.36331	.	.	.	.	.	T	0.47710	0.1460	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35871	-0.9771	4	.	.	.	-2.2178	4.411	0.11432	0.1594:0.5773:0.0:0.2632	.	.	.	.	Y	224	.	.	D	-	1	0	PLAA	26915951	0.997000	0.39634	1.000000	0.80357	0.994000	0.84299	0.336000	0.19823	0.817000	0.34445	0.585000	0.79938	GAC	.	.	.	none		0.373	PLAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051958.2	NM_001031689	
TLN1	7094	hgsc.bcm.edu	37	9	35711276	35711276	+	Missense_Mutation	SNP	T	T	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:35711276T>A	ENST00000314888.9	-	30	4348	c.3995A>T	c.(3994-3996)aAg>aTg	p.K1332M	TLN1_ENST00000540444.1_Missense_Mutation_p.K1332M	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1332	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CAGCTGACTCTTGAGGTTAGG	0.562																																					p.K1332M		Atlas-SNP	.											.	TLN1	185	.	0			c.A3995T						PASS	.						51.0	49.0	50.0					9																	35711276		2203	4300	6503	SO:0001583	missense	7094	exon30			TGACTCTTGAGGT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.3995A>T	chr9.hg19:g.35711276T>A	ENSP00000316029:p.Lys1332Met	61.0	0.0	.		57.0	21.0	.	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.775730	0.90195	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.18810	2.19;2.19	5.82	5.82	0.92795	Vinculin-binding site-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.44138	0.1279	M	0.83953	2.67	0.80722	D	1	P	0.52316	0.952	P	0.53954	0.738	T	0.48234	-0.9053	10	0.62326	D	0.03	-24.4418	16.1778	0.81874	0.0:0.0:0.0:1.0	.	1332	Q9Y490	TLN1_HUMAN	M	1332	ENSP00000316029:K1332M;ENSP00000442981:K1332M	ENSP00000316029:K1332M	K	-	2	0	TLN1	35701276	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	8.040000	0.89188	2.225000	0.72522	0.459000	0.35465	AAG	.	.	.	none		0.562	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
RNF20	56254	hgsc.bcm.edu	37	9	104302538	104302538	+	Missense_Mutation	SNP	G	G	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:104302538G>C	ENST00000389120.3	+	3	273	c.183G>C	c.(181-183)atG>atC	p.M61I	RNF20_ENST00000481046.1_3'UTR	NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	61					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		TGGCAGAAATGTTGGATCAGC	0.438																																					p.M61I		Atlas-SNP	.											.	RNF20	110	.	0			c.G183C						PASS	.						98.0	88.0	92.0					9																	104302538		2203	4300	6503	SO:0001583	missense	56254	exon3			AGAAATGTTGGAT	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"""RING-type (C3HC4) zinc fingers"""	10062	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"""	607699	"""ring finger protein 20"""			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.183G>C	chr9.hg19:g.104302538G>C	ENSP00000373772:p.Met61Ile	92.0	0.0	.		76.0	48.0	.	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	hg19	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.120440	0.37436	.	.	ENSG00000155827	ENST00000389120;ENST00000478347;ENST00000488264;ENST00000374819;ENST00000479306;ENST00000466817	T	0.29655	1.56	4.17	3.28	0.37604	.	0.193183	0.56097	D	0.000035	T	0.21387	0.0515	N	0.22421	0.69	0.36185	D	0.849654	B	0.02656	0.0	B	0.01281	0.0	T	0.16453	-1.0402	10	0.87932	D	0	-19.2966	11.9251	0.52814	0.0866:0.0:0.9134:0.0	.	61	Q5VTR2	BRE1A_HUMAN	I	61;49;47;61;61;61	ENSP00000373772:M61I	ENSP00000363952:M61I	M	+	3	0	RNF20	103342359	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	4.058000	0.57463	1.125000	0.41998	-0.379000	0.06801	ATG	.	.	.	none		0.438	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592	
ABCA1	19	hgsc.bcm.edu	37	9	107573100	107573100	+	Missense_Mutation	SNP	C	C	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:107573100C>G	ENST00000374736.3	-	29	4550	c.4156G>C	c.(4156-4158)Gaa>Caa	p.E1386Q		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1386					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	GTGTACTGTTCGTTGTACATC	0.507																																					p.E1386Q		Atlas-SNP	.											.	ABCA1	244	.	0			c.G4156C						PASS	.						198.0	175.0	183.0					9																	107573100		2203	4300	6503	SO:0001583	missense	19	exon29			ACTGTTCGTTGTA	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.4156G>C	chr9.hg19:g.107573100C>G	ENSP00000363868:p.Glu1386Gln	103.0	0.0	.		146.0	24.0	.	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	hg19	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077801	0.36662	.	.	ENSG00000165029	ENST00000374736	D	0.92299	-3.01	5.55	5.55	0.83447	.	0.095616	0.64402	D	0.000001	D	0.88840	0.6546	L	0.37466	1.105	0.80722	D	1	B	0.21309	0.054	B	0.26416	0.069	D	0.83736	0.0201	10	0.15499	T	0.54	.	19.8667	0.96806	0.0:1.0:0.0:0.0	.	1386	O95477	ABCA1_HUMAN	Q	1386	ENSP00000363868:E1386Q	ENSP00000363868:E1386Q	E	-	1	0	ABCA1	106612921	1.000000	0.71417	0.988000	0.46212	0.947000	0.59692	6.015000	0.70791	2.773000	0.95371	0.655000	0.94253	GAA	.	.	.	none		0.507	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
RPL7A	6130	hgsc.bcm.edu	37	9	136216489	136216489	+	Missense_Mutation	SNP	C	C	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:136216489C>A	ENST00000323345.6	+	3	238	c.208C>A	c.(208-210)Ctc>Atc	p.L70I	MED22_ENST00000471524.1_5'Flank|SNORD36B_ENST00000363961.1_RNA|MED22_ENST00000491289.1_5'Flank|MED22_ENST00000371999.1_5'Flank|SURF1_ENST00000495952.1_5'Flank|RPL7A_ENST00000315731.4_Intron|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000476080.1_5'Flank|MED22_ENST00000343730.5_5'Flank|SNORD36A_ENST00000362874.1_RNA|SNORD24_ENST00000383884.1_RNA|MED22_ENST00000344469.5_5'Flank|RPL7A_ENST00000463740.1_3'UTR	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a	70					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		GAGAGCCATCCTCTATAAGCG	0.552																																					p.L70I		Atlas-SNP	.											.	RPL7A	9	.	0			c.C208A						PASS	.						43.0	48.0	46.0					9																	136216489		2203	4294	6497	SO:0001583	missense	6130	exon3			GCCATCCTCTATA	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"""L ribosomal proteins"""	10364	protein-coding gene	gene with protein product	"""surfeit 3"", ""PLA-X polypeptide"", ""surfeit locus protein 3"", ""60S ribosomal protein L7a"", "";"", ""thyroid hormone receptor uncoupling protein"""	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.208C>A	chr9.hg19:g.136216489C>A	ENSP00000361076:p.Leu70Ile	80.0	0.0	.		88.0	31.0	.	NM_000972	P11518|Q5T8U4	Missense_Mutation	SNP	ENST00000323345.6	hg19	CCDS6965.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.158547	0.57368	.	.	ENSG00000148303	ENST00000323345;ENST00000426651	T;T	0.70164	-0.46;-0.13	4.03	4.03	0.46877	.	0.000000	0.85682	D	0.000000	T	0.75539	0.3863	M	0.89287	3.02	0.80722	D	1	B	0.22604	0.072	B	0.34346	0.18	T	0.78841	-0.2045	10	0.66056	D	0.02	.	15.1827	0.72972	0.0:1.0:0.0:0.0	.	70	P62424	RL7A_HUMAN	I	70;97	ENSP00000361076:L70I;ENSP00000416638:L97I	ENSP00000361076:L70I	L	+	1	0	RPL7A	135206310	1.000000	0.71417	0.648000	0.29521	0.115000	0.19883	5.276000	0.65580	1.816000	0.52996	0.313000	0.20887	CTC	.	.	.	none		0.552	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972	
LHX3	8022	hgsc.bcm.edu	37	9	139089398	139089398	+	Missense_Mutation	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:139089398C>T	ENST00000371748.5	-	6	1063	c.967G>A	c.(967-969)Gcc>Acc	p.A323T	LHX3_ENST00000371746.3_Missense_Mutation_p.A328T	NM_178138.4	NP_835258.1	Q9UBR4	LHX3_HUMAN	LIM homeobox 3	323					inner ear development (GO:0048839)|lung development (GO:0030324)|medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|placenta development (GO:0001890)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron cell fate specification (GO:0021520)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Myeloproliferative disorder(178;0.0511)		Epithelial(140;8.43e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.26e-07)		CTCTGCGGGGCGGCGGGGGAT	0.736																																					p.A328T		Atlas-SNP	.											.	LHX3	23	.	0			c.G982A						PASS	.						2.0	2.0	2.0					9																	139089398		1495	3217	4712	SO:0001583	missense	8022	exon6			GCGGGGCGGCGGG	AF096169	CCDS6994.1, CCDS6995.1	9q34.3	2011-06-20			ENSG00000107187	ENSG00000107187		"""Homeoboxes / LIM class"""	6595	protein-coding gene	gene with protein product		600577				10598593, 10717474	Standard	NM_178138		Approved		uc004cgz.3	Q9UBR4	OTTHUMG00000020924	ENST00000371748.5:c.967G>A	chr9.hg19:g.139089398C>T	ENSP00000360813:p.Ala323Thr	7.0	0.0	.		12.0	6.0	.	NM_014564	Q5TB39|Q5TB40|Q9NZB5|Q9P0I8|Q9P0I9	Missense_Mutation	SNP	ENST00000371748.5	hg19	CCDS6994.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.336|6.336	0.430180|0.430180	0.12045|0.12045	.|.	.|.	ENSG00000107187|ENSG00000107187	ENST00000371748;ENST00000371746|ENST00000325195	D;D|.	0.88818|.	-2.27;-2.43|.	4.04|4.04	1.96|1.96	0.26148|0.26148	.|.	0.152719|.	0.45361|.	N|.	0.000361|.	T|T	0.28433|0.28433	0.0703|0.0703	L|L	0.36672|0.36672	1.1|1.1	0.22961|0.22961	N|N	0.998502|0.998502	B;P|.	0.34462|.	0.308;0.454|.	B;B|.	0.29942|.	0.109;0.075|.	T|T	0.20371|0.20371	-1.0277|-1.0277	10|6	0.17369|0.33940	T|T	0.5|0.23	.|.	4.7565|4.7565	0.13086|0.13086	0.3922:0.4882:0.0:0.1196|0.3922:0.4882:0.0:0.1196	.|.	323;328|.	Q9UBR4;F1T0D9|.	LHX3_HUMAN;.|.	T|H	323;328|324	ENSP00000360813:A323T;ENSP00000360811:A328T|.	ENSP00000360811:A328T|ENSP00000319224:R324H	A|R	-|-	1|2	0|0	LHX3|LHX3	138229219|138229219	0.831000|0.831000	0.29352|0.29352	0.042000|0.042000	0.18584|0.18584	0.173000|0.173000	0.22820|0.22820	1.670000|1.670000	0.37502|0.37502	0.891000|0.891000	0.36235|0.36235	0.491000|0.491000	0.48974|0.48974	GCC|CGC	.	.	.	none		0.736	LHX3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055048.3		
OPTN	10133	hgsc.bcm.edu	37	10	13160994	13160994	+	Nonsense_Mutation	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:13160994C>T	ENST00000378748.3	+	8	1095	c.733C>T	c.(733-735)Cag>Tag	p.Q245*	OPTN_ENST00000378757.2_Nonsense_Mutation_p.Q245*|OPTN_ENST00000378747.3_Nonsense_Mutation_p.Q245*|OPTN_ENST00000378764.2_Nonsense_Mutation_p.Q239*|OPTN_ENST00000378752.3_Nonsense_Mutation_p.Q239*|OPTN_ENST00000263036.5_Nonsense_Mutation_p.Q245*	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	245					cell death (GO:0008219)|defense response to Gram-negative bacterium (GO:0050829)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi organization (GO:0007030)|Golgi ribbon formation (GO:0090161)|Golgi to plasma membrane protein transport (GO:0043001)|macroautophagy (GO:0016236)|mitotic cell cycle (GO:0000278)|negative regulation of receptor recycling (GO:0001920)|protein targeting to Golgi (GO:0000042)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	polyubiquitin binding (GO:0031593)|protein C-terminus binding (GO:0008022)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						GGAAGGGAATCAGAAGGTGGA	0.428																																					p.Q245X		Atlas-SNP	.											.	OPTN	57	.	0			c.C733T						PASS	.						93.0	91.0	91.0					10																	13160994		2203	4300	6503	SO:0001587	stop_gained	10133	exon7			GGGAATCAGAAGG	AF420371	CCDS7094.1	10p14	2014-01-28	2003-09-08		ENSG00000123240	ENSG00000123240			17142	protein-coding gene	gene with protein product		602432	"""glaucoma 1, open angle, E (adult-onset)"""	GLC1E		11834836, 9488477	Standard	NM_001008211		Approved	FIP2, HYPL, FIP-2, TFIIIA-INTP, NRP, HIP7	uc001ilx.1	Q96CV9	OTTHUMG00000017690	ENST00000378748.3:c.733C>T	chr10.hg19:g.13160994C>T	ENSP00000368022:p.Gln245*	199.0	0.0	.		175.0	100.0	.	NM_001008212	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Nonsense_Mutation	SNP	ENST00000378748.3	hg19	CCDS7094.1	.	.	.	.	.	.	.	.	.	.	C	39	7.381482	0.98248	.	.	ENSG00000123240	ENST00000263036;ENST00000378764;ENST00000378757;ENST00000378752;ENST00000378748;ENST00000378747	.	.	.	6.16	6.16	0.99307	.	0.099240	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-22.7994	19.6313	0.95704	0.0:1.0:0.0:0.0	.	.	.	.	X	245;239;245;239;245;245	.	ENSP00000263036:Q245X	Q	+	1	0	OPTN	13201000	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	2.672000	0.46850	2.937000	0.99478	0.650000	0.86243	CAG	.	.	.	none		0.428	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980	
KIAA1462	57608	hgsc.bcm.edu	37	10	30336674	30336674	+	Missense_Mutation	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:30336674C>T	ENST00000375377.1	-	2	169	c.68G>A	c.(67-69)cGc>cAc	p.R23H		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	23					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						GTTATCCTCGCGTGATGCTGG	0.607																																					p.R23H		Atlas-SNP	.											.	KIAA1462	162	.	0			c.G68A						PASS	.						73.0	79.0	77.0					10																	30336674		2036	4192	6228	SO:0001583	missense	57608	exon2			TCCTCGCGTGATG	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.68G>A	chr10.hg19:g.30336674C>T	ENSP00000364526:p.Arg23His	116.0	0.0	.		128.0	6.0	.	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	hg19	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	C	7.772	0.707679	0.15239	.	.	ENSG00000165757	ENST00000375377	T	0.11604	2.76	5.3	-1.25	0.09405	.	0.823638	0.10809	N	0.631817	T	0.03434	0.0099	N	0.03115	-0.41	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.46992	-0.9151	10	0.11794	T	0.64	-5.5506	5.0393	0.14451	0.0:0.4095:0.1523:0.4382	.	23	Q9P266	K1462_HUMAN	H	23	ENSP00000364526:R23H	ENSP00000364526:R23H	R	-	2	0	KIAA1462	30376680	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.154000	0.10130	-0.048000	0.13401	-0.373000	0.07131	CGC	.	.	.	none		0.607	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
KNDC1	85442	hgsc.bcm.edu	37	10	135013012	135013012	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:135013012G>A	ENST00000304613.3	+	15	2830	c.2809G>A	c.(2809-2811)Gcc>Acc	p.A937T	KNDC1_ENST00000368572.2_Missense_Mutation_p.A939T|KNDC1_ENST00000368571.2_Missense_Mutation_p.A872T			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	937					cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.A937T(1)		NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TTTCTGTGGCGCCATTTCCGA	0.532																																					p.A937T		Atlas-SNP	.											KNDC1,rectum,carcinoma,0,2	KNDC1	155	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2809A						PASS	.						177.0	150.0	159.0					10																	135013012		2203	4300	6503	SO:0001583	missense	85442	exon15			TGTGGCGCCATTT	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.2809G>A	chr10.hg19:g.135013012G>A	ENSP00000304437:p.Ala937Thr	151.0	0.0	.		192.0	14.0	.	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.244556	0.59103	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.12984	2.63;2.63;2.63	3.99	3.99	0.46301	.	0.479232	0.18727	N	0.132851	T	0.34571	0.0902	M	0.66939	2.045	0.41003	D	0.984944	D;D;D	0.89917	0.993;1.0;0.997	D;D;P	0.72338	0.919;0.977;0.74	T	0.18116	-1.0347	10	0.72032	D	0.01	-25.397	13.9012	0.63804	0.0:0.0:1.0:0.0	.	937;872;937	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	T	937;939;872	ENSP00000304437:A937T;ENSP00000357561:A939T;ENSP00000357560:A872T	ENSP00000304437:A937T	A	+	1	0	KNDC1	134863002	0.937000	0.31787	0.821000	0.32701	0.124000	0.20399	2.706000	0.47135	1.957000	0.56846	0.313000	0.20887	GCC	.	.	.	none		0.532	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
OR51D1	390038	hgsc.bcm.edu	37	11	4661643	4661643	+	Missense_Mutation	SNP	A	A	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:4661643A>T	ENST00000357605.2	+	1	699	c.623A>T	c.(622-624)aAt>aTt	p.N208I		NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, member 1	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACCAGGGTCAATGTGGTTTAT	0.468																																					p.N208I		Atlas-SNP	.											.	OR51D1	49	.	0			c.A623T						PASS	.						290.0	242.0	259.0					11																	4661643		2201	4298	6499	SO:0001583	missense	390038	exon1			GGGTCAATGTGGT	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"""GPCR / Class A : Olfactory receptors"""	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.623A>T	chr11.hg19:g.4661643A>T	ENSP00000350222:p.Asn208Ile	141.0	0.0	.		172.0	74.0	.	NM_001004751	B9EIK4	Missense_Mutation	SNP	ENST00000357605.2	hg19	CCDS31357.1	.	.	.	.	.	.	.	.	.	.	A	11.92	1.781247	0.31502	.	.	ENSG00000197428	ENST00000357605	T	0.00231	8.49	4.29	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000197	T	0.00580	0.0019	M	0.88906	2.99	0.43330	D	0.995366	P	0.44877	0.845	D	0.63793	0.918	T	0.66272	-0.5965	10	0.87932	D	0	.	9.16	0.37016	0.9102:0.0:0.0898:0.0	.	208	Q8NGF3	O51D1_HUMAN	I	208	ENSP00000350222:N208I	ENSP00000350222:N208I	N	+	2	0	OR51D1	4618219	0.644000	0.27277	0.752000	0.31206	0.008000	0.06430	1.567000	0.36407	0.752000	0.32923	0.460000	0.39030	AAT	.	.	.	none		0.468	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751	
EIF4G2	1982	hgsc.bcm.edu	37	11	10820842	10820842	+	Missense_Mutation	SNP	T	T	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:10820842T>G	ENST00000526148.1	-	20	2964	c.2454A>C	c.(2452-2454)aaA>aaC	p.K818N	SNORD97_ENST00000459187.1_RNA|EIF4G2_ENST00000339995.5_Missense_Mutation_p.K818N|RP11-685M7.5_ENST00000532365.1_RNA|EIF4G2_ENST00000525681.1_Missense_Mutation_p.K818N|EIF4G2_ENST00000396525.2_Missense_Mutation_p.K780N	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		CATGAAGAAATTTCTGCATTA	0.443																																					p.K818N		Atlas-SNP	.											.	EIF4G2	89	.	0			c.A2454C						PASS	.						154.0	144.0	148.0					11																	10820842		2201	4294	6495	SO:0001583	missense	1982	exon20			AAGAAATTTCTGC	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.2454A>C	chr11.hg19:g.10820842T>G	ENSP00000433664:p.Lys818Asn	101.0	0.0	.		120.0	61.0	.	NM_001172705		Missense_Mutation	SNP	ENST00000526148.1	hg19	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	T	19.81	3.896251	0.72639	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000528839;ENST00000379653	T;T;T;T	0.22743	1.94;1.94;1.94;1.96	6.07	0.912	0.19349	eIF4-gamma/eIF5/eIF2-epsilon (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.31040	0.0784	M	0.76727	2.345	0.53005	D	0.999965	P;D	0.63880	0.949;0.993	P;P	0.52109	0.493;0.69	T	0.47086	-0.9144	9	0.59425	D	0.04	-9.3023	8.4006	0.32583	0.0:0.5799:0.0:0.4201	.	818;891	P78344;B4DZF2	IF4G2_HUMAN;.	N	818;818;818;780;891;166;200	ENSP00000433664:K818N;ENSP00000433371:K818N;ENSP00000340281:K818N;ENSP00000379778:K780N	ENSP00000340281:K818N	K	-	3	2	EIF4G2	10777418	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.781000	0.26774	0.149000	0.19098	0.533000	0.62120	AAA	.	.	.	none		0.443	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418	
CKAP5	9793	hgsc.bcm.edu	37	11	46799004	46799004	+	Silent	SNP	G	G	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:46799004G>C	ENST00000529230.1	-	23	2893	c.2847C>G	c.(2845-2847)gtC>gtG	p.V949V	CKAP5_ENST00000312055.5_Silent_p.V949V|CKAP5_ENST00000354558.3_Silent_p.V949V|CKAP5_ENST00000415402.1_Silent_p.V949V			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	949					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						TGTCTCCAAGGACTGTGATGA	0.413																																					p.V949V	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.C2847G						PASS	.						137.0	125.0	129.0					11																	46799004		2201	4299	6500	SO:0001819	synonymous_variant	9793	exon23			TCCAAGGACTGTG		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.2847C>G	chr11.hg19:g.46799004G>C		81.0	0.0	.		104.0	43.0	.	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Silent	SNP	ENST00000529230.1	hg19	CCDS31477.1																																																																																			.	.	.	none		0.413	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756	
NUP160	23279	hgsc.bcm.edu	37	11	47837537	47837537	+	Silent	SNP	A	A	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:47837537A>G	ENST00000378460.2	-	12	1522	c.1476T>C	c.(1474-1476)agT>agC	p.S492S	NUP160_ENST00000531016.1_5'UTR|NUP160_ENST00000528501.1_Silent_p.S56S|NUP160_ENST00000528071.1_Silent_p.S378S|NUP160_ENST00000530326.1_Silent_p.S378S	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa	492					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|biliary_tract(2)|breast(7)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(6)|prostate(2)|skin(2)|urinary_tract(2)	53						TCTTCAGTTCACTCCAGGAAA	0.363																																					p.S492S		Atlas-SNP	.											.	NUP160	116	.	0			c.T1476C						PASS	.						92.0	89.0	90.0					11																	47837537		2201	4298	6499	SO:0001819	synonymous_variant	23279	exon12			CAGTTCACTCCAG	D83781	CCDS31484.1	11p11.12	2008-07-21	2002-08-29		ENSG00000030066	ENSG00000030066			18017	protein-coding gene	gene with protein product		607614	"""nucleoporin 160kD"""			11684705	Standard	NM_015231		Approved	KIAA0197, FLJ22583	uc001ngm.3	Q12769	OTTHUMG00000166534	ENST00000378460.2:c.1476T>C	chr11.hg19:g.47837537A>G		264.0	0.0	.		361.0	175.0	.	NM_015231	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Silent	SNP	ENST00000378460.2	hg19	CCDS31484.1																																																																																			.	.	.	none		0.363	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231	
PTPRJ	5795	hgsc.bcm.edu	37	11	48142728	48142728	+	Missense_Mutation	SNP	T	T	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:48142728T>G	ENST00000418331.2	+	4	878	c.526T>G	c.(526-528)Tta>Gta	p.L176V	PTPRJ_ENST00000440289.2_Missense_Mutation_p.L176V	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	176	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CATCACAGGCTTACGTCCAGC	0.423																																					p.L176V		Atlas-SNP	.											.	PTPRJ	225	.	0			c.T526G						PASS	.						163.0	147.0	153.0					11																	48142728		2201	4298	6499	SO:0001583	missense	5795	exon4			ACAGGCTTACGTC	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.526T>G	chr11.hg19:g.48142728T>G	ENSP00000400010:p.Leu176Val	282.0	1.0	.		323.0	131.0	.	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	hg19	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.149018	0.57151	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289;ENST00000534219	D;D;D	0.84800	-1.9;-1.9;-1.9	5.41	1.8	0.24995	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	D	0.89894	0.6847	M	0.75615	2.305	0.09310	N	1	D;D	0.71674	0.992;0.998	P;D	0.72338	0.908;0.977	T	0.78858	-0.2038	9	0.72032	D	0.01	.	6.633	0.22867	0.0:0.2796:0.0:0.7204	.	176;176	Q12913;Q6P4H4	PTPRJ_HUMAN;.	V	176;176;176;97	ENSP00000400010:L176V;ENSP00000409733:L176V;ENSP00000432686:L97V	ENSP00000278456:L176V	L	+	1	2	PTPRJ	48099304	0.000000	0.05858	0.014000	0.15608	0.075000	0.17131	-0.197000	0.09518	0.346000	0.23899	0.482000	0.46254	TTA	.	.	.	none		0.423	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
ANKK1	255239	hgsc.bcm.edu	37	11	113265705	113265705	+	Missense_Mutation	SNP	A	A	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:113265705A>C	ENST00000303941.3	+	3	629	c.535A>C	c.(535-537)Atc>Ctc	p.I179L		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	179	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		GATGCAGTACATCGAGAGGTC	0.552																																					p.I179L		Atlas-SNP	.											.	ANKK1	83	.	0			c.A535C						PASS	.						52.0	51.0	51.0					11																	113265705		2003	4170	6173	SO:0001583	missense	255239	exon3			CAGTACATCGAGA	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.535A>C	chr11.hg19:g.113265705A>C	ENSP00000306678:p.Ile179Leu	113.0	0.0	.		192.0	87.0	.	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	hg19	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	A	7.078	0.569692	0.13560	.	.	ENSG00000170209	ENST00000303941	D	0.82167	-1.58	4.25	3.11	0.35812	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	U	0.000079	T	0.76786	0.4036	L	0.27053	0.805	0.42141	D	0.991513	P	0.43231	0.801	P	0.48089	0.566	T	0.72301	-0.4334	10	0.34782	T	0.22	-24.2177	9.4598	0.38778	0.8415:0.0:0.0:0.1585	.	179	Q8NFD2	ANKK1_HUMAN	L	179	ENSP00000306678:I179L	ENSP00000306678:I179L	I	+	1	0	ANKK1	112770915	0.995000	0.38212	0.250000	0.24296	0.020000	0.10135	3.696000	0.54757	0.654000	0.30846	-1.026000	0.02426	ATC	.	.	.	none		0.552	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
B4GALNT3	283358	hgsc.bcm.edu	37	12	660177	660177	+	Missense_Mutation	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:660177C>T	ENST00000266383.5	+	11	1100	c.1087C>T	c.(1087-1089)Cgc>Tgc	p.R363C		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	363					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			TCCTCTGCAGCGCTACCAGGG	0.607																																					p.R363C		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.C1087T						PASS	.						172.0	151.0	158.0					12																	660177		2203	4300	6503	SO:0001583	missense	283358	exon11			CTGCAGCGCTACC	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.1087C>T	chr12.hg19:g.660177C>T	ENSP00000266383:p.Arg363Cys	105.0	0.0	.		163.0	37.0	.	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	C	31	5.064455	0.93898	.	.	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.72725	-0.68;-0.68	5.22	5.22	0.72569	.	0.107194	0.64402	D	0.000004	D	0.84428	0.5470	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.68621	0.959;0.926	D	0.86089	0.1549	10	0.87932	D	0	-22.1916	18.9627	0.92682	0.0:1.0:0.0:0.0	.	265;363	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	C	363;265	ENSP00000266383:R363C;ENSP00000322953:R265C	ENSP00000266383:R363C	R	+	1	0	B4GALNT3	530438	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.267000	0.65530	2.715000	0.92844	0.655000	0.94253	CGC	.	.	.	none		0.607	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
LRTM2	654429	hgsc.bcm.edu	37	12	1940301	1940301	+	Missense_Mutation	SNP	A	A	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:1940301A>T	ENST00000543818.1	+	4	1110	c.268A>T	c.(268-270)Aac>Tac	p.N90Y	LRTM2_ENST00000299194.1_Missense_Mutation_p.N90Y|CACNA2D4_ENST00000586184.1_Intron|CACNA2D4_ENST00000587995.1_Intron|CACNA2D4_ENST00000585708.1_Intron|CACNA2D4_ENST00000588077.1_Intron|CACNA2D4_ENST00000585732.1_Intron|LRTM2_ENST00000535041.1_Missense_Mutation_p.N90Y|LRTM2_ENST00000543730.1_Intron|CACNA2D4_ENST00000382722.5_Intron	NM_001039029.2|NM_001163925.1|NM_001163926.1	NP_001034118.1|NP_001157397.1|NP_001157398.1	Q8N967	LRTM2_HUMAN	leucine-rich repeats and transmembrane domains 2	90						integral component of membrane (GO:0016021)				NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	20	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000834)			GGCTTTCGCCAACCTCTCCAG	0.617																																					p.N90Y		Atlas-SNP	.											.	LRTM2	43	.	0			c.A268T						PASS	.						57.0	65.0	62.0					12																	1940301		2203	4300	6503	SO:0001583	missense	654429	exon4			TTCGCCAACCTCT	AK095610	CCDS31726.1	12p13.33	2008-02-05				ENSG00000166159			32443	protein-coding gene	gene with protein product							Standard	NM_001039029		Approved		uc010sdx.1	Q8N967		ENST00000543818.1:c.268A>T	chr12.hg19:g.1940301A>T	ENSP00000446278:p.Asn90Tyr	47.0	0.0	.		59.0	30.0	.	NM_001039029	A7E2U6	Missense_Mutation	SNP	ENST00000543818.1	hg19	CCDS31726.1	.	.	.	.	.	.	.	.	.	.	A	17.40	3.379726	0.61845	.	.	ENSG00000166159	ENST00000543818;ENST00000299194;ENST00000535041;ENST00000546167;ENST00000543694	T;T;T;D;D	0.85013	0.52;0.52;0.52;-1.93;-1.93	5.04	3.87	0.44632	.	0.000000	0.85682	D	0.000000	D	0.88224	0.6379	L	0.54323	1.7	0.58432	D	0.999996	D	0.59357	0.985	P	0.61328	0.887	D	0.87459	0.2406	10	0.62326	D	0.03	.	10.9074	0.47088	0.925:0.0:0.075:0.0	.	90	Q8N967	LRTM2_HUMAN	Y	90	ENSP00000446278:N90Y;ENSP00000299194:N90Y;ENSP00000444737:N90Y;ENSP00000438678:N90Y;ENSP00000444104:N90Y	ENSP00000299194:N90Y	N	+	1	0	LRTM2	1810562	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.182000	0.58310	0.748000	0.32831	0.459000	0.35465	AAC	.	.	.	none		0.617	LRTM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398055.1		
WBP11	51729	hgsc.bcm.edu	37	12	14943406	14943406	+	Silent	SNP	A	A	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:14943406A>G	ENST00000261167.2	-	10	1526	c.1293T>C	c.(1291-1293)ccT>ccC	p.P431P		NM_016312.2	NP_057396.1	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	431	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein phosphatase type 1 regulator activity (GO:0008599)|single-stranded DNA binding (GO:0003697)|WW domain binding (GO:0050699)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)	30						GTGGACCAGGAGGAAGGCCTG	0.473																																					p.P431P		Atlas-SNP	.											.	WBP11	66	.	0			c.T1293C						PASS	.						99.0	103.0	102.0					12																	14943406		2203	4300	6503	SO:0001819	synonymous_variant	51729	exon10			ACCAGGAGGAAGG	AB029309	CCDS8666.1	12p12.3	2014-06-13			ENSG00000084463	ENSG00000084463			16461	protein-coding gene	gene with protein product	"""splicing factor, PQBP1 and PP1 interacting"", ""protein phosphatase 1, regulatory subunit 165"""					10593949	Standard	NM_016312		Approved	NPWBP, SIPP1, PPP1R165	uc001rci.3	Q9Y2W2	OTTHUMG00000168737	ENST00000261167.2:c.1293T>C	chr12.hg19:g.14943406A>G		97.0	0.0	.		134.0	24.0	.	NM_016312	Q96AY8	Silent	SNP	ENST00000261167.2	hg19	CCDS8666.1																																																																																			.	.	.	none		0.473	WBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400850.1	NM_016312	
KCNH3	23416	hgsc.bcm.edu	37	12	49944077	49944077	+	Missense_Mutation	SNP	A	A	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:49944077A>C	ENST00000257981.6	+	10	2143	c.1883A>C	c.(1882-1884)gAg>gCg	p.E628A		NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	628					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						GGCTCCATGGAGGTGCTCAAG	0.647																																					p.E628A		Atlas-SNP	.											.	KCNH3	88	.	0			c.A1883C						PASS	.						73.0	66.0	68.0					12																	49944077		2203	4300	6503	SO:0001583	missense	23416	exon10			CCATGGAGGTGCT	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.1883A>C	chr12.hg19:g.49944077A>C	ENSP00000257981:p.Glu628Ala	17.0	0.0	.		93.0	48.0	.	NM_012284	Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	hg19	CCDS8786.1	.	.	.	.	.	.	.	.	.	.	A	31	5.069017	0.93950	.	.	ENSG00000135519	ENST00000257981	D	0.93307	-3.2	5.48	5.48	0.80851	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.48767	D	0.000161	D	0.96620	0.8897	M	0.84219	2.685	0.58432	D	0.999997	D	0.76494	0.999	D	0.87578	0.998	D	0.97133	0.9819	10	0.87932	D	0	.	13.8224	0.63331	1.0:0.0:0.0:0.0	.	628	Q9ULD8	KCNH3_HUMAN	A	628	ENSP00000257981:E628A	ENSP00000257981:E628A	E	+	2	0	KCNH3	48230344	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.224000	0.72417	0.533000	0.62120	GAG	.	.	.	none		0.647	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284	
CSAD	51380	hgsc.bcm.edu	37	12	53554015	53554015	+	Missense_Mutation	SNP	T	T	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:53554015T>C	ENST00000444623.1	-	14	1322	c.1055A>G	c.(1054-1056)aAg>aGg	p.K352R	CSAD_ENST00000379846.1_Missense_Mutation_p.K205R|CSAD_ENST00000453446.2_Missense_Mutation_p.K352R|CSAD_ENST00000267085.4_Missense_Mutation_p.K379R|CSAD_ENST00000379843.3_Missense_Mutation_p.K205R|RP11-1136G11.8_ENST00000550908.1_lincRNA	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	352					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)		pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	CTGCACCACCTTGTCTCCCGT	0.612																																					p.K379R	Ovarian(109;252 1546 16882 28524 44645)	Atlas-SNP	.											.	CSAD	66	.	0			c.A1136G						PASS	.						117.0	104.0	108.0					12																	53554015		2203	4300	6503	SO:0001583	missense	51380	exon14			ACCACCTTGTCTC	AB044561	CCDS8848.2, CCDS58235.1	12q13.11-q14.3	2008-08-04			ENSG00000139631	ENSG00000139631			18966	protein-coding gene	gene with protein product	"""P-selectin cytoplasmic tail-associated protein"""					15489334	Standard	NM_015989		Approved	PCAP, CSD	uc001sbz.3	Q9Y600	OTTHUMG00000048076	ENST00000444623.1:c.1055A>G	chr12.hg19:g.53554015T>C	ENSP00000415485:p.Lys352Arg	63.0	0.0	.		120.0	60.0	.	NM_015989	A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	Missense_Mutation	SNP	ENST00000444623.1	hg19	CCDS58235.1	.	.	.	.	.	.	.	.	.	.	T	33	5.207752	0.95033	.	.	ENSG00000139631	ENST00000308926;ENST00000379843;ENST00000267085;ENST00000379846;ENST00000444623;ENST00000398047;ENST00000453446	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	4.67	4.67	0.58626	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.047421	0.85682	D	0.000000	T	0.59376	0.2189	L	0.61387	1.9	0.80722	D	1	D;D;P	0.69078	0.997;0.994;0.871	D;D;B	0.68765	0.96;0.96;0.247	T	0.62062	-0.6933	10	0.56958	D	0.05	-26.8125	13.5402	0.61671	0.0:0.0:0.0:1.0	.	379;352;205	Q9Y600-3;Q9Y600;Q9Y600-2	.;CSAD_HUMAN;.	R	441;205;379;205;352;313;352	ENSP00000369172:K205R;ENSP00000267085:K379R;ENSP00000369175:K205R;ENSP00000415485:K352R;ENSP00000410648:K352R	ENSP00000267085:K379R	K	-	2	0	CSAD	51840282	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.430000	0.80321	2.100000	0.63781	0.533000	0.62120	AAG	.	.	.	none		0.612	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343697.1	NM_015989	
GPR84	53831	hgsc.bcm.edu	37	12	54756649	54756649	+	Silent	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:54756649G>A	ENST00000551809.1	-	1	1622	c.987C>T	c.(985-987)gcC>gcT	p.A329A	GPR84_ENST00000267015.3_Silent_p.A329A|RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	329						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						TGTAGCTCAGGGCAAAGCAGA	0.537																																					p.A329A		Atlas-SNP	.											.	GPR84	38	.	0			c.C987T						PASS	.						139.0	138.0	138.0					12																	54756649		2203	4300	6503	SO:0001819	synonymous_variant	53831	exon2			GCTCAGGGCAAAG	AF237762	CCDS8878.1	12q13.13	2012-08-20						"""GPCR / Class A : Fatty acid receptors"""	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.987C>T	chr12.hg19:g.54756649G>A		153.0	0.0	.		202.0	15.0	.	NM_020370	B6V9G7	Silent	SNP	ENST00000551809.1	hg19	CCDS8878.1																																																																																			.	.	.	none		0.537	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1		
SMARCC2	6601	hgsc.bcm.edu	37	12	56578005	56578005	+	Missense_Mutation	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:56578005G>T	ENST00000267064.4	-	6	602	c.516C>A	c.(514-516)aaC>aaA	p.N172K	SMARCC2_ENST00000550859.1_5'UTR|SMARCC2_ENST00000347471.4_Missense_Mutation_p.N172K|SMARCC2_ENST00000550164.1_Missense_Mutation_p.N172K|SMARCC2_ENST00000394023.3_Missense_Mutation_p.N172K|RP11-977G19.5_ENST00000553176.1_RNA	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	172					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			GGGAGGCATTGTTCTTATCCT	0.498																																					p.N172K		Atlas-SNP	.											.	SMARCC2	212	.	0			c.C516A						PASS	.						116.0	94.0	101.0					12																	56578005		2203	4300	6503	SO:0001583	missense	6601	exon6			GGCATTGTTCTTA	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.516C>A	chr12.hg19:g.56578005G>T	ENSP00000267064:p.Asn172Lys	136.0	0.0	.		135.0	55.0	.	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	hg19	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.028067	0.35797	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	5.38	4.49	0.54785	BRCT (1);	0.717108	0.14170	N	0.336810	T	0.28067	0.0692	N	0.04508	-0.205	0.22610	N	0.998937	B;B;B;B;B	0.18310	0.016;0.027;0.016;0.016;0.027	B;B;B;B;B	0.17098	0.007;0.017;0.007;0.007;0.017	T	0.14504	-1.0470	10	0.25751	T	0.34	-3.7705	7.6019	0.28081	0.2492:0.0:0.7508:0.0	.	61;172;177;172;172	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	K	172	ENSP00000377591:N172K;ENSP00000449396:N172K;ENSP00000302919:N172K;ENSP00000267064:N172K	ENSP00000267064:N172K	N	-	3	2	SMARCC2	54864272	0.956000	0.32656	0.998000	0.56505	0.994000	0.84299	1.519000	0.35888	1.412000	0.46977	0.561000	0.74099	AAC	.	.	.	none		0.498	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		
APAF1	317	hgsc.bcm.edu	37	12	99093184	99093184	+	Splice_Site	SNP	A	A	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:99093184A>C	ENST00000551964.1	+	17	3040		c.e17-1		APAF1_ENST00000333991.1_Intron|APAF1_ENST00000550527.1_Splice_Site|APAF1_ENST00000357310.1_Splice_Site|APAF1_ENST00000549007.1_Splice_Site|APAF1_ENST00000339433.3_Splice_Site|APAF1_ENST00000552268.1_Intron|APAF1_ENST00000359972.2_Splice_Site|APAF1_ENST00000547045.1_Splice_Site	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	TTTAATTCAAAGCTTTGGGAT	0.323																																					.		Atlas-SNP	.											.	APAF1	111	.	0			c.2272-2A>C						PASS	.						52.0	51.0	51.0					12																	99093184		2203	4300	6503	SO:0001630	splice_region_variant	317	exon17			ATTCAAAGCTTTG	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"""WD repeat domain containing"""	576	protein-coding gene	gene with protein product		602233	"""apoptotic protease activating factor"", ""apoptotic peptidase activating factor"""			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.2305-1A>C	chr12.hg19:g.99093184A>C		54.0	0.0	.		58.0	22.0	.	NM_001160	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Splice_Site	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.598135	0.46318	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000550527;ENST00000547045;ENST00000549007	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5583	0.61773	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	APAF1	97617315	1.000000	0.71417	0.949000	0.38748	0.676000	0.39594	7.031000	0.76491	2.186000	0.69663	0.533000	0.62120	.	.	.	.	none		0.323	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1	Intron
DCLK1	9201	hgsc.bcm.edu	37	13	36383187	36383187	+	Silent	SNP	A	A	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr13:36383187A>G	ENST00000360631.3	-	13	1945	c.1734T>C	c.(1732-1734)taT>taC	p.Y578Y	DCLK1_ENST00000379893.1_Silent_p.Y271Y|DCLK1_ENST00000255448.4_Silent_p.Y578Y			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	578	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		ACAGCAGGATATAAGTGATTA	0.473																																					p.Y578Y		Atlas-SNP	.											.	DCLK1	350	.	0			c.T1734C						PASS	.						101.0	88.0	92.0					13																	36383187		2203	4300	6503	SO:0001819	synonymous_variant	9201	exon13			CAGGATATAAGTG	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"""doublecortin and CaM kinase-like 1"""	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1734T>C	chr13.hg19:g.36383187A>G		93.0	0.0	.		150.0	51.0	.	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	hg19																																																																																				.	.	.	none		0.473	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734	
UGGT2	55757	hgsc.bcm.edu	37	13	96684163	96684163	+	Missense_Mutation	SNP	A	A	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr13:96684163A>G	ENST00000376747.3	-	2	291	c.221T>C	c.(220-222)tTa>tCa	p.L74S	UGGT2_ENST00000397618.3_Missense_Mutation_p.L74S|UGGT2_ENST00000376714.3_Missense_Mutation_p.L74S|UGGT2_ENST00000376712.4_Missense_Mutation_p.L74S	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	74					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						ATAAATTGCTAATTCTTGCAC	0.259																																					p.L74S		Atlas-SNP	.											.	UGGT2	127	.	0			c.T221C						PASS	.						59.0	62.0	61.0					13																	96684163		2198	4277	6475	SO:0001583	missense	55757	exon2			ATTGCTAATTCTT	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.221T>C	chr13.hg19:g.96684163A>G	ENSP00000365938:p.Leu74Ser	103.0	0.0	.		102.0	38.0	.	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	hg19	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	A	18.23	3.578856	0.65878	.	.	ENSG00000102595	ENST00000376747;ENST00000376722;ENST00000376714;ENST00000397618;ENST00000376712	T;T	0.32272	3.07;1.46	5.93	5.93	0.95920	.	0.075675	0.56097	D	0.000039	T	0.61565	0.2357	M	0.84683	2.71	0.53688	D	0.999975	D;D;P	0.89917	1.0;1.0;0.937	D;D;P	0.91635	0.999;0.999;0.512	T	0.67772	-0.5584	10	0.87932	D	0	-7.6383	16.3943	0.83563	1.0:0.0:0.0:0.0	.	74;74;74	Q2TAA6;E7EMU6;Q9NYU1	.;.;UGGG2_HUMAN	S	74	ENSP00000365938:L74S;ENSP00000380743:L74S	ENSP00000365902:L74S	L	-	2	0	UGGT2	95482164	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.701000	0.84566	2.281000	0.76405	0.533000	0.62120	TTA	.	.	.	none		0.259	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
RPGRIP1	57096	hgsc.bcm.edu	37	14	21769308	21769308	+	Silent	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:21769308C>T	ENST00000400017.2	+	3	402	c.402C>T	c.(400-402)gcC>gcT	p.A134A	RPGRIP1_ENST00000557771.1_Silent_p.A134A|RPGRIP1_ENST00000206660.6_Silent_p.A134A|RPGRIP1_ENST00000556336.1_Silent_p.A134A	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	134					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		TCGGCCCTGCCAGCCCCCGCC	0.682																																					p.A134A		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.C402T						PASS	.						10.0	14.0	13.0					14																	21769308		1990	4127	6117	SO:0001819	synonymous_variant	57096	exon3			CCCTGCCAGCCCC	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.402C>T	chr14.hg19:g.21769308C>T		114.0	0.0	.		229.0	57.0	.	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	hg19	CCDS45080.1																																																																																			.	.	.	none		0.682	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
EFS	10278	hgsc.bcm.edu	37	14	23828918	23828918	+	Silent	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:23828918G>A	ENST00000216733.3	-	4	1376	c.769C>T	c.(769-771)Ctg>Ttg	p.L257L	EFS_ENST00000429593.2_Intron|RP11-124D2.3_ENST00000554010.1_RNA|EFS_ENST00000351354.3_Silent_p.L164L	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	257	Pro-rich.				cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		GGCCCCAGCAGAGGCACATCG	0.642																																					p.L257L		Atlas-SNP	.											.	EFS	37	.	0			c.C769T						PASS	.						37.0	45.0	42.0					14																	23828918		2203	4300	6503	SO:0001819	synonymous_variant	10278	exon4			CCAGCAGAGGCAC	AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"""Cas scaffolding proteins"""	16898	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 3"""	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.769C>T	chr14.hg19:g.23828918G>A		50.0	0.0	.		62.0	19.0	.	NM_005864	B2RAJ7|B4DJ56|E9PGU2|O43282	Silent	SNP	ENST00000216733.3	hg19	CCDS9595.1																																																																																			.	.	.	none		0.642	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2		
LRR1	122769	hgsc.bcm.edu	37	14	50081041	50081041	+	Missense_Mutation	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:50081041G>T	ENST00000298288.6	+	4	1396	c.1072G>T	c.(1072-1074)Gtt>Ttt	p.V358F	LRR1_ENST00000318317.4_Missense_Mutation_p.C117F	NM_152329.3	NP_689542.2	Q96L50	LLR1_HUMAN	leucine rich repeat protein 1	358					protein ubiquitination (GO:0016567)					kidney(2)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						AAAAATTTGTGTTTGTGGAAG	0.368																																					p.V358F		Atlas-SNP	.											.	LRR1	35	.	0			c.G1072T						PASS	.						117.0	111.0	113.0					14																	50081041		2203	4300	6503	SO:0001583	missense	122769	exon4			ATTTGTGTTTGTG	BC030142	CCDS9686.1, CCDS9687.1	14q21.3	2011-02-02	2011-02-02	2011-02-02	ENSG00000165501	ENSG00000165501			19742	protein-coding gene	gene with protein product	"""LRR-repeat protein 1"""	609193	"""peptidylprolyl isomerase (cyclophilin)-like 5"""	PPIL5		11804328, 21074724	Standard	NR_037792		Approved	MGC20689, LRR-1	uc001wwn.3	Q96L50	OTTHUMG00000140273	ENST00000298288.6:c.1072G>T	chr14.hg19:g.50081041G>T	ENSP00000298288:p.Val358Phe	61.0	0.0	.		53.0	11.0	.	NM_152329	A5D6X3|B4DDE0|Q52M24|Q86SZ1|Q8N6H9	Missense_Mutation	SNP	ENST00000298288.6	hg19	CCDS9686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.98|12.98	2.100514|2.100514	0.37048|0.37048	.|.	.|.	ENSG00000165501|ENSG00000165501	ENST00000318317|ENST00000298288	.|T	.|0.42513	.|0.97	5.55|5.55	3.74|3.74	0.42951|0.42951	.|.	.|0.342603	.|0.30820	.|N	.|0.008808	T|T	0.29850|0.29850	0.0746|0.0746	L|L	0.48642|0.48642	1.525|1.525	0.23050|0.23050	N|N	0.998374|0.998374	P|P	0.48503|0.37864	0.911|0.61	B|B	0.42282|0.30646	0.382|0.118	T|T	0.12785|0.12785	-1.0534|-1.0534	7|10	.|0.33940	.|T	.|0.23	-1.8537|-1.8537	8.4558|8.4558	0.32899|0.32899	0.149:0.1617:0.6893:0.0|0.149:0.1617:0.6893:0.0	.|.	117|358	Q96L50-2|Q96L50	.|LLR1_HUMAN	F|F	117|358	.|ENSP00000298288:V358F	.|ENSP00000298288:V358F	C|V	+|+	2|1	0|0	LRR1|LRR1	49150791|49150791	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.566000|0.566000	0.35808|0.35808	4.799000|4.799000	0.62517|0.62517	0.839000|0.839000	0.34971|0.34971	-0.142000|-0.142000	0.14014|0.14014	TGT|GTT	.	.	.	none		0.368	LRR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410790.1	NM_203467	
ZC2HC1C	79696	hgsc.bcm.edu	37	14	75537677	75537677	+	Missense_Mutation	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:75537677G>T	ENST00000524913.1	+	2	890	c.401G>T	c.(400-402)gGa>gTa	p.G134V	ZC2HC1C_ENST00000439583.2_Missense_Mutation_p.G134V|ZC2HC1C_ENST00000238686.8_Missense_Mutation_p.G134V|ZC2HC1C_ENST00000526748.1_Intron|ACYP1_ENST00000555463.1_5'Flank	NM_024643.2	NP_078919.2	Q53FD0	ZC21C_HUMAN	zinc finger, C2HC-type containing 1C	134							metal ion binding (GO:0046872)										AAACGAGTTGGAGTGGACCGG	0.522																																					p.G134V		Atlas-SNP	.											.	.	.	.	0			c.G401T						PASS	.						98.0	96.0	97.0					14																	75537677		1869	4100	5969	SO:0001583	missense	79696	exon2			GAGTTGGAGTGGA	AK026746	CCDS41972.1, CCDS45138.1	14q24.3	2013-01-10	2012-02-03	2012-02-03	ENSG00000119703	ENSG00000119703		"""Zinc fingers, C2HC-type containing"""	20354	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 140"", ""family with sequence similarity 164, member C"""	C14orf140, FAM164C			Standard	XM_005268062		Approved		uc001xrh.3	Q53FD0	OTTHUMG00000167439	ENST00000524913.1:c.401G>T	chr14.hg19:g.75537677G>T	ENSP00000435550:p.Gly134Val	96.0	0.0	.		95.0	31.0	.	NM_024643	E9PJQ0|Q9BTA8|Q9H5S9	Missense_Mutation	SNP	ENST00000524913.1	hg19	CCDS41972.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.02|15.02	2.709290|2.709290	0.48517|0.48517	.|.	.|.	ENSG00000119703|ENSG00000119703	ENST00000532198|ENST00000524913;ENST00000238686;ENST00000554763;ENST00000439583;ENST00000526130	.|T	.|0.76578	.|-1.03	4.53|4.53	4.53|4.53	0.55603|0.55603	.|.	.|0.080328	.|0.49916	.|D	.|0.000121	.|D	.|0.87111	.|0.6096	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.997	.|D	.|0.87264	.|0.2281	.|9	.|.	.|.	.|.	-17.5211|-17.5211	17.4741|17.4741	0.87655|0.87655	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|134;134	.|Q53FD0;E9PJQ0	.|F164C_HUMAN;.	X|V	1|134	.|ENSP00000435550:G134V	.|.	E|G	+|+	1|2	0|0	FAM164C|FAM164C	74607430|74607430	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.325000|0.325000	0.28411|0.28411	6.888000|6.888000	0.75622|0.75622	2.356000|2.356000	0.79943|0.79943	0.557000|0.557000	0.71058|0.71058	GAG|GGA	.	.	.	none		0.522	ZC2HC1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394616.4	NM_001042430	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102478240	102478240	+	Missense_Mutation	SNP	T	T	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:102478240T>C	ENST00000360184.4	+	33	6811	c.6647T>C	c.(6646-6648)aTc>aCc	p.I2216T		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2216	AAA 2. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						ATCACCCAGATCAATCATGGC	0.602																																					p.I2216T		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.T6647C						PASS	.						86.0	74.0	78.0					14																	102478240		2203	4300	6503	SO:0001583	missense	1778	exon33			CCCAGATCAATCA	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.6647T>C	chr14.hg19:g.102478240T>C	ENSP00000348965:p.Ile2216Thr	80.0	0.0	.		87.0	27.0	.	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	T	18.82	3.705776	0.68615	.	.	ENSG00000197102	ENST00000360184	T	0.27402	1.67	5.8	5.8	0.92144	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.33265	0.0857	L	0.44542	1.39	0.80722	D	1	P	0.45348	0.856	P	0.44394	0.448	T	0.03423	-1.1038	10	0.40728	T	0.16	.	16.1547	0.81649	0.0:0.0:0.0:1.0	.	2216	Q14204	DYHC1_HUMAN	T	2216	ENSP00000348965:I2216T	ENSP00000348965:I2216T	I	+	2	0	DYNC1H1	101547993	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	7.991000	0.88244	2.221000	0.72209	0.528000	0.53228	ATC	.	.	.	none		0.602	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
TRIM69	140691	hgsc.bcm.edu	37	15	45048565	45048565	+	Splice_Site	SNP	G	G	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr15:45048565G>C	ENST00000559390.1	+	4	1411		c.e4-1		TRIM69_ENST00000558173.1_Splice_Site|TRIM69_ENST00000329464.4_Splice_Site|TRIM69_ENST00000558329.1_Splice_Site|TRIM69_ENST00000560442.1_Splice_Site|TRIM69_ENST00000338264.4_Splice_Site|TRIM69_ENST00000561043.1_Splice_Site			Q86WT6	TRI69_HUMAN	tripartite motif containing 69						apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		GATATTCCCAGGAGGAGCTTG	0.488																																					.	Pancreas(84;519 1450 1802 20427 34706)	Atlas-SNP	.											.	TRIM69	47	.	0			c.7-1G>C						PASS	.						41.0	39.0	40.0					15																	45048565		1927	3624	5551	SO:0001630	splice_region_variant	140691	exon2			TTCCCAGGAGGAG	AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	17857	protein-coding gene	gene with protein product			"""ring finger protein 36"", ""tripartite motif-containing 69"""	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.484-1G>C	chr15.hg19:g.45048565G>C		93.0	0.0	.		130.0	61.0	.	NM_080745	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Splice_Site	SNP	ENST00000559390.1	hg19	CCDS32220.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.350808	0.24512	.	.	ENSG00000185880	ENST00000329464;ENST00000338264	.	.	.	5.34	4.43	0.53597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9849	0.53142	0.0847:0.0:0.9153:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TRIM69	42835857	1.000000	0.71417	0.995000	0.50966	0.200000	0.23975	4.849000	0.62882	1.391000	0.46566	0.655000	0.94253	.	.	.	.	none		0.488	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1		Intron
FBN1	2200	hgsc.bcm.edu	37	15	48748937	48748937	+	Silent	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr15:48748937G>T	ENST00000316623.5	-	44	5774	c.5319C>A	c.(5317-5319)atC>atA	p.I1773I		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1773	EGF-like 29; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		AGACCCCTGGGATCTCCCGGC	0.468																																					p.I1773I		Atlas-SNP	.											.	FBN1	310	.	0			c.C5319A						PASS	.						112.0	99.0	103.0					15																	48748937		2198	4296	6494	SO:0001819	synonymous_variant	2200	exon44			CCCTGGGATCTCC	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.5319C>A	chr15.hg19:g.48748937G>T		70.0	0.0	.		112.0	44.0	.	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	ENST00000316623.5	hg19	CCDS32232.1																																																																																			.	.	.	none		0.468	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
SV2B	9899	hgsc.bcm.edu	37	15	91811781	91811781	+	Missense_Mutation	SNP	T	T	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr15:91811781T>A	ENST00000394232.1	+	9	1789	c.1319T>A	c.(1318-1320)aTc>aAc	p.I440N	SV2B_ENST00000545111.2_Missense_Mutation_p.I289N|SV2B_ENST00000330276.4_Missense_Mutation_p.I440N	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	440					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			GGCGCCACAATCAACTTCACG	0.428																																					p.I440N		Atlas-SNP	.											.	SV2B	98	.	0			c.T1319A						PASS	.						139.0	136.0	137.0					15																	91811781		2198	4298	6496	SO:0001583	missense	9899	exon10			CCACAATCAACTT	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1319T>A	chr15.hg19:g.91811781T>A	ENSP00000377779:p.Ile440Asn	176.0	0.0	.		271.0	21.0	.	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	hg19	CCDS10370.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.561903	0.86335	.	.	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.61980	0.06;0.06;0.06	5.49	5.49	0.81192	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.043947	0.85682	D	0.000000	T	0.55273	0.1910	L	0.34521	1.04	0.43761	D	0.99627	P	0.41159	0.74	B	0.43386	0.418	T	0.52260	-0.8599	10	0.24483	T	0.36	-35.1417	14.7146	0.69257	0.0:0.0:0.0:1.0	.	440	Q7L1I2	SV2B_HUMAN	N	289;440;440	ENSP00000443243:I289N;ENSP00000377779:I440N;ENSP00000332818:I440N	ENSP00000332818:I440N	I	+	2	0	SV2B	89612785	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.750000	0.85110	2.212000	0.71576	0.533000	0.62120	ATC	.	.	.	none		0.428	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
RPL3L	6123	hgsc.bcm.edu	37	16	1995884	1995884	+	Silent	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:1995884C>T	ENST00000268661.7	-	8	1093	c.999G>A	c.(997-999)ctG>ctA	p.L333L	MSRB1_ENST00000399753.2_5'Flank|MSRB1_ENST00000361871.3_5'Flank|MSRB1_ENST00000564908.1_5'Flank	NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	333					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						TACAACCCTTCAGCATGACGA	0.602																																					p.L333L		Atlas-SNP	.											.	RPL3L	42	.	0			c.G999A						PASS	.						164.0	138.0	147.0					16																	1995884		2199	4300	6499	SO:0001819	synonymous_variant	6123	exon8			ACCCTTCAGCATG	U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"""L ribosomal proteins"""	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685	ENST00000268661.7:c.999G>A	chr16.hg19:g.1995884C>T		35.0	0.0	.		74.0	5.0	.	NM_005061		Silent	SNP	ENST00000268661.7	hg19	CCDS10450.1																																																																																			.	.	.	none		0.602	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061	
PKMYT1	9088	hgsc.bcm.edu	37	16	3025761	3025761	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:3025761G>A	ENST00000262300.8	-	4	939	c.431C>T	c.(430-432)cCa>cTa	p.P144L	PKMYT1_ENST00000574385.1_Missense_Mutation_p.P135L|PKMYT1_ENST00000440027.2_Missense_Mutation_p.P144L|PKMYT1_ENST00000573944.1_Missense_Mutation_p.P135L|PKMYT1_ENST00000574730.1_Missense_Mutation_p.P75L|PKMYT1_ENST00000431515.2_Missense_Mutation_p.P144L	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	144	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						GCCCCGGAATGGTGACATGGA	0.667																																					p.P144L		Atlas-SNP	.											.	PKMYT1	23	.	0			c.C431T						PASS	.						25.0	27.0	26.0					16																	3025761		2153	4235	6388	SO:0001583	missense	9088	exon4			CGGAATGGTGACA	AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"""membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase"", ""protein phosphatase 1, regulatory subunit 126"""	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.431C>T	chr16.hg19:g.3025761G>A	ENSP00000262300:p.Pro144Leu	5.0	0.0	.		86.0	33.0	.	NM_182687	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000262300.8	hg19	CCDS10486.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.938404	0.52972	.	.	ENSG00000127564	ENST00000431515;ENST00000262300;ENST00000440027;ENST00000402679;ENST00000382240	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.69	5.69	0.88448	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.059815	0.64402	D	0.000002	T	0.47266	0.1436	N	0.11818	0.18	0.80722	D	1	P;P;P;P	0.43701	0.56;0.704;0.56;0.815	B;B;B;B	0.39068	0.217;0.217;0.217;0.289	T	0.56498	-0.7969	10	0.66056	D	0.02	-14.3456	17.2983	0.87175	0.0:0.0:1.0:0.0	.	135;75;144;144	A6NHV6;B4DXD4;Q99640;F8W164	.;.;PMYT1_HUMAN;.	L	144;144;144;144;135	ENSP00000392855:P144L;ENSP00000262300:P144L;ENSP00000397739:P144L;ENSP00000371675:P135L	ENSP00000262300:P144L	P	-	2	0	PKMYT1	2965762	1.000000	0.71417	0.237000	0.24090	0.956000	0.61745	4.915000	0.63355	2.676000	0.91093	0.655000	0.94253	CCA	.	.	.	none		0.667	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250963.2	NM_004203	
NLRC3	197358	hgsc.bcm.edu	37	16	3614323	3614323	+	RNA	SNP	G	G	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:3614323G>C	ENST00000301749.7	-	0	1020				NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCACCGCCAGGCTGGGCTCCC	0.662																																					p.S205R		Atlas-SNP	.											.	NLRC3	103	.	0			c.C615G						PASS	.						31.0	37.0	35.0					16																	3614323		2003	4170	6173			197358	exon5			CGCCAGGCTGGGC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		chr16.hg19:g.3614323G>C		57.0	0.0	.		95.0	32.0	.	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	hg19		.	.	.	.	.	.	.	.	.	.	G	1.295	-0.606481	0.03717	.	.	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23	4.84	0.17	0.15021	.	0.625501	0.16533	N	0.210300	T	0.55625	0.1932	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.15870	0.014	T	0.32107	-0.9919	9	0.17832	T	0.49	.	4.5952	0.12325	0.0829:0.2788:0.4949:0.1434	.	252	C9JLH9	.	R	205;205;205;252;187	ENSP00000301749:S205R;ENSP00000352039:S205R;ENSP00000414415:S252R;ENSP00000323897:S187R	ENSP00000301749:S205R	S	-	3	2	NLRC3	3554324	0.000000	0.05858	0.004000	0.12327	0.008000	0.06430	0.471000	0.22100	0.074000	0.16767	0.655000	0.94253	AGC	.	.	.	none		0.662	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
CREBBP	1387	hgsc.bcm.edu	37	16	3779018	3779018	+	Silent	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:3779018C>T	ENST00000262367.5	-	31	6839	c.6030G>A	c.(6028-6030)ggG>ggA	p.G2010G	CREBBP_ENST00000382070.3_Silent_p.G1972G	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2010					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)		GCATGACGGGCCCGCTCACCT	0.692			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.G2010G		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.G6030A						PASS	.						12.0	14.0	13.0					16																	3779018		2185	4287	6472	SO:0001819	synonymous_variant	1387	exon31			GACGGGCCCGCTC	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.6030G>A	chr16.hg19:g.3779018C>T		14.0	0.0	.		58.0	18.0	.	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	hg19	CCDS10509.1																																																																																			.	.	.	none		0.692	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
METTL22	79091	hgsc.bcm.edu	37	16	8736394	8736394	+	Missense_Mutation	SNP	T	T	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:8736394T>C	ENST00000381920.3	+	9	1240	c.982T>C	c.(982-984)Tgc>Cgc	p.C328R	METTL22_ENST00000561758.1_Missense_Mutation_p.C272R|METTL22_ENST00000568967.1_3'UTR	NM_024109.2	NP_077014.2	Q9BUU2	MET22_HUMAN	methyltransferase like 22	328						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			large_intestine(5)|lung(4)	9						GAAAAATGCCTGCACAGCCAT	0.532																																					p.C328R		Atlas-SNP	.											.	METTL22	23	.	0			c.T982C						PASS	.						124.0	139.0	134.0					16																	8736394		2055	4190	6245	SO:0001583	missense	79091	exon9			AATGCCTGCACAG	AK022495	CCDS10533.2	16p13.2	2014-07-15	2011-03-03	2011-03-03	ENSG00000067365	ENSG00000067365			28368	protein-coding gene	gene with protein product		615261	"""chromosome 16 open reading frame 68"""	C16orf68		24140279	Standard	XM_005255570		Approved	FLJ12433,MGC2654	uc002cyz.3	Q9BUU2	OTTHUMG00000129694	ENST00000381920.3:c.982T>C	chr16.hg19:g.8736394T>C	ENSP00000371345:p.Cys328Arg	103.0	0.0	.		157.0	65.0	.	NM_024109	B2RD29|D3DUF2|Q6XYB4|Q9HA03	Missense_Mutation	SNP	ENST00000381920.3	hg19	CCDS10533.2	.	.	.	.	.	.	.	.	.	.	T	10.28	1.307330	0.23821	.	.	ENSG00000067365	ENST00000381920	T	0.40756	1.02	5.18	5.18	0.71444	.	0.177884	0.49305	D	0.000145	T	0.43590	0.1254	L	0.41710	1.295	0.80722	D	1	D;P	0.53462	0.96;0.752	P;P	0.54312	0.748;0.469	T	0.19976	-1.0289	10	0.14252	T	0.57	-39.2838	11.4298	0.50034	0.0:0.0:0.0:1.0	.	103;328	Q9BUU2-3;Q9BUU2	.;MET22_HUMAN	R	328	ENSP00000371345:C328R	ENSP00000371345:C328R	C	+	1	0	METTL22	8643895	1.000000	0.71417	1.000000	0.80357	0.286000	0.27126	2.384000	0.44362	1.956000	0.56807	0.533000	0.62120	TGC	.	.	.	none		0.532	METTL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251901.1	NM_024109	
DHRS7C	201140	hgsc.bcm.edu	37	17	9683157	9683157	+	Missense_Mutation	SNP	T	T	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:9683157T>A	ENST00000330255.5	-	3	478	c.466A>T	c.(466-468)Atc>Ttc	p.I156F	DHRS7C_ENST00000571134.1_Missense_Mutation_p.I155F	NM_001105571.2|NM_001220493.1	NP_001099041.1|NP_001207422.1	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	156					regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	extracellular region (GO:0005576)|longitudinal sarcoplasmic reticulum (GO:0014801)|sarcoplasmic reticulum membrane (GO:0033017)	retinol dehydrogenase activity (GO:0004745)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	15						GTCAATGTGATGGGGCCAAAG	0.478																																					p.I156F		Atlas-SNP	.											.	DHRS7C	34	.	0			c.A466T						PASS	.						49.0	47.0	47.0					17																	9683157		1906	4125	6031	SO:0001583	missense	201140	exon3			ATGTGATGGGGCC		CCDS56020.1, CCDS58517.1	17p13.1	2011-09-20				ENSG00000184544		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	32423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 32C, member 2"""					19027726	Standard	NM_001105571		Approved	SDR32C2	uc010vvb.2	A6NNS2		ENST00000330255.5:c.466A>T	chr17.hg19:g.9683157T>A	ENSP00000327975:p.Ile156Phe	95.0	0.0	.		108.0	8.0	.	NM_001220493	B7ZW74|B9EJH3	Missense_Mutation	SNP	ENST00000330255.5	hg19	CCDS56020.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.223879	0.39300	.	.	ENSG00000184544	ENST00000330255	D	0.86865	-2.18	5.75	5.75	0.90469	NAD(P)-binding domain (1);	0.045861	0.85682	D	0.000000	D	0.90000	0.6878	L	0.37630	1.12	0.47511	D	0.999443	D;D	0.71674	0.998;0.998	D;D	0.71184	0.972;0.94	D	0.91167	0.4965	10	0.87932	D	0	.	15.0365	0.71751	0.0:0.0:0.0:1.0	.	156;152	A6NNS2;B9EJH3	DRS7C_HUMAN;.	F	156	ENSP00000327975:I156F	ENSP00000327975:I156F	I	-	1	0	DHRS7C	9623882	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.823000	0.69272	2.193000	0.70182	0.533000	0.62120	ATC	.	.	.	none		0.478	DHRS7C-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439863.1	XM_113912	
COX10	1352	hgsc.bcm.edu	37	17	13980322	13980322	+	Missense_Mutation	SNP	G	G	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:13980322G>C	ENST00000261643.3	+	3	525	c.448G>C	c.(448-450)Gtg>Ctg	p.V150L	COX10_ENST00000536205.1_5'UTR|COX10_ENST00000429152.2_Missense_Mutation_p.V150L|COX10_ENST00000537334.1_Intron	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	150					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		GAAGCTGCAAGTGTATGATTT	0.368																																					p.V150L		Atlas-SNP	.											.	COX10	36	.	0			c.G448C						PASS	.						83.0	88.0	87.0					17																	13980322		2203	4300	6503	SO:0001583	missense	1352	exon3			CTGCAAGTGTATG	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"""Mitochondrial respiratory chain complex assembly factors"""	2260	protein-coding gene	gene with protein product	"""heme A: farnesyltransferase"", ""protoheme IX farnesyltransferase, mitochondrial"", ""heme O synthase"""	602125	"""COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)"", ""COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"""			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.448G>C	chr17.hg19:g.13980322G>C	ENSP00000261643:p.Val150Leu	146.0	0.0	.		161.0	69.0	.	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Missense_Mutation	SNP	ENST00000261643.3	hg19	CCDS11166.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.143|0.143	-1.100268|-1.100268	0.01843|0.01843	.|.	.|.	ENSG00000006695|ENSG00000006695	ENST00000429152|ENST00000261643	T|T	0.37235|0.61980	1.21|0.06	5.35|5.35	-6.73|-6.73	0.01749|0.01749	.|.	.|1.554890	.|0.03407	.|N	.|0.204147	T|T	0.36880|0.36880	0.0983|0.0983	N|N	0.25890|0.25890	0.77|0.77	0.34746|0.34746	D|D	0.731242|0.731242	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.49978|0.49978	-0.8881|-0.8881	6|10	.|0.02654	.|T	.|1	0.0067|0.0067	3.698|3.698	0.08372|0.08372	0.2638:0.4606:0.1338:0.1418|0.2638:0.4606:0.1338:0.1418	.|.	.|150	.|Q12887	.|COX10_HUMAN	T|L	110|150	ENSP00000397750:S110T|ENSP00000261643:V150L	.|ENSP00000261643:V150L	S|V	+|+	2|1	0|0	COX10|COX10	13921047|13921047	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.223000|0.223000	0.24884|0.24884	-0.888000|-0.888000	0.04148|0.04148	-0.666000|-0.666000	0.05310|0.05310	0.655000|0.655000	0.94253|0.94253	AGT|GTG	.	.	.	none		0.368	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303	
SLFN12L	100506736	hgsc.bcm.edu	37	17	33807110	33807110	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:33807110G>A	ENST00000260908.7	-	2	236	c.119C>T	c.(118-120)aCt>aTt	p.T40I	SLFN12L_ENST00000361112.4_Missense_Mutation_p.T69I|RP11-686D22.9_ENST00000587076.1_RNA|SLFN12L_ENST00000449046.1_Missense_Mutation_p.T71I	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	40						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						CTCTCCAAGAGTGACTCTTCC	0.403																																					p.T40I		Atlas-SNP	.											.	SLFN12L	140	.	0			c.C119T						PASS	.						57.0	44.0	48.0					17																	33807110		692	1591	2283	SO:0001583	missense	100506736	exon2			CCAAGAGTGACTC	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.119C>T	chr17.hg19:g.33807110G>A	ENSP00000437635:p.Thr40Ile	74.0	0.0	.		103.0	8.0	.	NM_001195790	F5H6G3	Missense_Mutation	SNP	ENST00000260908.7	hg19	CCDS56026.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.968021	0.53507	.	.	ENSG00000205045	ENST00000260908;ENST00000361112;ENST00000449046	T;T;T	0.06528	3.32;3.64;3.29	2.72	2.72	0.32119	.	.	.	.	.	T	0.16599	0.0399	L	0.57536	1.79	0.09310	N	1	D	0.65815	0.995	D	0.63703	0.917	T	0.03993	-1.0986	9	0.48119	T	0.1	.	8.9486	0.35773	0.0:0.0:1.0:0.0	.	69	Q6IEE8-2	.	I	40;69;71	ENSP00000437635:T40I;ENSP00000354412:T69I;ENSP00000389348:T71I	ENSP00000437635:T40I	T	-	2	0	SLFN12L	30831223	0.000000	0.05858	0.017000	0.16124	0.662000	0.39071	-0.169000	0.09911	1.504000	0.48704	0.205000	0.17691	ACT	.	.	.	none		0.403	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206	
KRT38	8687	hgsc.bcm.edu	37	17	39596920	39596920	+	Missense_Mutation	SNP	A	A	C			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:39596920A>C	ENST00000246646.3	-	1	253	c.254T>G	c.(253-255)aTt>aGt	p.I85S		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	85	Head.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				GTTGCCAGGAATGTGGCAGGT	0.607																																					p.I85S		Atlas-SNP	.											.	KRT38	63	.	0			c.T254G						PASS	.						73.0	68.0	70.0					17																	39596920		2203	4300	6503	SO:0001583	missense	8687	exon1			CCAGGAATGTGGC	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6456	protein-coding gene	gene with protein product		604542	"""keratin, hair, acidic, 8"""	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.254T>G	chr17.hg19:g.39596920A>C	ENSP00000246646:p.Ile85Ser	109.0	0.0	.		212.0	88.0	.	NM_006771	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	hg19	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.337461	0.41398	.	.	ENSG00000171360	ENST00000246646	D	0.82167	-1.58	4.89	3.82	0.43975	.	0.130125	0.34460	N	0.003941	D	0.84511	0.5488	L	0.50333	1.59	0.09310	N	1	D	0.89917	1.0	D	0.69307	0.963	T	0.72830	-0.4174	10	0.28530	T	0.3	.	5.4631	0.16627	0.6239:0.2845:0.0915:0.0	.	85	O76015	KRT38_HUMAN	S	85	ENSP00000246646:I85S	ENSP00000246646:I85S	I	-	2	0	KRT38	36850446	0.089000	0.21612	0.031000	0.17742	0.359000	0.29487	1.205000	0.32308	0.906000	0.36621	0.528000	0.53228	ATT	.	.	.	none		0.607	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771	
JUP	3728	hgsc.bcm.edu	37	17	39925817	39925817	+	Missense_Mutation	SNP	C	C	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:39925817C>G	ENST00000393931.3	-	3	439	c.321G>C	c.(319-321)gaG>gaC	p.E107D	JUP_ENST00000393930.1_Missense_Mutation_p.E107D|JUP_ENST00000310706.5_Missense_Mutation_p.E107D|JUP_ENST00000540235.1_Missense_Mutation_p.E107D	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	junction plakoglobin	107					adherens junction organization (GO:0034332)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell-cell junction organization (GO:0045216)|cellular response to indole-3-methanol (GO:0071681)|cytoskeletal anchoring at plasma membrane (GO:0007016)|desmosome assembly (GO:0002159)|detection of mechanical stimulus (GO:0050982)|ectoderm development (GO:0007398)|endothelial cell-cell adhesion (GO:0071603)|establishment of protein localization to plasma membrane (GO:0090002)|gastrulation (GO:0007369)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|nervous system development (GO:0007399)|oocyte development (GO:0048599)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein heterooligomerization (GO:0051291)|regulation of cell proliferation (GO:0042127)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)|ventricular cardiac muscle cell action potential (GO:0086005)	actin cytoskeleton (GO:0015629)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gamma-catenin-TCF7L2 complex (GO:0071665)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|cadherin binding (GO:0045296)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|structural constituent of cell wall (GO:0005199)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	23		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		TGGCCTGCCCCTCCACCTGGG	0.647																																					p.E107D	Colon(16;42 520 6044 17852 28530)	Atlas-SNP	.											.	JUP	64	.	0			c.G321C						PASS	.						31.0	29.0	29.0					17																	39925817		2201	4297	6498	SO:0001583	missense	3728	exon3			CTGCCCCTCCACC	AF233882	CCDS11407.1	17q21	2014-09-17	2004-08-09		ENSG00000173801	ENSG00000173801		"""Armadillo repeat containing"""	6207	protein-coding gene	gene with protein product		173325	"""catenin (cadherin-associated protein), gamma 80kDa"""	CTNNG		1889810, 7604000	Standard	NM_021991		Approved	DP3, PDGB, PKGB, DPIII	uc002hxs.2	P14923	OTTHUMG00000133494	ENST00000393931.3:c.321G>C	chr17.hg19:g.39925817C>G	ENSP00000377508:p.Glu107Asp	67.0	0.0	.		123.0	27.0	.	NM_021991	Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	Missense_Mutation	SNP	ENST00000393931.3	hg19	CCDS11407.1	.	.	.	.	.	.	.	.	.	.	c	8.550	0.875277	0.17395	.	.	ENSG00000173801	ENST00000540235;ENST00000393930;ENST00000310706;ENST00000393931;ENST00000449889;ENST00000437187;ENST00000420370;ENST00000424457	T;T;T;T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06;-0.06;-0.06;-0.06	5.52	-7.03	0.01584	.	0.239681	0.42053	D	0.000764	T	0.27454	0.0674	N	0.08118	0	0.22591	N	0.998951	D;B	0.54207	0.965;0.001	B;B	0.43950	0.437;0.003	T	0.51663	-0.8677	10	0.22109	T	0.4	-21.4947	1.588	0.02648	0.2613:0.236:0.089:0.4138	.	107;107	B4DE59;P14923	.;PLAK_HUMAN	D	107	ENSP00000441751:E107D;ENSP00000377507:E107D;ENSP00000311113:E107D;ENSP00000377508:E107D;ENSP00000389886:E107D;ENSP00000394146:E107D;ENSP00000411449:E107D;ENSP00000401034:E107D	ENSP00000311113:E107D	E	-	3	2	JUP	37179343	0.000000	0.05858	0.979000	0.43373	0.992000	0.81027	-4.131000	0.00289	-0.505000	0.06568	0.556000	0.70494	GAG	.	.	.	none		0.647	JUP-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257406.1		
HELZ	9931	hgsc.bcm.edu	37	17	65105385	65105385	+	Missense_Mutation	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:65105385C>T	ENST00000358691.5	-	29	4502	c.4336G>A	c.(4336-4338)Gaa>Aaa	p.E1446K	HELZ_ENST00000580168.1_Missense_Mutation_p.E1447K	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1446						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					ATTACAGCTTCTGCAGGAGGA	0.547																																					p.E1446K		Atlas-SNP	.											.	HELZ	160	.	0			c.G4336A						PASS	.						65.0	73.0	70.0					17																	65105385		2028	4202	6230	SO:0001583	missense	9931	exon29			CAGCTTCTGCAGG	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"""Zinc fingers, CCCH-type domain containing"""	16878	protein-coding gene	gene with protein product	"""down-regulated in human cancers"""	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.4336G>A	chr17.hg19:g.65105385C>T	ENSP00000351524:p.Glu1446Lys	105.0	0.0	.		111.0	43.0	.	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.701438	0.48307	.	.	ENSG00000198265	ENST00000358691	D	0.83419	-1.72	5.9	4.92	0.64577	.	0.199043	0.53938	D	0.000060	T	0.74801	0.3764	N	0.19112	0.55	0.43777	D	0.996308	B;B	0.20261	0.043;0.043	B;B	0.19391	0.025;0.025	T	0.70945	-0.4734	10	0.62326	D	0.03	-11.4842	16.9692	0.86294	0.0:0.8723:0.1277:0.0	.	1447;1446	B7ZLW2;P42694	.;HELZ_HUMAN	K	1446	ENSP00000351524:E1446K	ENSP00000351524:E1446K	E	-	1	0	HELZ	62535847	0.991000	0.36638	0.996000	0.52242	0.966000	0.64601	2.728000	0.47319	1.460000	0.47911	0.549000	0.68633	GAA	.	.	.	none		0.547	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877	
EXOC7	23265	hgsc.bcm.edu	37	17	74081440	74081440	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:74081440G>A	ENST00000335146.7	-	16	1873	c.1820C>T	c.(1819-1821)tCc>tTc	p.S607F	EXOC7_ENST00000589210.1_Missense_Mutation_p.S556F|EXOC7_ENST00000332065.5_Missense_Mutation_p.S525F|EXOC7_ENST00000467929.2_Missense_Mutation_p.S528F|EXOC7_ENST00000405575.4_Missense_Mutation_p.S579F|EXOC7_ENST00000607838.1_Missense_Mutation_p.S579F|EXOC7_ENST00000411744.2_Missense_Mutation_p.S548F|EXOC7_ENST00000591724.1_5'Flank			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	607					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			CTCCCGGTAGGAGCGCTCAGC	0.637																																					p.S607F		Atlas-SNP	.											EXOC7,NS,malignant_melanoma,0,1	EXOC7	47	.	0			c.C1820T						PASS	.						57.0	47.0	50.0					17																	74081440		2202	4300	6502	SO:0001583	missense	23265	exon16			CGGTAGGAGCGCT	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.1820C>T	chr17.hg19:g.74081440G>A	ENSP00000334100:p.Ser607Phe	30.0	0.0	.		45.0	4.0	.	NM_001145297	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	g	11.91	1.778418	0.31502	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	4.43	4.43	0.53597	Cullin repeat-like-containing domain (1);	0.133958	0.50627	D	0.000114	T	0.54615	0.1869	L	0.40543	1.245	0.80722	D	1	P;B;P;B;P;P;P	0.51653	0.947;0.006;0.844;0.059;0.918;0.809;0.578	B;B;P;B;B;B;B	0.46389	0.283;0.028;0.515;0.028;0.384;0.317;0.129	T	0.54200	-0.8329	9	0.30078	T	0.28	-19.663	17.099	0.86644	0.0:0.0:1.0:0.0	.	548;579;528;493;607;525;556	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	F	525;445;579;607;556;493;548	.	ENSP00000333806:S525F	S	-	2	0	EXOC7	71593035	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	6.700000	0.74619	2.035000	0.60131	0.479000	0.44913	TCC	.	.	.	none		0.637	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219	
SETBP1	26040	hgsc.bcm.edu	37	18	42533244	42533244	+	Silent	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr18:42533244C>T	ENST00000282030.5	+	4	4235	c.3939C>T	c.(3937-3939)gaC>gaT	p.D1313D		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1313						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		GGGAAAAGGACATCCAAGCCT	0.443									Schinzel-Giedion syndrome																												p.D1313D		Atlas-SNP	.											.	SETBP1	577	.	0			c.C3939T						PASS	.						130.0	120.0	123.0					18																	42533244		2203	4300	6503	SO:0001819	synonymous_variant	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AAAGGACATCCAA	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.3939C>T	chr18.hg19:g.42533244C>T		158.0	0.0	.		144.0	38.0	.	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Silent	SNP	ENST00000282030.5	hg19	CCDS11923.2																																																																																			.	.	.	none		0.443	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
PTPRS	5802	hgsc.bcm.edu	37	19	5286082	5286082	+	Missense_Mutation	SNP	C	C	A	rs200430287	byFrequency	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:5286082C>A	ENST00000587303.1	-	1	169	c.70G>T	c.(70-72)Gtt>Ttt	p.V24F	PTPRS_ENST00000353284.2_Missense_Mutation_p.V24F|PTPRS_ENST00000357368.4_Missense_Mutation_p.V24F|PTPRS_ENST00000262963.6_Missense_Mutation_p.V24F|PTPRS_ENST00000588012.1_Missense_Mutation_p.V24F|PTPRS_ENST00000592099.1_Missense_Mutation_p.V24F|PTPRS_ENST00000372412.4_Missense_Mutation_p.V24F|PTPRS_ENST00000348075.2_Missense_Mutation_p.V24F|PTPRS_ENST00000590509.1_Missense_Mutation_p.V24F|PTPRS_ENST00000588552.1_5'UTR			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	24					cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	CAGCCTCCAACGAGCAGGACC	0.617																																					p.V24F		Atlas-SNP	.											.	PTPRS	169	.	0			c.G70T						PASS	.						52.0	46.0	48.0					19																	5286082		2203	4299	6502	SO:0001583	missense	5802	exon2			CTCCAACGAGCAG	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.70G>T	chr19.hg19:g.5286082C>A	ENSP00000467537:p.Val24Phe	150.0	0.0	.		160.0	81.0	.	NM_130854	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	hg19	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	C	6.878	0.531372	0.13127	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	T;T;T;T;T	0.56776	0.62;0.61;0.57;0.44;0.53	4.14	1.83	0.25207	.	1.741500	0.04678	U	0.411808	T	0.32971	0.0847	N	0.08118	0	0.09310	N	0.999997	B;B;B;B;P;B;B	0.34462	0.275;0.207;0.275;0.275;0.454;0.089;0.18	B;B;B;B;B;B;B	0.34138	0.091;0.176;0.091;0.091;0.045;0.017;0.025	T	0.35251	-0.9796	10	0.59425	D	0.04	.	5.1867	0.15187	0.0:0.6502:0.2297:0.1202	.	24;24;24;24;24;24;50	F8W800;Q8NHS7;Q13332-7;F5H2T4;Q13332-6;Q13332;Q59FX6	.;.;.;.;.;PTPRS_HUMAN;.	F	50;24;24;24;24;24;24;24;24;24	ENSP00000361489:V24F;ENSP00000349932:V24F;ENSP00000262963:V24F;ENSP00000269907:V24F;ENSP00000327313:V24F	ENSP00000262963:V24F	V	-	1	0	PTPRS	5237082	0.861000	0.29849	0.878000	0.34440	0.011000	0.07611	1.123000	0.31308	0.973000	0.38340	-0.362000	0.07510	GTT	.	C|0.999;T|0.001	.	alt		0.617	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
KEAP1	9817	hgsc.bcm.edu	37	19	10610178	10610178	+	Nonsense_Mutation	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:10610178G>A	ENST00000171111.5	-	2	1079	c.532C>T	c.(532-534)Cag>Tag	p.Q178*	KEAP1_ENST00000588024.1_5'UTR|KEAP1_ENST00000393623.2_Nonsense_Mutation_p.Q178*	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	178					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	GGGTCCAGCTGCTGCACCAGG	0.572																																					p.Q178X		Atlas-SNP	.											.	KEAP1	182	.	0			c.C532T						PASS	.						137.0	109.0	118.0					19																	10610178		2203	4300	6503	SO:0001587	stop_gained	9817	exon2			CCAGCTGCTGCAC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.532C>T	chr19.hg19:g.10610178G>A	ENSP00000171111:p.Gln178*	141.0	1.0	.		104.0	91.0	.	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Nonsense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	G	38	6.966030	0.97967	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	.	.	.	4.81	4.81	0.61882	.	0.116198	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	15.3825	0.74669	0.0:0.0:1.0:0.0	.	.	.	.	X	178	.	ENSP00000171111:Q178X	Q	-	1	0	KEAP1	10471178	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.704000	0.84595	2.232000	0.73038	0.561000	0.74099	CAG	.	.	.	none		0.572	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289	
SLC7A9	11136	hgsc.bcm.edu	37	19	33350841	33350841	+	Missense_Mutation	SNP	A	A	G			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:33350841A>G	ENST00000023064.4	-	8	970	c.779T>C	c.(778-780)aTc>aCc	p.I260T	SLC7A9_ENST00000587772.1_Missense_Mutation_p.I260T|RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000590341.1_Missense_Mutation_p.I260T	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	260					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	CACCAGGGGGATCCCGATGAT	0.607																																					p.I260T	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											.	SLC7A9	78	.	0			c.T779C						PASS	.						100.0	82.0	88.0					19																	33350841		2203	4300	6503	SO:0001583	missense	11136	exon8			AGGGGGATCCCGA	AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"""Solute carriers"""	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.779T>C	chr19.hg19:g.33350841A>G	ENSP00000023064:p.Ile260Thr	185.0	0.0	.		210.0	108.0	.	NM_001243036	B2R9A6	Missense_Mutation	SNP	ENST00000023064.4	hg19	CCDS12425.1	.	.	.	.	.	.	.	.	.	.	A	19.17	3.776707	0.70107	.	.	ENSG00000021488	ENST00000023064	D	0.90620	-2.7	5.64	5.64	0.86602	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.95799	0.8633	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	D	0.96469	0.9347	10	0.87932	D	0	.	15.8639	0.79047	1.0:0.0:0.0:0.0	.	260;260	Q53FY4;P82251	.;BAT1_HUMAN	T	260	ENSP00000023064:I260T	ENSP00000023064:I260T	I	-	2	0	SLC7A9	38042681	1.000000	0.71417	1.000000	0.80357	0.388000	0.30384	9.192000	0.94947	2.161000	0.67846	0.379000	0.24179	ATC	.	.	.	none		0.607	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1		
CEBPA	1050	hgsc.bcm.edu	37	19	33793108	33793108	+	Silent	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:33793108G>T	ENST00000498907.2	-	1	362	c.213C>A	c.(211-213)gcC>gcA	p.A71A	CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.11_ENST00000589932.1_RNA|CTD-2540B15.9_ENST00000593041.1_lincRNA|CTD-2540B15.7_ENST00000587312.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	71					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A72fs*89(1)|p.Y7_G130del(1)|p.A72fs*90(1)|p.A72fs*37(1)|p.S61fs*88(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					CGTTGAAGGCGGCCGGGTCGA	0.751			"""Mis, N, F"""		"""AML, MDS"""				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.A71A		Atlas-SNP	.		Dom	yes		19	19q13.1	1050	"""CCAAT/enhancer binding protein (C/EBP), alpha"""		L	.,1	CEBPA	986	.	5	Insertion - Frameshift(3)|Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(5)	c.C213A						PASS	.						4.0	5.0	4.0					19																	33793108		1229	2522	3751	SO:0001819	synonymous_variant	1050	exon1	Familial Cancer Database	Familial AML	GAAGGCGGCCGGG	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"""basic leucine zipper proteins"""	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.213C>A	chr19.hg19:g.33793108G>T		26.0	0.0	.		83.0	30.0	.	NM_004364	A7LNP2|P78319|Q05CA4	Silent	SNP	ENST00000498907.2	hg19	CCDS54243.1																																																																																			.	.	.	none		0.751	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364	
CEBPA	1050	hgsc.bcm.edu	37	19	33793120	33793120	+	Nonsense_Mutation	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:33793120G>T	ENST00000498907.2	-	1	350	c.201C>A	c.(199-201)taC>taA	p.Y67*	CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.11_ENST00000589932.1_RNA|CTD-2540B15.9_ENST00000593041.1_lincRNA|CTD-2540B15.7_ENST00000587312.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	67					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.I68fs*41(4)|p.Y67fs*92(2)|p.S61fs*88(1)|p.Y67fs*95(1)|p.I68fs*39(1)|p.Y7_G130del(1)|p.Y67fs*42(1)|p.Y67fs*37(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					CCGGGTCGATGTAGGCGCTGA	0.751			"""Mis, N, F"""		"""AML, MDS"""				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.Y67X		Atlas-SNP	.		Dom	yes		19	19q13.1	1050	"""CCAAT/enhancer binding protein (C/EBP), alpha"""		L	.,2	CEBPA	986	.	12	Insertion - Frameshift(6)|Deletion - Frameshift(5)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(12)	c.C201A						PASS	.						4.0	5.0	5.0					19																	33793120		1255	2546	3801	SO:0001587	stop_gained	1050	exon1	Familial Cancer Database	Familial AML	GTCGATGTAGGCG	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"""basic leucine zipper proteins"""	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.201C>A	chr19.hg19:g.33793120G>T	ENSP00000427514:p.Tyr67*	26.0	0.0	.		84.0	29.0	.	NM_004364	A7LNP2|P78319|Q05CA4	Nonsense_Mutation	SNP	ENST00000498907.2	hg19	CCDS54243.1	.	.	.	.	.	.	.	.	.	.	g	33	5.204863	0.95033	.	.	ENSG00000245848	ENST00000498907	.	.	.	3.93	2.89	0.33648	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1768	0.25749	0.2127:0.0:0.7873:0.0	.	.	.	.	X	67	.	ENSP00000427514:Y67X	Y	-	3	2	CEBPA	38484960	1.000000	0.71417	1.000000	0.80357	0.663000	0.39108	5.273000	0.65564	0.631000	0.30412	0.282000	0.19409	TAC	.	.	.	none		0.751	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364	
WTIP	126374	hgsc.bcm.edu	37	19	34991065	34991065	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:34991065G>A	ENST00000590071.2	+	8	1521	c.1184G>A	c.(1183-1185)gGa>gAa	p.G395E	WTIP_ENST00000270288.6_Missense_Mutation_p.G619E	NM_001080436.1	NP_001073905.1	A6NIX2	WTIP_HUMAN	Wilms tumor 1 interacting protein	395	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|negative regulation of hippo signaling (GO:0035331)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)	4	all_lung(56;5.94e-07)|Lung NSC(56;9.35e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			GGGGAGGAGGGACGCCGTTGC	0.667																																					p.G395E		Atlas-SNP	.											.	WTIP	12	.	0			c.G1184A						PASS	.						32.0	40.0	38.0					19																	34991065		2142	4235	6377	SO:0001583	missense	126374	exon8			AGGAGGGACGCCG	AK130059	CCDS59375.1	19q13.11	2012-03-16			ENSG00000142279	ENSG00000142279			20964	protein-coding gene	gene with protein product	"""WT1-interacting protein"""	614790				14736876	Standard	NM_001080436		Approved		uc002nvm.3	A6NIX2		ENST00000590071.2:c.1184G>A	chr19.hg19:g.34991065G>A	ENSP00000466953:p.Gly395Glu	21.0	0.0	.		41.0	20.0	.	NM_001080436		Missense_Mutation	SNP	ENST00000590071.2	hg19	CCDS59375.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.337153	0.60963	.	.	ENSG00000142279	ENST00000270288	T	0.63580	-0.05	4.35	4.35	0.52113	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	T	0.72835	0.3510	M	0.76838	2.35	0.80722	D	1	P	0.37370	0.592	P	0.47528	0.549	T	0.77760	-0.2467	10	0.66056	D	0.02	.	15.9833	0.80130	0.0:0.0:1.0:0.0	.	619	A6NIX2	WTIP_HUMAN	E	619	ENSP00000270288:G619E	ENSP00000270288:G619E	G	+	2	0	WTIP	39682905	1.000000	0.71417	0.991000	0.47740	0.294000	0.27393	9.098000	0.94202	2.101000	0.63845	0.305000	0.20034	GGA	.	.	.	none		0.667	WTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459381.3	XM_059037	
LSR	51599	hgsc.bcm.edu	37	19	35758028	35758028	+	Silent	SNP	C	C	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:35758028C>A	ENST00000361790.3	+	9	1464	c.1305C>A	c.(1303-1305)acC>acA	p.T435T	USF2_ENST00000343550.5_5'Flank|LSR_ENST00000347609.4_Silent_p.T377T|USF2_ENST00000222305.3_5'Flank|USF2_ENST00000379134.3_5'Flank|LSR_ENST00000354900.3_Silent_p.T416T|LSR_ENST00000602122.1_Silent_p.T415T|USF2_ENST00000594064.1_5'Flank|LSR_ENST00000360798.3_Silent_p.T367T|USF2_ENST00000595068.1_5'Flank|LSR_ENST00000427250.1_Silent_p.T279T|AD000684.2_ENST00000602262.1_RNA	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	435					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GTGAAGTCACCTCCCTCCACG	0.677																																					p.T435T		Atlas-SNP	.											.	LSR	60	.	0			c.C1305A						PASS	.						31.0	40.0	37.0					19																	35758028		2134	4246	6380	SO:0001819	synonymous_variant	51599	exon9			AGTCACCTCCCTC	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29572	protein-coding gene	gene with protein product	"""lipolysis-stimulated remnant"", ""immunoglobulin-like domain containing receptor 3"""					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.1305C>A	chr19.hg19:g.35758028C>A		110.0	0.0	.		161.0	93.0	.	NM_205834	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Silent	SNP	ENST00000361790.3	hg19	CCDS12450.1																																																																																			.	.	.	none		0.677	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925	
FCGBP	8857	hgsc.bcm.edu	37	19	40357745	40357745	+	Missense_Mutation	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:40357745G>T	ENST00000221347.6	-	34	15575	c.15568C>A	c.(15568-15570)Ctg>Atg	p.L5190M		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	5190	Cys-rich.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TCTGAGGTCAGCAGGGAGGAG	0.577																																					p.L5190M		Atlas-SNP	.											.	FCGBP	416	.	0			c.C15568A						PASS	.						52.0	48.0	49.0					19																	40357745		2203	4300	6503	SO:0001583	missense	8857	exon34			AGGTCAGCAGGGA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.15568C>A	chr19.hg19:g.40357745G>T	ENSP00000221347:p.Leu5190Met	166.0	0.0	.		199.0	23.0	.	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.321017	0.41096	.	.	ENSG00000090920	ENST00000221347	T	0.05649	3.41	4.69	1.09	0.20402	.	0.754197	0.11458	N	0.562013	T	0.07728	0.0194	L	0.28694	0.88	0.22796	N	0.99872	P	0.46395	0.877	P	0.51016	0.656	T	0.39702	-0.9601	10	0.23302	T	0.38	.	7.3143	0.26491	0.0:0.3807:0.4452:0.1741	.	5190	Q9Y6R7	FCGBP_HUMAN	M	5190	ENSP00000221347:L5190M	ENSP00000221347:L5190M	L	-	1	2	FCGBP	45049585	0.892000	0.30473	0.997000	0.53966	0.846000	0.48090	0.111000	0.15458	0.563000	0.29222	0.655000	0.94253	CTG	.	.	.	none		0.577	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
HRC	3270	hgsc.bcm.edu	37	19	49657889	49657889	+	Silent	SNP	T	T	C	rs57199624|rs147238387|rs551367394|rs542091249		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:49657889T>C	ENST00000252825.4	-	1	792	c.606A>G	c.(604-606)gaA>gaG	p.E202E	HRC_ENST00000595625.1_Silent_p.E202E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	202	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		AGGcctcctcttcctcctcct	0.567																																					p.E202E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.,1	HRC	85	.	0			c.A606G						PASS	.						122.0	91.0	101.0					19																	49657889		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCCTCC		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.606A>G	chr19.hg19:g.49657889T>C		55.0	0.0	.		58.0	6.0	.	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.	.	none		0.567	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
NUP62	23636	hgsc.bcm.edu	37	19	50412996	50412996	+	Silent	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:50412996C>T	ENST00000596217.1	-	2	1956	c.69G>A	c.(67-69)acG>acA	p.T23T	NUP62_ENST00000413454.1_Silent_p.T23T|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000422090.2_Silent_p.T23T|CTC-326K19.6_ENST00000451973.1_3'UTR|NUP62_ENST00000597029.1_Silent_p.T23T|NUP62_ENST00000600583.1_5'UTR|NUP62_ENST00000597723.1_Silent_p.T23T|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000352066.3_Silent_p.T23T			P37198	NUP62_HUMAN	nucleoporin 62kDa	23	15 X 9 AA approximate repeats.|Thr-rich.				carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		TGGTTGTTGCCGTCTTTGCAG	0.567																																					p.T23T		Atlas-SNP	.											.	NUP62	50	.	0			c.G69A						PASS	.						48.0	55.0	53.0					19																	50412996		2203	4300	6503	SO:0001819	synonymous_variant	23636	exon3			TGTTGCCGTCTTT	X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"""nuclear pore glycoprotein p62"""	605815	"""nucleoporin 62kD"""			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.69G>A	chr19.hg19:g.50412996C>T		82.0	0.0	.		88.0	50.0	.	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Silent	SNP	ENST00000596217.1	hg19	CCDS12788.1																																																																																			.	.	.	none		0.567	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719	
MBOAT7	79143	hgsc.bcm.edu	37	19	54687463	54687463	+	Missense_Mutation	SNP	T	T	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:54687463T>A	ENST00000245615.1	-	5	914	c.434A>T	c.(433-435)gAc>gTc	p.D145V	MBOAT7_ENST00000391754.1_Missense_Mutation_p.D145V|MBOAT7_ENST00000474910.1_5'UTR|MBOAT7_ENST00000431666.2_Missense_Mutation_p.D72V|MBOAT7_ENST00000338624.6_Missense_Mutation_p.D72V	NM_024298.3	NP_077274.3	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain containing 7	145					glycerophospholipid biosynthetic process (GO:0046474)|layer formation in cerebral cortex (GO:0021819)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|ventricular system development (GO:0021591)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipid acyltransferase activity (GO:0071617)			endometrium(4)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	10	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GGAGGGCACGTCGGGCAGCAG	0.617																																					p.D145V	NSCLC(97;826 2151 10470 22540)	Atlas-SNP	.											.	MBOAT7	37	.	0			c.A434T						PASS	.						105.0	84.0	91.0					19																	54687463		2203	4300	6503	SO:0001583	missense	79143	exon5			GGCACGTCGGGCA	AF211969	CCDS12883.1, CCDS54315.1, CCDS54316.1	19q13.4	2008-12-15	2008-01-17	2008-01-17	ENSG00000125505	ENSG00000125505			15505	protein-coding gene	gene with protein product	"""lysophosphatidylinositol acyltransferase"""	606048	"""leukocyte receptor cluster (LRC) member 4"""	LENG4		10941842, 8702217, 18094042	Standard	NM_024298		Approved	BB1, hMBOA-7, LPIAT	uc002qdr.3	Q96N66	OTTHUMG00000066516	ENST00000245615.1:c.434A>T	chr19.hg19:g.54687463T>A	ENSP00000245615:p.Asp145Val	101.0	0.0	.		97.0	52.0	.	NM_001146082	A9C4B6|B0V3I5|B4DQ87|Q05DF0|Q7L5N2|Q99908|Q9BPV2|Q9BRE9	Missense_Mutation	SNP	ENST00000245615.1	hg19	CCDS12883.1	.	.	.	.	.	.	.	.	.	.	T	8.074	0.770996	0.15983	.	.	ENSG00000125505	ENST00000431666;ENST00000338624;ENST00000245615;ENST00000449249;ENST00000391754;ENST00000414665;ENST00000453320	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69;-0.69	4.2	1.95	0.26073	.	0.659654	0.15733	N	0.247337	T	0.46718	0.1407	N	0.20685	0.6	0.09310	N	1	B;B;B	0.30973	0.033;0.302;0.033	B;B;B	0.21917	0.023;0.037;0.023	T	0.28650	-1.0037	10	0.40728	T	0.16	-2.1121	4.0508	0.09795	0.0:0.1914:0.1877:0.6209	.	127;72;145	B4DDH8;Q96N66-2;Q96N66	.;.;MBOA7_HUMAN	V	72;72;145;97;145;145;145	ENSP00000410503:D72V;ENSP00000344377:D72V;ENSP00000245615:D145V;ENSP00000375634:D145V;ENSP00000388250:D145V	ENSP00000245615:D145V	D	-	2	0	MBOAT7	59379275	0.001000	0.12720	0.058000	0.19502	0.792000	0.44763	1.025000	0.30090	1.714000	0.51371	0.363000	0.22086	GAC	.	.	.	none		0.617	MBOAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142203.1	NM_024298	
RIMS4	140730	hgsc.bcm.edu	37	20	43378853	43378853	+	IGR	SNP	G	G	A			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr20:43378853G>A	ENST00000372851.3	-	0	5203				KCNK15_ENST00000372861.3_Missense_Mutation_p.V123I	NM_001205317.1|NM_182970.3	NP_001192246.1|NP_892015.1	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4						exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)|synaptic membrane (GO:0097060)				central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(5)|urinary_tract(1)	29		Myeloproliferative disorder(115;0.0122)				GCTGACGCTGGTCACTTTCCA	0.682																																					p.V123I		Atlas-SNP	.											.	KCNK15	19	.	0			c.G367A						PASS	.						35.0	31.0	33.0					20																	43378853		2203	4300	6503	SO:0001628	intergenic_variant	60598	exon2			ACGCTGGTCACTT		CCDS13338.1, CCDS56191.1	20q13.12	2005-02-03	2003-06-18	2003-06-20	ENSG00000101098	ENSG00000101098			16183	protein-coding gene	gene with protein product		611601	"""chromosome 20 open reading frame 190"""	C20orf190		12620390	Standard	NM_182970		Approved	dJ781B1.3	uc010ggu.3	Q9H426	OTTHUMG00000032546		chr20.hg19:g.43378853G>A		61.0	0.0	.		136.0	40.0	.	NM_022358	A4FU94|E1P613|Q3MI44|Q5JWT7	Missense_Mutation	SNP	ENST00000372851.3	hg19	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.418600	0.83559	.	.	ENSG00000124249	ENST00000372861	T	0.28454	1.61	4.08	4.08	0.47627	Ion transport 2 (1);	0.000000	0.64402	U	0.000004	T	0.43100	0.1232	L	0.31578	0.945	0.54753	D	0.999989	D	0.69078	0.997	D	0.72075	0.976	T	0.38351	-0.9665	10	0.45353	T	0.12	.	16.4786	0.84151	0.0:0.0:1.0:0.0	.	123	Q9H427	KCNKF_HUMAN	I	123	ENSP00000361952:V123I	ENSP00000361952:V123I	V	+	1	0	KCNK15	42812267	1.000000	0.71417	0.999000	0.59377	0.904000	0.53231	6.347000	0.73004	2.095000	0.63458	0.655000	0.94253	GTC	.	.	.	none		0.682	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970	
LIPI	149998	hgsc.bcm.edu	37	21	15554119	15554119	+	Silent	SNP	C	C	T	rs368826576		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr21:15554119C>T	ENST00000536861.1	-	4	602	c.603G>A	c.(601-603)acG>acA	p.T201T	LIPI_ENST00000344577.2_Silent_p.T222T			Q6XZB0	LIPI_HUMAN	lipase, member I	201					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		ACTTTGCATCCGTGTAATCTA	0.388																																					p.T222T		Atlas-SNP	.											LIPI,NS,carcinoma,-1,1	LIPI	95	.	0			c.G666A						PASS	.	A		0,4406		0,0,2203	104.0	98.0	100.0		666	-5.4	0.9	21		100	1,8599		0,1,4299	no	coding-synonymous	LIPI	NM_198996.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		222/482	15554119	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	149998	exon4			TGCATCCGTGTAA	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"""membrane-associated phospholipase A1 beta"", ""cancer/testis antigen 17"""	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.603G>A	chr21.hg19:g.15554119C>T		52.0	0.0	.		66.0	18.0	.	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Silent	SNP	ENST00000536861.1	hg19		.	.	.	.	.	.	.	.	.	.	A	8.536	0.872084	0.17322	0.0	1.16E-4	ENSG00000188992	ENST00000400211	.	.	.	5.46	-5.41	0.02648	.	.	.	.	.	T	0.35508	0.0934	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36648	-0.9739	4	.	.	.	.	1.1112	0.01704	0.2909:0.094:0.2357:0.3795	.	.	.	.	R	81	.	.	G	-	1	0	LIPI	14475990	0.021000	0.18746	0.905000	0.35620	0.056000	0.15407	-0.820000	0.04457	-1.108000	0.03000	-4.655000	0.00004	GGA	.	.	.	weak		0.388	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996	
NCAM2	4685	hgsc.bcm.edu	37	21	22906941	22906941	+	Missense_Mutation	SNP	A	A	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr21:22906941A>T	ENST00000400546.1	+	17	2615	c.2366A>T	c.(2365-2367)aAt>aTt	p.N789I	NCAM2_ENST00000284894.7_Missense_Mutation_p.N647I	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	789					axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AGCCCAGTAAATGAGCCAAAT	0.393																																					p.N789I		Atlas-SNP	.											.	NCAM2	220	.	0			c.A2366T						PASS	.						113.0	108.0	109.0					21																	22906941		1920	4124	6044	SO:0001583	missense	4685	exon17			CAGTAAATGAGCC		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.2366A>T	chr21.hg19:g.22906941A>T	ENSP00000383392:p.Asn789Ile	132.0	0.0	.		122.0	35.0	.	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	hg19	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.935591	0.73442	.	.	ENSG00000154654	ENST00000400546;ENST00000284894	T;T	0.44083	0.93;0.93	5.49	5.49	0.81192	.	0.210687	0.48286	D	0.000186	T	0.49729	0.1574	L	0.41236	1.265	0.80722	D	1	D;D	0.61697	0.99;0.985	P;P	0.56398	0.797;0.724	T	0.49978	-0.8881	10	0.54805	T	0.06	-29.9197	14.4086	0.67101	1.0:0.0:0.0:0.0	.	647;789	B7Z5K2;O15394	.;NCAM2_HUMAN	I	789;647	ENSP00000383392:N789I;ENSP00000284894:N647I	ENSP00000284894:N647I	N	+	2	0	NCAM2	21828812	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.778000	0.75043	2.088000	0.63022	0.377000	0.23210	AAT	.	.	.	none		0.393	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540	
BACE2	25825	hgsc.bcm.edu	37	21	42551431	42551431	+	Intron	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr21:42551431C>T	ENST00000330333.6	+	1	775				PLAC4_ENST00000430327.2_RNA|PLAC4_ENST00000414699.1_RNA|PLAC4_ENST00000440221.2_RNA|BACE2_ENST00000347667.5_Intron|PLAC4_ENST00000536486.1_RNA|BACE2-IT1_ENST00000433378.1_RNA|BACE2_ENST00000328735.6_Intron	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2						membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				GTGACGGTGTCTGGGGTGAGT	0.607																																					p.R42K		Atlas-SNP	.											.	.	.	.	0			c.G125A						PASS	.						125.0	109.0	114.0					21																	42551431		2196	4274	6470	SO:0001627	intron_variant	191585	exon1			CGGTGTCTGGGGT	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.312+10929C>T	chr21.hg19:g.42551431C>T		137.0	0.0	.		179.0	49.0	.	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Missense_Mutation	SNP	ENST00000330333.6	hg19	CCDS13668.1																																																																																			.	.	.	none		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1		
SHANK3	85358	hgsc.bcm.edu	37	22	51160316	51160316	+	Missense_Mutation	SNP	C	C	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr22:51160316C>T	ENST00000414786.2	+	21	4240	c.4013C>T	c.(4012-4014)gCa>gTa	p.A1338V	SHANK3_ENST00000262795.3_Missense_Mutation_p.A1368V|SHANK3_ENST00000445220.2_Missense_Mutation_p.A1354V			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1352	Pro-rich.				adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CCTGAGTCTGCAGCCGACTCT	0.701																																					p.A1338V		Atlas-SNP	.											.	SHANK3	96	.	0			c.C4013T						PASS	.						9.0	11.0	10.0					22																	51160316		1919	4032	5951	SO:0001583	missense	85358	exon21			AGTCTGCAGCCGA	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.4013C>T	chr22.hg19:g.51160316C>T	ENSP00000464552:p.Ala1338Val	30.0	0.0	.		87.0	53.0	.	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	C	8.474	0.858312	0.17178	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.13089	2.62;2.62	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.13543	0.0328	N	0.24115	0.695	0.27140	N	0.961671	D;P;D	0.56521	0.97;0.941;0.976	P;B;B	0.51895	0.683;0.43;0.441	T	0.12837	-1.0532	10	0.02654	T	1	.	16.0382	0.80645	0.0:1.0:0.0:0.0	.	1352;1353;1368	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	V	1368;1354	ENSP00000442518:A1368V;ENSP00000446078:A1354V	ENSP00000442518:A1368V	A	+	2	0	SHANK3	49507182	1.000000	0.71417	0.900000	0.35374	0.856000	0.48823	5.501000	0.66950	2.381000	0.81170	0.462000	0.41574	GCA	.	.	.	none		0.701	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
DMD	1756	hgsc.bcm.edu	37	X	32305751	32305751	+	Missense_Mutation	SNP	G	G	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:32305751G>T	ENST00000357033.4	-	43	6391	c.6185C>A	c.(6184-6186)gCa>gAa	p.A2062E	DMD_ENST00000378677.2_Missense_Mutation_p.A2058E	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2062					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				ACTTTGCAATGCTGCTGTCTT	0.368																																					p.A2062E		Atlas-SNP	.											.	DMD	2127	.	0			c.C6185A						PASS	.						131.0	105.0	114.0					X																	32305751		2202	4300	6502	SO:0001583	missense	1756	exon43			TGCAATGCTGCTG	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.6185C>A	chrX.hg19:g.32305751G>T	ENSP00000354923:p.Ala2062Glu	31.0	0.0	.		29.0	28.0	.	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	8.237	0.805865	0.16467	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.35048	1.33;1.33	4.36	2.59	0.31030	.	0.000000	0.36778	U	0.002408	T	0.28830	0.0715	L	0.53249	1.67	0.80722	D	1	B;P;B;B;B	0.38677	0.275;0.642;0.322;0.259;0.44	B;B;B;B;B	0.34418	0.088;0.182;0.144;0.138;0.096	T	0.05835	-1.0861	10	0.72032	D	0.01	.	7.2118	0.25937	0.3674:0.0:0.6326:0.0	.	2054;2062;2058;721;718	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	E	2054;721;718;2058;2062;2062;1939	ENSP00000367948:A2058E;ENSP00000354923:A2062E	ENSP00000354923:A2062E	A	-	2	0	DMD	32215672	0.996000	0.38824	0.224000	0.23877	0.172000	0.22775	2.060000	0.41394	0.416000	0.25844	-0.191000	0.12829	GCA	.	.	.	none		0.368	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
BMP15	9210	hgsc.bcm.edu	37	X	50658768	50658768	+	Missense_Mutation	SNP	A	A	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:50658768A>T	ENST00000252677.3	+	2	340	c.340A>T	c.(340-342)Ata>Tta	p.I114L		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	114					female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1)	26	Ovarian(276;0.236)					TACCTGGCATATACAGATCCT	0.438																																					p.I114L		Atlas-SNP	.											.	BMP15	62	.	0			c.A340T						PASS	.						95.0	90.0	91.0					X																	50658768		2203	4299	6502	SO:0001583	missense	9210	exon2			TGGCATATACAGA	AF082349	CCDS14334.1	Xp11.2	2013-02-06			ENSG00000130385	ENSG00000130385		"""Bone morphogenetic proteins"""	1068	protein-coding gene	gene with protein product		300247				9849956	Standard	NM_005448		Approved	GDF9B	uc011mnw.2	O95972	OTTHUMG00000021525	ENST00000252677.3:c.340A>T	chrX.hg19:g.50658768A>T	ENSP00000252677:p.Ile114Leu	81.0	0.0	.		113.0	108.0	.	NM_005448	Q17RM6|Q5JST1|Q9UMS1	Missense_Mutation	SNP	ENST00000252677.3	hg19	CCDS14334.1	.	.	.	.	.	.	.	.	.	.	a	2.291	-0.362548	0.05103	.	.	ENSG00000130385	ENST00000252677	T	0.77489	-1.1	5.42	-3.73	0.04398	.	1.153060	0.05985	N	0.645013	T	0.69006	0.3063	M	0.65975	2.015	0.09310	N	1	B	0.19583	0.037	B	0.16289	0.015	T	0.49214	-0.8963	10	0.10377	T	0.69	.	6.9598	0.24591	0.3592:0.0:0.4995:0.1413	.	114	O95972	BMP15_HUMAN	L	114	ENSP00000252677:I114L	ENSP00000252677:I114L	I	+	1	0	BMP15	50675508	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.129000	0.10515	-0.754000	0.04715	-0.670000	0.03821	ATA	.	.	.	none		0.438	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448	
ZBTB38	253461	hgsc.bcm.edu	37	3	141162052	141162058	+	Frame_Shift_Del	DEL	TTCGGAT	TTCGGAT	-	rs549239683		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TTCGGAT	TTCGGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:141162052_141162058delTTCGGAT	ENST00000514251.1	+	4	1101_1107	c.822_828delTTCGGAT	c.(820-828)gattcggatfs	p.DSD274fs	ZBTB38_ENST00000441582.2_Frame_Shift_Del_p.DSD274fs|ZBTB38_ENST00000321464.5_Frame_Shift_Del_p.DSD275fs					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						TACCACAGGATTCGGATTCAGCCACAG	0.459																																					p.274_276del		Atlas-Indel,Pindel	.											.	ZBTB38	92	.	0			c.821_827del						PASS	.																																			SO:0001589	frameshift_variant	253461	exon8			.	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.822_828delTTCGGAT	chr3.hg19:g.141162052_141162058delTTCGGAT	ENSP00000426387:p.Asp274fs	74.0	0.0	0		65.0	14.0	0.215385	NM_001080412		Frame_Shift_Del	DEL	ENST00000514251.1	hg19	CCDS43157.1																																																																																			.	.	.	none		0.459	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
TJP2	9414	hgsc.bcm.edu	37	9	71869284	71869285	+	Frame_Shift_Ins	INS	-	-	T			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:71869284_71869285insT	ENST00000377245.4	+	23	3775_3776	c.3567_3568insT	c.(3568-3570)ttafs	p.L1190fs	TJP2_ENST00000539225.1_Frame_Shift_Ins_p.L1221fs|TJP2_ENST00000535702.1_Frame_Shift_Ins_p.L1157fs|TJP2_ENST00000348208.4_Frame_Shift_Ins_p.L1043fs|TJP2_ENST00000453658.2_Frame_Shift_Ins_p.L1020fs	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	1190	Interaction with SCRIB.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						GGGACACAGAATTATAGATGTC	0.579																																					p.E1220fs		Atlas-Indel,Pindel	.											.	TJP2	120	.	0			c.3660_3661insT						PASS	.																																			SO:0001589	frameshift_variant	9414	exon23			.	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.3569dupT	chr9.hg19:g.71869286_71869286dupT	ENSP00000366453:p.Leu1190fs	79.0	0.0	0		78.0	21.0	0.269231	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Frame_Shift_Ins	INS	ENST00000377245.4	hg19	CCDS6627.1																																																																																			.	.	.	none		0.579	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
FAM186A	121006	hgsc.bcm.edu	37	12	50748961	50748961	+	Frame_Shift_Del	DEL	G	G	-	rs564349682		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:50748961delG	ENST00000327337.5	-	4	1653	c.1654delC	c.(1654-1656)cgtfs	p.R552fs	FAM186A_ENST00000543111.1_Frame_Shift_Del_p.R552fs	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	552																	GGAGATTCACGTTTGACCTTC	0.413																																					p.R552fs	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-Indel,Pindel	.											.	FAM186A	181	.	0			c.1655delG						PASS	.						158.0	122.0	133.0					12																	50748961		692	1591	2283	SO:0001589	frameshift_variant	121006	exon4			.		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.1654delC	chr12.hg19:g.50748961delG	ENSP00000329995:p.Arg552fs	129.0	0.0	0		141.0	53.0	0.375887	NM_001145475		Frame_Shift_Del	DEL	ENST00000327337.5	hg19	CCDS44878.1																																																																																			.	.	.	none		0.413	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
RBAK	57786	hgsc.bcm.edu	37	7	5104550	5104550	+	Frame_Shift_Del	DEL	G	G	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:5104550delG	ENST00000353796.3	+	6	1787	c.1463delG	c.(1462-1464)agtfs	p.S488fs	RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK_ENST00000396912.1_Frame_Shift_Del_p.S488fs|RBAK-RBAKDN_ENST00000407184.1_Intron	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	488	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		CATGAATGTAGTGAATGTGGA	0.373																																					p.S488fs		Atlas-Indel,Pindel	.											.	RBAK	82	.	0			c.1462delA						PASS	.						64.0	64.0	64.0					7																	5104550		2203	4299	6502	SO:0001589	frameshift_variant	57786	exon5			.	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"""Zinc fingers, C2H2-type"", ""-"""	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.1463delG	chr7.hg19:g.5104550delG	ENSP00000275423:p.Ser488fs	114.0	0.0	0		105.0	58.0	0.552381	NM_021163	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Frame_Shift_Del	DEL	ENST00000353796.3	hg19	CCDS5337.1																																																																																			.	.	.	none		0.373	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163	
DNAH8	1769	hgsc.bcm.edu	37	6	38818063	38818080	+	In_Frame_Del	DEL	ATAAAAATAATGCAGCGA	ATAAAAATAATGCAGCGA	-	rs200056261|rs201568629|rs547165959		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	ATAAAAATAATGCAGCGA	ATAAAAATAATGCAGCGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:38818063_38818080delATAAAAATAATGCAGCGA	ENST00000359357.3	+	36	4839_4856	c.4585_4602delATAAAAATAATGCAGCGA	c.(4585-4602)ataaaaataatgcagcgadel	p.IKIMQR1529del	DNAH8_ENST00000449981.2_In_Frame_Del_p.IKIMQR1746del|DNAH8_ENST00000441566.1_In_Frame_Del_p.IKIMQR1529del			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1529					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.I1529I(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						CAAGTCTTGGATAAAAATAATGCAGCGAGCTCATGAGA	0.362																																					p.1745_1751del		Atlas-Indel,Pindel	.											.	DNAH8	1239	.	2	Substitution - coding silent(2)	lung(2)	c.5235_5252del						PASS	.																																			SO:0001651	inframe_deletion	1769	exon38			.	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.4585_4602delATAAAAATAATGCAGCGA	chr6.hg19:g.38818063_38818080delATAAAAATAATGCAGCGA	ENSP00000352312:p.Ile1529_Arg1534del	89.0	0.0	0		65.0	25.0	0.384615	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	In_Frame_Del	DEL	ENST00000359357.3	hg19																																																																																				.	.	.	none		0.362	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
ZNF814	730051	hgsc.bcm.edu	37	19	58385280	58385281	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:58385280_58385281delTG	ENST00000435989.2	-	3	1711_1712	c.1477_1478delCA	c.(1477-1479)cagfs	p.Q493fs	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	493					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						TTCTCCACACTGATAAGGTCTT	0.47																																					p.493_493del		Atlas-INDEL	.											.	ZNF814	93	.	0			c.1478_1479del						PASS	.																																			SO:0001589	frameshift_variant	730051	exon3			.		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.1477_1478delCA	chr19.hg19:g.58385280_58385281delTG	ENSP00000410545:p.Gln493fs	130.0	0.0	0		124.0	12.0	0.0967742	NM_001144989	A6NF35	Frame_Shift_Del	DEL	ENST00000435989.2	hg19	CCDS46212.1																																																																																			.	.	.	none		0.470	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
PCSK9	255738	hgsc.bcm.edu	37	1	55529096	55529096	+	Frame_Shift_Del	DEL	G	G	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:55529096delG	ENST00000302118.5	+	12	2208	c.1918delG	c.(1918-1920)gggfs	p.G640fs	PCSK9_ENST00000543384.1_3'UTR|PCSK9_ENST00000490692.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	640	C-terminal domain.				apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						TGCCCTCCCTGGGACCTCCCA	0.662																																					p.P639fs	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-Indel,Pindel	.											.	PCSK9	76	.	0			c.1917delT						PASS	.						34.0	34.0	34.0					1																	55529096		2203	4300	6503	SO:0001589	frameshift_variant	255738	exon12			.	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.1918delG	chr1.hg19:g.55529096delG	ENSP00000303208:p.Gly640fs	177.0	0.0	0		232.0	129.0	0.556035	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Frame_Shift_Del	DEL	ENST00000302118.5	hg19	CCDS603.1																																																																																			.	.	.	none		0.662	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
AKT2	208	hgsc.bcm.edu	37	19	40788466	40788466	+	Intron	DEL	A	A	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:40788466delA	ENST00000392038.2	-	1	215				AKT2_ENST00000579047.1_Intron|MIR641_ENST00000384899.1_RNA|AKT2_ENST00000581582.1_Intron	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2						activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			AAGAGGAAGGAAAGACATAGG	0.542			A		"""ovarian, pancreatic """																																.		Atlas-INDEL	.		Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	.	.	.	.	0			.						PASS	.						48.0	49.0	49.0					19																	40788466		1568	3582	5150	SO:0001627	intron_variant	693226	.			.	M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	392	protein-coding gene	gene with protein product		164731				1409633	Standard	NM_001626		Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.83+2621T>-	chr19.hg19:g.40788466delA		47.0	0.0	0		56.0	17.0	0.303571	.	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	RNA	DEL	ENST00000392038.2	hg19	CCDS12552.1																																																																																			.	.	.	none		0.542	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626	
UBQLN2	29978	hgsc.bcm.edu	37	X	56592091	56592092	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:56592091_56592092delAA	ENST00000338222.5	+	1	2066_2067	c.1785_1786delAA	c.(1783-1788)ttaaacfs	p.N596fs		NM_013444.3	NP_038472.2	Q9UHD9	UBQL2_HUMAN	ubiquilin 2	596	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)	21						TGGGGTTCTTAAACCGTGAAGC	0.515																																					p.595_595del	Esophageal Squamous(104;218 1492 6022 10838 28884)	Atlas-Indel,Pindel	.											.	UBQLN2	55	.	0			c.1784_1785del						PASS	.																																			SO:0001589	frameshift_variant	29978	exon1			.	AF189009	CCDS14374.1	Xp11.21	2014-09-17			ENSG00000188021	ENSG00000188021		"""Ubiquilin family"""	12509	protein-coding gene	gene with protein product	"""NEDD4 binding protein 4"""	300264				10675567	Standard	NM_013444		Approved	Chap1, Dsk2, RIHFB2157, LIC-2, CHAP1/DSK2, PLIC-2, N4BP4, PLIC2	uc004dus.3	Q9UHD9	OTTHUMG00000021669	ENST00000338222.5:c.1785_1786delAA	chrX.hg19:g.56592091_56592092delAA	ENSP00000345195:p.Asn596fs	106.0	0.0	0		167.0	146.0	0.874251	NM_013444	O94798|Q5D027|Q9H3W6|Q9HAZ4	Frame_Shift_Del	DEL	ENST00000338222.5	hg19	CCDS14374.1																																																																																			.	.	.	none		0.515	UBQLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056891.1	NM_013444	
PPP2R5E	5529	hgsc.bcm.edu	37	14	63881922	63881922	+	Frame_Shift_Del	DEL	A	A	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:63881922delA	ENST00000337537.3	-	5	1087	c.485delT	c.(484-486)ttgfs	p.L162fs	PPP2R5E_ENST00000553266.1_5'UTR|PPP2R5E_ENST00000422769.2_Frame_Shift_Del_p.L86fs|PPP2R5E_ENST00000555899.1_Frame_Shift_Del_p.L162fs	NM_001282179.1|NM_001282180.1|NM_001282181.1|NM_001282182.1|NM_006246.2	NP_001269108.1|NP_001269109.1|NP_001269110.1|NP_001269111.1|NP_006237.1	Q16537	2A5E_HUMAN	protein phosphatase 2, regulatory subunit B', epsilon isoform	162					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)	15				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		TTGGCTTTCCAAAAATCGTAT	0.313																																					p.L162fs		Atlas-Indel,Pindel	.											.	PPP2R5E	43	.	0			c.486delG						PASS	.						87.0	91.0	90.0					14																	63881922		2202	4298	6500	SO:0001589	frameshift_variant	5529	exon5			.	L76703	CCDS9758.1, CCDS61467.1, CCDS61468.1	14q23.2	2010-06-18	2007-01-22		ENSG00000154001	ENSG00000154001		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9313	protein-coding gene	gene with protein product		601647	"""protein phosphatase 2, regulatory subunit B (B56), epsilon isoform"""			7592815	Standard	NM_006246		Approved		uc001xgd.1	Q16537	OTTHUMG00000140341	ENST00000337537.3:c.485delT	chr14.hg19:g.63881922delA	ENSP00000337641:p.Leu162fs	113.0	0.0	0		95.0	51.0	0.536842	NM_006246	A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4	Frame_Shift_Del	DEL	ENST00000337537.3	hg19	CCDS9758.1																																																																																			.	.	.	none		0.313	PPP2R5E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276973.1	NM_006246	
HECA	51696	hgsc.bcm.edu	37	6	139487930	139487930	+	Frame_Shift_Del	DEL	G	G	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:139487930delG	ENST00000367658.2	+	2	1066	c.781delG	c.(781-783)ggtfs	p.G261fs	RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.3_ENST00000585874.1_RNA|RP1-225E12.2_ENST00000591102.1_RNA|RP1-225E12.2_ENST00000586229.1_RNA|RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000589192.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.2_ENST00000590679.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	261					respiratory tube development (GO:0030323)	membrane (GO:0016020)				endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		CGCAGCCTACGGTGCCCGTTC	0.682																																					p.Y260X		Atlas-Indel,Pindel	.											.	HECA	45	.	0			c.780delC						PASS	.						15.0	18.0	17.0					6																	139487930		2203	4297	6500	SO:0001589	frameshift_variant	51696	exon2			.	AB033492	CCDS5194.1	6q23-q24	2010-11-25			ENSG00000112406	ENSG00000112406			21041	protein-coding gene	gene with protein product		607977				11696983, 19643820	Standard	NM_016217		Approved	HDCL, hHDC, HDC, dJ225E12.1	uc003qin.3	Q9UBI9	OTTHUMG00000015686	ENST00000367658.2:c.781delG	chr6.hg19:g.139487930delG	ENSP00000356630:p.Gly261fs	75.0	0.0	0		66.0	21.0	0.318182	NM_016217		Frame_Shift_Del	DEL	ENST00000367658.2	hg19	CCDS5194.1																																																																																			.	.	.	none		0.682	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217	
RAPH1	65059	hgsc.bcm.edu	37	2	204304774	204304775	+	Frame_Shift_Del	DEL	AC	AC	-	rs201752703		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:204304774_204304775delAC	ENST00000319170.5	-	14	3437_3438	c.3138_3139delGT	c.(3136-3141)gtgtcafs	p.S1047fs	RAPH1_ENST00000374493.3_Frame_Shift_Del_p.S1099fs|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000295851.5_3'UTR	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	1047					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GCTTTTGCTGACACACACCCTT	0.545																																					p.1047_1047del		Atlas-Indel,Pindel	.											.	RAPH1	118	.	0			c.3139_3140del						PASS	.																																			SO:0001589	frameshift_variant	65059	exon14			.	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"""Pleckstrin homology (PH) domain containing"""	14436	protein-coding gene	gene with protein product	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"""	609035	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"""	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.3138_3139delGT	chr2.hg19:g.204304780_204304781delAC	ENSP00000316543:p.Ser1047fs	75.0	0.0	0		79.0	37.0	0.468354	NM_213589	Q96Q37|Q9C0I2	Frame_Shift_Del	DEL	ENST00000319170.5	hg19	CCDS2359.1																																																																																			.	.	.	none		0.545	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252	
SPEG	10290	hgsc.bcm.edu	37	2	220354060	220354064	+	Frame_Shift_Del	DEL	TCTTC	TCTTC	-	rs78622154	byFrequency	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TCTTC	TCTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:220354060_220354064delTCTTC	ENST00000312358.7	+	36	8452_8456	c.8320_8324delTCTTC	c.(8320-8325)tcttcafs	p.SS2774fs	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2774	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TCTCTTAGATTCTTCAGCTGTGCCA	0.62																																					p.2773_2775del		Atlas-Indel,Pindel	.											.	SPEG	272	.	0			c.8319_8323del						PASS	.																																			SO:0001589	frameshift_variant	10290	exon36			.	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.8320_8324delTCTTC	chr2.hg19:g.220354060_220354064delTCTTC	ENSP00000311684:p.Ser2774fs	54.0	0.0	0		61.0	25.0	0.409836	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Frame_Shift_Del	DEL	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.	.	none		0.620	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
RCHY1	25898	hgsc.bcm.edu	37	4	76416940	76416940	+	Frame_Shift_Del	DEL	A	A	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:76416940delA	ENST00000324439.5	-	6	901	c.503delT	c.(502-504)ttafs	p.L168fs	RCHY1_ENST00000380840.2_Frame_Shift_Del_p.L128fs|RCHY1_ENST00000512706.1_Frame_Shift_Del_p.L146fs|RCHY1_ENST00000451788.1_Frame_Shift_Del_p.L168fs|RCHY1_ENST00000513257.1_Frame_Shift_Del_p.L168fs|RCHY1_ENST00000514021.1_5'Flank	NM_001278536.1|NM_001278538.1|NM_001278539.1	NP_001265465.1|NP_001265467.1|NP_001265468.1	Q96PM5	ZN363_HUMAN	ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase	168					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(2)|pancreas(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TTACCTATGTAAAAGATGTCC	0.308																																					p.L168fs		Atlas-Indel,Pindel	.											.	RCHY1	17	.	0			c.504delA						PASS	.						59.0	59.0	59.0					4																	76416940		2203	4297	6500	SO:0001589	frameshift_variant	25898	exon6			.	AF255666	CCDS3567.1, CCDS34012.1, CCDS63990.1, CCDS63991.1, CCDS63992.1	4q21.1-q21.3	2014-02-17	2012-02-23	2004-03-30	ENSG00000163743	ENSG00000163743		"""RING-type (C3HC4) zinc fingers"""	17479	protein-coding gene	gene with protein product	"""androgen-receptor N-terminal-interacting protein"", ""p53-induced protein with a RING-H2 domain"", ""zinc finger, CHY-type"""	607680	"""zinc finger protein 363"", ""ring finger and CHY zinc finger domain containing 1"""	ZNF363		12654245	Standard	NM_015436		Approved	CHIMP, DKFZp586C1620, PRO1996, RNF199, ARNIP, PIRH2, ZCHY	uc003hik.3	Q96PM5	OTTHUMG00000130105	ENST00000324439.5:c.503delT	chr4.hg19:g.76416940delA	ENSP00000321239:p.Leu168fs	282.0	0.0	0		221.0	125.0	0.565611	NM_001008925	B3KRG3|C7E541|C7E542|C7E543|D3YRV2|E7EMC8|E7ETW5|J3KPI0|Q2KN33|Q59GN7|Q86X26|Q96PR5	Frame_Shift_Del	DEL	ENST00000324439.5	hg19	CCDS3567.1																																																																																			.	.	.	none		0.308	RCHY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252411.2	NM_015436	
HPS3	84343	hgsc.bcm.edu	37	3	148857880	148857881	+	Frame_Shift_Ins	INS	-	-	GT	rs541164156		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:148857880_148857881insGT	ENST00000296051.2	+	2	447_448	c.307_308insGT	c.(307-309)cgtfs	p.R103fs	HPS3_ENST00000460120.1_Intron	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	103					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)		p.R103S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TGAAAACTCTCGTGTGTGTATC	0.426									Hermansky-Pudlak syndrome																												p.R103fs		Atlas-Indel,Pindel	.											HPS3,NS,carcinoma,0,1	HPS3	104	.	1	Substitution - Missense(1)	lung(1)	c.307_308insGT						PASS	.																																			SO:0001589	frameshift_variant	84343	exon2	Familial Cancer Database	HPS, HPS1-8	.	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.314_315dupGT	chr3.hg19:g.148857887_148857888dupGT	ENSP00000296051:p.Arg103fs	145.0	0.0	0		131.0	30.0	0.229008	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Frame_Shift_Ins	INS	ENST00000296051.2	hg19	CCDS3140.1																																																																																			.	.	.	none		0.426	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
VSTM2A	222008	hgsc.bcm.edu	37	7	54612346	54612346	+	Frame_Shift_Del	DEL	G	G	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:54612346delG	ENST00000407838.3	+	2	517	c.111delG	c.(109-111)acgfs	p.T37fs	VSTM2A_ENST00000302287.3_Frame_Shift_Del_p.T37fs|VSTM2A_ENST00000402613.3_Frame_Shift_Del_p.T37fs|VSTM2A_ENST00000404951.1_Frame_Shift_Del_p.T37fs|VSTM2A_ENST00000402026.2_Frame_Shift_Del_p.T36fs	NM_182546.2	NP_872352.2	Q8TAG5	VTM2A_HUMAN	V-set and transmembrane domain containing 2A	37	Ig-like V-type.					extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(12)|prostate(1)	16			STAD - Stomach adenocarcinoma(5;0.0525)			GGAACGTGACGGCGACCGAGG	0.577																																					p.T37fs		Atlas-Indel,Pindel	.											.	VSTM2A	53	.	0			c.110delC						PASS	.						61.0	60.0	60.0					7																	54612346		2203	4300	6503	SO:0001589	frameshift_variant	222008	exon2			.	BC028404	CCDS5512.2, CCDS75604.1	7p11.2	2013-01-11	2007-08-10	2007-08-10	ENSG00000170419	ENSG00000170419		"""Immunoglobulin superfamily / V-set domain containing"""	28499	protein-coding gene	gene with protein product			"""V-set and transmembrane domain containing 2"""	VSTM2		12477932	Standard	XM_006715663		Approved	MGC33530	uc010kzf.3	Q8TAG5	OTTHUMG00000129271	ENST00000407838.3:c.111delG	chr7.hg19:g.54612346delG	ENSP00000384967:p.Thr37fs	128.0	0.0	0		167.0	50.0	0.299401	NM_182546	A4D2E9|B5MC94	Frame_Shift_Del	DEL	ENST00000407838.3	hg19	CCDS5512.2																																																																																			.	.	.	none		0.577	VSTM2A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318694.1	NM_182546	
MLEC	9761	hgsc.bcm.edu	37	12	121132908	121132908	+	Frame_Shift_Del	DEL	A	A	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:121132908delA	ENST00000228506.3	+	4	1030	c.602delA	c.(601-603)gacfs	p.D201fs	MLEC_ENST00000412616.2_Intron|RP11-173P15.3_ENST00000541383.1_RNA	NM_014730.2	NP_055545.1	Q14165	MLEC_HUMAN	malectin	201					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|enzyme binding (GO:0019899)	p.D201G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	16						GGGTACTATGACAATCCCAAG	0.498																																					p.D201fs		Atlas-Indel,Pindel	.											.	MLEC	33	.	1	Substitution - Missense(1)	lung(1)	c.601delG						PASS	.						381.0	352.0	362.0					12																	121132908		2203	4300	6503	SO:0001589	frameshift_variant	9761	exon4			.	BC000371	CCDS9206.1	12q24.31	2013-03-06	2008-11-05	2008-11-05	ENSG00000110917	ENSG00000110917			28973	protein-coding gene	gene with protein product	"""oligosaccharyltransferase complex subunit (non-catalytic)"""	613802	"""KIAA0152"""	KIAA0152		18524852	Standard	NM_014730		Approved		uc001tyy.1	Q14165	OTTHUMG00000169187	ENST00000228506.3:c.602delA	chr12.hg19:g.121132908delA	ENSP00000228506:p.Asp201fs	123.0	0.0	0		162.0	72.0	0.444444	NM_014730		Frame_Shift_Del	DEL	ENST00000228506.3	hg19	CCDS9206.1																																																																																			.	.	.	none		0.498	MLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402781.2	NM_014730	
RUSC2	9853	hgsc.bcm.edu	37	9	35547875	35547875	+	Frame_Shift_Del	DEL	G	G	-	rs375840925		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:35547875delG	ENST00000455600.1	+	2	1926	c.1357delG	c.(1357-1359)gtcfs	p.V453fs		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	453						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			GAAGCCAGAAGTCCAGCCAGA	0.572																																					p.E452fs		Atlas-Indel,Pindel	.											.	RUSC2	88	.	0			c.1356delA						PASS	.						107.0	127.0	120.0					9																	35547875		2203	4300	6503	SO:0001589	frameshift_variant	9853	exon2			.	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.1357delG	chr9.hg19:g.35547875delG	ENSP00000393922:p.Val453fs	76.0	0.0	0		86.0	53.0	0.616279	NM_014806	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Frame_Shift_Del	DEL	ENST00000455600.1	hg19	CCDS35008.1																																																																																			.	.	.	none		0.572	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462	
TYSND1	219743	hgsc.bcm.edu	37	10	71905802	71905819	+	In_Frame_Del	DEL	CTCTCAGTTGATCCGCCT	CTCTCAGTTGATCCGCCT	-	rs370610523|rs572542997|rs562289648|rs553877350	byFrequency	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	CTCTCAGTTGATCCGCCT	CTCTCAGTTGATCCGCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:71905802_71905819delCTCTCAGTTGATCCGCCT	ENST00000287078.6	-	1	523_540	c.524_541delAGGCGGATCAACTGAGAG	c.(523-543)gaggcggatcaactgagagcg>gcg	p.EADQLR175del	TYSND1_ENST00000335494.5_In_Frame_Del_p.EADQLR175del|TYSND1_ENST00000494143.1_5'Flank	NM_173555.2	NP_775826.2	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1	175					protein homooligomerization (GO:0051260)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of fatty acid beta-oxidation (GO:0031998)	membrane (GO:0016020)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1)	9						CAGCCCAGCGCTCTCAGTTGATCCGCCTCCTCGTCCTC	0.711														5	0.000998403	0.0008	0.0	5008	,	,		14648	0.002		0.0	False		,,,				2504	0.002				p.175_181del		Pindel	.											.	TYSND1	20	.	0			c.525_542del						PASS	.		,	1,4251		0,1,2125					,	3.9	1.0			26	18,8216		0,18,4099	no	coding,coding	TYSND1	NM_173555.2,NM_001040273.1	,	0,19,6224	A1A1,A1R,RR		0.2186,0.0235,0.1522	,	,		19,12467				SO:0001651	inframe_deletion	219743	exon1			.	BC016840	CCDS31213.1, CCDS31214.1	10q22.1	2009-11-06		2006-09-21	ENSG00000156521	ENSG00000156521			28531	protein-coding gene	gene with protein product		611017				17255948	Standard	NM_173555		Approved	MGC34695, NET41	uc001jqr.4	Q2T9J0	OTTHUMG00000018397	ENST00000287078.6:c.524_541delAGGCGGATCAACTGAGAG	chr10.hg19:g.71905802_71905819delCTCTCAGTTGATCCGCCT	ENSP00000287078:p.Glu175_Arg180del	24.0	0.0	.		112.0	32.0	0.286	NM_001040273	Q5SQT4|Q5SQU1|Q8N6H2|Q96AR5	In_Frame_Del	DEL	ENST00000287078.6	hg19	CCDS31213.1																																																																																			.	.	.	none		0.711	TYSND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048483.1	NM_173555	
MAST2	23139	hgsc.bcm.edu	37	1	46496701	46496702	+	Frame_Shift_Del	DEL	TC	TC	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:46496701_46496702delTC	ENST00000361297.2	+	23	3014_3015	c.2731_2732delTC	c.(2731-2733)tctfs	p.S911fs	MAST2_ENST00000372009.2_Frame_Shift_Del_p.S841fs	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					GCTGTCGGTGTCTGAGTCATCC	0.629																																					p.910_911del		Pindel	.											.	MAST2	136	.	0			c.2730_2731del						PASS	.																																			SO:0001589	frameshift_variant	23139	exon23			.	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.2731_2732delTC	chr1.hg19:g.46496701_46496702delTC	ENSP00000354671:p.Ser911fs	111.0	0.0	.		99.0	34.0	0.343	NM_015112		Frame_Shift_Del	DEL	ENST00000361297.2	hg19	CCDS41326.1																																																																																			.	.	.	none		0.629	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
UPRT	139596	hgsc.bcm.edu	37	X	74494317	74494318	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:74494317_74494318delAG	ENST00000373383.4	+	1	395_396	c.228_229delAG	c.(226-231)tcagagfs	p.E77fs	UPRT_ENST00000530743.1_5'Flank|UPRT_ENST00000373379.1_Frame_Shift_Del_p.E77fs|UPRT_ENST00000531704.1_3'UTR	NM_145052.3	NP_659489.1	Q96BW1	UPP_HUMAN	uracil phosphoribosyltransferase (FUR1) homolog (S. cerevisiae)	77					female pregnancy (GO:0007565)|lactation (GO:0007595)|response to insulin (GO:0032868)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(4)|lung(4)	18						GCCTCAACTCAGAGGGCAACAG	0.639																																					p.76_76del		Pindel	.											.	UPRT	46	.	0			c.227_228del						PASS	.																																			SO:0001589	frameshift_variant	139596	exon1			.	BC015116	CCDS14429.1	Xq13.3	2009-01-14			ENSG00000094841	ENSG00000094841			28334	protein-coding gene	gene with protein product		300656				12477932	Standard	NM_145052		Approved	DKFZp781E1243, MGC23937, FUR1, RP11-311P8.3	uc004ecb.2	Q96BW1	OTTHUMG00000021864	ENST00000373383.4:c.228_229delAG	chrX.hg19:g.74494319_74494320delAG	ENSP00000362481:p.Glu77fs	82.0	0.0	.		146.0	23.0	0.158	NM_145052	Q5JRL1|Q5JRL3|Q68DN0|Q96MW2	Frame_Shift_Del	DEL	ENST00000373383.4	hg19	CCDS14429.1																																																																																			.	.	.	none		0.639	UPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057278.1	NM_145052	
OFD1	8481	hgsc.bcm.edu	37	X	13762547	13762547	+	Frame_Shift_Del	DEL	T	T	-			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:13762547delT	ENST00000340096.6	+	6	753	c.426delT	c.(424-426)catfs	p.H142fs	OFD1_ENST00000398395.3_Frame_Shift_Del_p.H142fs|OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000380550.3_Frame_Shift_Del_p.H142fs|OFD1_ENST00000380567.1_Frame_Shift_Del_p.H2fs	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	142					axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						TTCTTATGCATTTTTTAAAAG	0.308																																					p.H142fs		Pindel	.											.	OFD1	109	.	0			c.425delA						PASS	.						66.0	59.0	61.0					X																	13762547		2203	4299	6502	SO:0001589	frameshift_variant	8481	exon6			.	Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"""retinitis pigmentosa 23 (X-linked recessive)"""	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.426delT	chrX.hg19:g.13762547delT	ENSP00000344314:p.His142fs	225.0	0.0	.		290.0	96.0	0.331	NM_003611	B9ZVU5|O75666|Q4VAK4	Frame_Shift_Del	DEL	ENST00000340096.6	hg19	CCDS14157.1																																																																																			.	.	.	none		0.308	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611	
