#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
SYNC	81493	hgsc.bcm.edu	37	1	33160953	33160953	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr1:33160953A>G	ENST00000409190.3	-	2	1204	c.746T>C	c.(745-747)gTg>gCg	p.V249A	SYNC_ENST00000373484.3_Missense_Mutation_p.V249A	NM_030786.2	NP_110413	Q9H7C4	SYNCI_HUMAN	syncoilin, intermediate filament protein	249	Coil 1b.				intermediate filament-based process (GO:0045103)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						TTCCTTTGTCACTTTGAAAAG	0.557																																					p.V249A		Atlas-SNP	.											.	SYNC	36	.	0			c.T746C						.						33.0	28.0	30.0					1																	33160953		692	1591	2283	SO:0001583	missense	81493	exon2			TTTGTCACTTTGA	AK024707	CCDS367.2, CCDS53294.1	1p35.1	2013-01-16	2008-09-19	2008-09-19	ENSG00000162520	ENSG00000162520		"""Intermediate filaments type III"""	28897	protein-coding gene	gene with protein product		611750	"""syncoilin, intermediate filament 1"""	SYNC1		11053421	Standard	NM_030786		Approved	SYNCOILIN	uc001bvt.2	Q9H7C4	OTTHUMG00000008087	ENST00000409190.3:c.746T>C	chr1.hg19:g.33160953A>G	ENSP00000386439:p.Val249Ala	67.0	0.0		71.0	35.0	NM_001161708	B4DNK8|B4DY58|C9IY41	Missense_Mutation	SNP	ENST00000409190.3	hg19	CCDS367.2	.	.	.	.	.	.	.	.	.	.	A	15.51	2.854954	0.51376	.	.	ENSG00000162520	ENST00000373484;ENST00000409190	D;D	0.88201	-2.35;-2.35	4.57	4.57	0.56435	Filament (1);	.	.	.	.	D	0.88800	0.6535	N	0.14661	0.345	0.30562	N	0.764398	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.994	D	0.85621	0.1264	9	0.37606	T	0.19	-10.6603	13.45	0.61165	1.0:0.0:0.0:0.0	.	249;249	Q9H7C4-2;Q9H7C4	.;SYNCI_HUMAN	A	249	ENSP00000362583:V249A;ENSP00000386439:V249A	ENSP00000362583:V249A	V	-	2	0	SYNC	32933540	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	4.376000	0.59556	1.853000	0.53794	0.459000	0.35465	GTG	.	.		0.557	SYNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022129.3	NM_030786	
RBM15	64783	hgsc.bcm.edu	37	1	110882218	110882218	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr1:110882218C>G	ENST00000369784.3	+	1	1091	c.191C>G	c.(190-192)tCg>tGg	p.S64W	RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000602849.1_Missense_Mutation_p.S64W|RBM15_ENST00000487146.2_Missense_Mutation_p.S64W	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	64	Gly/Ser-rich.				negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		GGTGAGGACTCGACTTCCCGC	0.637			T	MKL1	acute megakaryocytic leukemia																																p.S64W		Atlas-SNP	.		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	.	RBM15	93	.	0			c.C191G						.						40.0	41.0	40.0					1																	110882218		2203	4300	6503	SO:0001583	missense	64783	exon1			AGGACTCGACTTC	AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"""RNA binding motif (RRM) containing"""	14959	protein-coding gene	gene with protein product	"""one twenty-two"""	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.191C>G	chr1.hg19:g.110882218C>G	ENSP00000358799:p.Ser64Trp	240.0	0.0		280.0	112.0	NM_022768	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Missense_Mutation	SNP	ENST00000369784.3	hg19	CCDS822.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.042262	0.75732	.	.	ENSG00000162775	ENST00000369784	T	0.20069	2.1	5.31	5.31	0.75309	.	0.000000	0.39909	N	0.001222	T	0.23926	0.0579	N	0.19112	0.55	0.58432	D	0.999999	D;D	0.61080	0.989;0.981	D;P	0.65684	0.937;0.867	T	0.07233	-1.0783	10	0.72032	D	0.01	-6.0825	18.7537	0.91825	0.0:1.0:0.0:0.0	.	64;64	Q96T37-3;Q96T37	.;RBM15_HUMAN	W	64	ENSP00000358799:S64W	ENSP00000358799:S64W	S	+	2	0	RBM15	110683741	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.911000	0.48774	2.763000	0.94921	0.655000	0.94253	TCG	.	.		0.637	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768	
NUP210L	91181	hgsc.bcm.edu	37	1	154062058	154062058	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr1:154062058G>A	ENST00000368559.3	-	16	2271	c.2200C>T	c.(2200-2202)Cga>Tga	p.R734*	NUP210L_ENST00000271854.3_Nonsense_Mutation_p.R734*	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	734					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			TTTCCAATTCGGAATGTGAGA	0.423																																					p.R734X		Atlas-SNP	.											.	NUP210L	181	.	0			c.C2200T						.						74.0	75.0	75.0					1																	154062058		1891	4124	6015	SO:0001587	stop_gained	91181	exon16			CAATTCGGAATGT	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2200C>T	chr1.hg19:g.154062058G>A	ENSP00000357547:p.Arg734*	123.0	0.0		282.0	58.0	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Nonsense_Mutation	SNP	ENST00000368559.3	hg19	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	G	39	7.522494	0.98335	.	.	ENSG00000143552	ENST00000368559;ENST00000271854	.	.	.	4.57	4.57	0.56435	.	0.150747	0.30752	N	0.008943	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-27.8864	15.3044	0.73982	0.0:0.0:1.0:0.0	.	.	.	.	X	734	.	ENSP00000271854:R734X	R	-	1	2	NUP210L	152328682	0.996000	0.38824	0.954000	0.39281	0.941000	0.58515	4.027000	0.57239	2.363000	0.80096	0.467000	0.42956	CGA	.	.		0.423	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308	
SHCBP1L	81626	hgsc.bcm.edu	37	1	182922018	182922018	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr1:182922018G>T	ENST00000367547.3	-	1	487	c.251C>A	c.(250-252)gCg>gAg	p.A84E	SHCBP1L_ENST00000423786.1_5'Flank|SHCBP1L_ENST00000488956.1_5'UTR	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	156										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						cgccgccgccgccTCTCCCGT	0.751																																					p.A84E		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.C251A						.						3.0	5.0	4.0					1																	182922018		1575	3339	4914	SO:0001583	missense	81626	exon1			GCCGCCGCCTCTC	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 14"""	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.251C>A	chr1.hg19:g.182922018G>T	ENSP00000356518:p.Ala84Glu	97.0	0.0		226.0	12.0	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	hg19	CCDS30955.1	.	.	.	.	.	.	.	.	.	.	G	2.175	-0.388855	0.04932	.	.	ENSG00000157060	ENST00000367547;ENST00000287709	T	0.49720	0.77	3.09	-0.43	0.12299	.	1.097780	0.07237	N	0.863539	T	0.20536	0.0494	N	0.03608	-0.345	0.20074	N	0.999933	B	0.02656	0.0	B	0.06405	0.002	T	0.17167	-1.0378	10	0.25106	T	0.35	.	3.5265	0.07761	0.0:0.3945:0.3188:0.2868	.	84	Q9BZQ2-3	.	E	84;153	ENSP00000356518:A84E	ENSP00000287709:A153E	A	-	2	0	SHCBP1L	181188641	0.000000	0.05858	0.012000	0.15200	0.187000	0.23431	-0.880000	0.04183	-0.078000	0.12730	0.205000	0.17691	GCG	.	.		0.751	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933	
DLEC1	9940	hgsc.bcm.edu	37	3	38103672	38103672	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:38103672C>A	ENST00000308059.6	+	4	707	c.686C>A	c.(685-687)cCt>cAt	p.P229H	DLEC1_ENST00000452631.2_Missense_Mutation_p.P229H|DLEC1_ENST00000346219.3_Missense_Mutation_p.P229H					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		ATCTCCCTACCTGGATGTTCA	0.453																																					p.P229H		Atlas-SNP	.											.	DLEC1	278	.	0			c.C686A						.						106.0	94.0	98.0					3																	38103672		1970	4157	6127	SO:0001583	missense	9940	exon4			CCCTACCTGGATG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.686C>A	chr3.hg19:g.38103672C>A	ENSP00000308597:p.Pro229His	79.0	0.0		86.0	34.0	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	C	13.77	2.336703	0.41398	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.07327	3.23;3.2;3.45	3.92	3.03	0.35002	.	0.163073	0.41194	D	0.000937	T	0.23965	0.0580	M	0.75777	2.31	0.19300	N	0.999979	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.992;0.992	T	0.01549	-1.1327	10	0.87932	D	0	-8.3179	8.0406	0.30519	0.0:0.8863:0.0:0.1137	.	229;229;229	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	H	229	ENSP00000308597:P229H;ENSP00000315914:P229H;ENSP00000410427:P229H	ENSP00000308597:P229H	P	+	2	0	DLEC1	38078676	0.078000	0.21339	0.109000	0.21407	0.016000	0.09150	1.634000	0.37123	1.193000	0.43086	0.655000	0.94253	CCT	.	.		0.453	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
KIAA1407	57577	hgsc.bcm.edu	37	3	113755465	113755465	+	Missense_Mutation	SNP	C	C	T	rs529892538		TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:113755465C>T	ENST00000295878.3	-	5	730	c.584G>A	c.(583-585)aGa>aAa	p.R195K	KIAA1407_ENST00000545063.1_Missense_Mutation_p.R26K	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	195										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						CTGCTTATGTCTCATCTCCAT	0.373													C|||	1	0.000199681	0.0	0.0	5008	,	,		14349	0.0		0.001	False		,,,				2504	0.0				p.R195K		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G584A						.						243.0	227.0	232.0					3																	113755465		2203	4300	6503	SO:0001583	missense	57577	exon5			TTATGTCTCATCT	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.584G>A	chr3.hg19:g.113755465C>T	ENSP00000295878:p.Arg195Lys	137.0	0.0		195.0	74.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.750109	0.89753	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000;ENST00000483766	T;T;T	0.78003	-0.82;-1.14;-0.19	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.87669	0.6235	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.83275	0.996;0.99;0.996	D	0.86626	0.1882	10	0.44086	T	0.13	.	19.1032	0.93282	0.0:1.0:0.0:0.0	.	182;71;195	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	K	195;26;182;159	ENSP00000295878:R195K;ENSP00000446381:R26K;ENSP00000418099:R182K	ENSP00000295878:R195K	R	-	2	0	KIAA1407	115238155	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.748000	0.68697	2.734000	0.93682	0.650000	0.86243	AGA	.	.		0.373	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817	
KIAA1407	57577	hgsc.bcm.edu	37	3	113755521	113755521	+	Silent	SNP	C	C	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:113755521C>T	ENST00000295878.3	-	5	674	c.528G>A	c.(526-528)agG>agA	p.R176R	KIAA1407_ENST00000545063.1_Silent_p.R7R	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	176										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						GGTTTTCCTTCCTTCCAAGAT	0.398																																					p.R176R		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G528A						.						242.0	220.0	227.0					3																	113755521		2203	4300	6503	SO:0001819	synonymous_variant	57577	exon5			TTCCTTCCTTCCA	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.528G>A	chr3.hg19:g.113755521C>T		150.0	0.0		207.0	81.0	NM_020817	B4DYL1|Q9P2E0	Silent	SNP	ENST00000295878.3	hg19	CCDS2977.1																																																																																			.	.		0.398	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817	
KIAA1407	57577	hgsc.bcm.edu	37	3	113755536	113755536	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:113755536C>T	ENST00000295878.3	-	5	659	c.513G>A	c.(511-513)atG>atA	p.M171I	KIAA1407_ENST00000545063.1_Missense_Mutation_p.M2I	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	171										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						CAAGATCTTCCATCATTGCAG	0.413																																					p.M171I		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G513A						.						211.0	191.0	197.0					3																	113755536		2203	4300	6503	SO:0001583	missense	57577	exon5			ATCTTCCATCATT	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.513G>A	chr3.hg19:g.113755536C>T	ENSP00000295878:p.Met171Ile	148.0	0.0		208.0	83.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	14.15	2.449946	0.43531	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000;ENST00000483766	T;T;T	0.47869	1.53;0.83;0.96	5.28	5.28	0.74379	.	0.308811	0.33040	N	0.005341	T	0.31009	0.0783	N	0.14661	0.345	0.80722	D	1	B;B;B	0.15719	0.002;0.014;0.003	B;B;B	0.12837	0.005;0.008;0.005	T	0.07654	-1.0761	10	0.36615	T	0.2	.	12.4291	0.55563	0.0:0.9237:0.0:0.0763	.	158;47;171	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	I	171;2;158;135	ENSP00000295878:M171I;ENSP00000446381:M2I;ENSP00000418099:M158I	ENSP00000295878:M171I	M	-	3	0	KIAA1407	115238226	0.998000	0.40836	0.998000	0.56505	0.987000	0.75469	1.375000	0.34295	2.734000	0.93682	0.650000	0.86243	ATG	.	.		0.413	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817	
KIAA1407	57577	hgsc.bcm.edu	37	3	113755539	113755539	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:113755539C>T	ENST00000295878.3	-	5	656	c.510G>A	c.(508-510)atG>atA	p.M170I	KIAA1407_ENST00000545063.1_Start_Codon_SNP_p.M1I	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	170										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						GATCTTCCATCATTGCAGAAT	0.428																																					p.M170I		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G510A						.						201.0	182.0	188.0					3																	113755539		2203	4300	6503	SO:0001583	missense	57577	exon5			TTCCATCATTGCA	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.510G>A	chr3.hg19:g.113755539C>T	ENSP00000295878:p.Met170Ile	151.0	0.0		204.0	81.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	5.721	0.317595	0.10845	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000;ENST00000483766	T;T;T	0.55413	1.68;0.52;1.1	5.28	-0.347	0.12617	.	0.411620	0.29087	N	0.013190	T	0.24586	0.0596	N	0.19112	0.55	0.31370	N	0.680314	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.31251	-0.9950	10	0.02654	T	1	.	4.2143	0.10526	0.1732:0.2622:0.0:0.5646	.	157;46;170	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	I	170;1;157;134	ENSP00000295878:M170I;ENSP00000446381:M1I;ENSP00000418099:M157I	ENSP00000295878:M170I	M	-	3	0	KIAA1407	115238229	0.144000	0.22641	0.261000	0.24466	0.969000	0.65631	0.371000	0.20450	0.028000	0.15324	0.650000	0.86243	ATG	.	.		0.428	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817	
KIAA1407	57577	hgsc.bcm.edu	37	3	113755550	113755550	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:113755550C>T	ENST00000295878.3	-	5	645	c.499G>A	c.(499-501)Gat>Aat	p.D167N	KIAA1407_ENST00000545063.1_5'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	167										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						ATTGCAGAATCTACCACATTT	0.428																																					p.D167N		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G499A						.						174.0	158.0	164.0					3																	113755550		2203	4300	6503	SO:0001583	missense	57577	exon5			CAGAATCTACCAC	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.499G>A	chr3.hg19:g.113755550C>T	ENSP00000295878:p.Asp167Asn	156.0	0.0		204.0	75.0	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.737220	0.49045	.	.	ENSG00000163617	ENST00000295878;ENST00000491000;ENST00000483766	T;T	0.49139	1.38;0.79	5.28	4.41	0.53225	.	0.313039	0.33382	N	0.004973	T	0.48892	0.1525	L	0.43152	1.355	0.80722	D	1	B;D;B	0.61080	0.084;0.989;0.084	B;P;B	0.55923	0.037;0.787;0.037	T	0.39099	-0.9630	10	0.24483	T	0.36	.	8.5385	0.33377	0.0:0.7835:0.0:0.2165	.	154;43;167	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	N	167;154;131	ENSP00000295878:D167N;ENSP00000418099:D154N	ENSP00000295878:D167N	D	-	1	0	KIAA1407	115238240	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.821000	0.39041	1.443000	0.47586	0.650000	0.86243	GAT	.	.		0.428	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817	
ADAMTS3	9508	hgsc.bcm.edu	37	4	73169792	73169792	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr4:73169792T>G	ENST00000286657.4	-	17	2302	c.2266A>C	c.(2266-2268)Aag>Cag	p.K756Q		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	756	Spacer.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GCCTGGTTCTTAATAGCTAAA	0.373																																					p.K756Q	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-SNP	.											.	ADAMTS3	164	.	0			c.A2266C						.						113.0	119.0	117.0					4																	73169792		2203	4300	6503	SO:0001583	missense	9508	exon17			GGTTCTTAATAGC	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"""ADAM metallopeptidases with thrombospondin type 1 motif"""	219	protein-coding gene	gene with protein product		605011	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"""			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.2266A>C	chr4.hg19:g.73169792T>G	ENSP00000286657:p.Lys756Gln	102.0	0.0		112.0	49.0	NM_014243	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	hg19	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.402314	0.83230	.	.	ENSG00000156140	ENST00000286657	T	0.59083	0.29	5.57	5.57	0.84162	ADAM-TS Spacer 1 (1);	0.000000	0.85682	D	0.000000	T	0.77445	0.4131	M	0.82056	2.57	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.80656	-0.1285	10	0.66056	D	0.02	.	15.7409	0.77894	0.0:0.0:0.0:1.0	.	756	O15072	ATS3_HUMAN	Q	756	ENSP00000286657:K756Q	ENSP00000286657:K756Q	K	-	1	0	ADAMTS3	73388656	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	7.950000	0.87804	2.120000	0.65058	0.533000	0.62120	AAG	.	.		0.373	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2		
DSPP	1834	hgsc.bcm.edu	37	4	88536436	88536436	+	Silent	SNP	C	C	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr4:88536436C>T	ENST00000282478.7	+	4	2655	c.2622C>T	c.(2620-2622)agC>agT	p.S874S	DSPP_ENST00000399271.1_Silent_p.S874S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	874	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagcaacagcagtg	0.502																																					p.S874S		Atlas-SNP	.											.	DSPP	174	.	0			c.C2622T						.						70.0	85.0	79.0					4																	88536436		1641	2936	4577	SO:0001819	synonymous_variant	1834	exon5			CAGCAGCAACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2622C>T	chr4.hg19:g.88536436C>T		265.0	0.0		348.0	28.0	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.502	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
FSTL5	56884	hgsc.bcm.edu	37	4	162421233	162421233	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr4:162421233T>C	ENST00000306100.5	-	12	1829	c.1393A>G	c.(1393-1395)Ata>Gta	p.I465V	FSTL5_ENST00000427802.2_Missense_Mutation_p.I455V|FSTL5_ENST00000379164.4_Missense_Mutation_p.I464V|FSTL5_ENST00000536695.1_Missense_Mutation_p.I464V	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	465						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		ATGGGTTGTATCACTTTGATT	0.323																																					p.I465V		Atlas-SNP	.											.	FSTL5	207	.	0			c.A1393G						.						104.0	98.0	100.0					4																	162421233		2203	4299	6502	SO:0001583	missense	56884	exon12			GTTGTATCACTTT	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.1393A>G	chr4.hg19:g.162421233T>C	ENSP00000305334:p.Ile465Val	123.0	0.0		182.0	18.0	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	hg19	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	T	14.04	2.416852	0.42918	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.72505	-0.62;-0.6;-0.66;-0.6	5.29	4.11	0.48088	.	0.041760	0.85682	N	0.000000	T	0.66636	0.2809	M	0.62723	1.935	0.53005	D	0.999968	B;B;B	0.31077	0.083;0.307;0.172	B;B;B	0.33620	0.037;0.167;0.058	T	0.63278	-0.6673	10	0.38643	T	0.18	.	10.1207	0.42618	0.0:0.0799:0.0:0.9201	.	455;464;465	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	V	465;464;455;464	ENSP00000305334:I465V;ENSP00000368462:I464V;ENSP00000389270:I455V;ENSP00000440409:I464V	ENSP00000305334:I465V	I	-	1	0	FSTL5	162640683	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.761000	0.62243	0.961000	0.38030	0.460000	0.39030	ATA	.	.		0.323	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
TCERG1	10915	hgsc.bcm.edu	37	5	145847914	145847914	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr5:145847914G>T	ENST00000296702.5	+	6	1184	c.1146G>T	c.(1144-1146)atG>atT	p.M382I	TCERG1_ENST00000394421.2_Intron	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	382					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTGTAGCAATGATGCAAATAG	0.413																																					p.M382I		Atlas-SNP	.											.	TCERG1	148	.	0			c.G1146T						.						120.0	103.0	109.0					5																	145847914		2203	4300	6503	SO:0001583	missense	10915	exon6			AGCAATGATGCAA	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"""transcription factor CA150"", ""co-activator of 150 kDa"", ""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"", ""TATA box-binding protein-associated factor 2S"""	605409	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"""	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.1146G>T	chr5.hg19:g.145847914G>T	ENSP00000296702:p.Met382Ile	125.0	0.0		209.0	10.0	NM_006706	Q2NKN2|Q59EA1	Missense_Mutation	SNP	ENST00000296702.5	hg19	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.036131	0.54896	.	.	ENSG00000113649	ENST00000296702	T	0.25414	1.8	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.24084	0.0583	N	0.19112	0.55	0.80722	D	1	P	0.35872	0.525	B	0.42214	0.38	T	0.03473	-1.1033	10	0.20519	T	0.43	-12.432	19.3205	0.94236	0.0:0.0:1.0:0.0	.	382	O14776	TCRG1_HUMAN	I	382	ENSP00000296702:M382I	ENSP00000296702:M382I	M	+	3	0	TCERG1	145828107	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.567000	0.86603	0.563000	0.77884	ATG	.	.		0.413	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006	
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156941	26156941	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr6:26156941A>C	ENST00000304218.3	+	1	383	c.323A>C	c.(322-324)aAc>aCc	p.N108T	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	108	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						TTCAAACTCAACAAGAAGGCG	0.612																																					p.N108T		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.A323C						.						34.0	40.0	38.0					6																	26156941		2203	4300	6503	SO:0001583	missense	3008	exon1			AACTCAACAAGAA	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"""Histones / Replication-dependent"""	4718	protein-coding gene	gene with protein product		142220	"""H1 histone family, member 4"", ""histone 1, H1e"""	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.323A>C	chr6.hg19:g.26156941A>C	ENSP00000307705:p.Asn108Thr	202.0	0.0		239.0	95.0	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	hg19	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	17.47	3.397487	0.62177	.	.	ENSG00000168298	ENST00000304218	T	0.09723	2.95	5.35	5.35	0.76521	Histone H1/H5 (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.153236	0.56097	D	0.000029	T	0.20901	0.0503	M	0.77103	2.36	0.58432	D	0.99999	D	0.60160	0.987	D	0.69142	0.962	T	0.01294	-1.1393	10	0.72032	D	0.01	-12.771	9.2621	0.37619	0.9099:0.0:0.0901:0.0	.	108	P10412	H14_HUMAN	T	108	ENSP00000307705:N108T	ENSP00000307705:N108T	N	+	2	0	HIST1H1E	26264920	0.848000	0.29623	1.000000	0.80357	0.940000	0.58332	0.218000	0.17622	2.146000	0.66826	0.459000	0.35465	AAC	.	.		0.612	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
CALCR	799	hgsc.bcm.edu	37	7	93073038	93073038	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr7:93073038T>A	ENST00000394441.1	-	8	995	c.680A>T	c.(679-681)cAg>cTg	p.Q227L	CALCR_ENST00000426151.1_Missense_Mutation_p.Q227L|CALCR_ENST00000359558.2_Missense_Mutation_p.Q261L|CALCR_ENST00000360249.4_Missense_Mutation_p.Q243L|CALCR_ENST00000421592.1_Missense_Mutation_p.Q243L	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	261					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	CATCATGTACTGGTGGAAAAA	0.453																																					p.Q261L		Atlas-SNP	.											.	CALCR	200	.	0			c.A782T						.						119.0	112.0	114.0					7																	93073038		2203	4300	6503	SO:0001583	missense	799	exon11			ATGTACTGGTGGA	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.680A>T	chr7.hg19:g.93073038T>A	ENSP00000377959:p.Gln227Leu	135.0	0.0		186.0	67.0	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000394441.1	hg19	CCDS5631.1	.	.	.	.	.	.	.	.	.	.	T	6.496	0.459721	0.12342	.	.	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85	4.94	4.94	0.65067	.	.	.	.	.	T	0.32882	0.0844	N	0.24115	0.695	0.47123	D	0.999323	B;B	0.26195	0.144;0.023	B;B	0.31547	0.132;0.09	T	0.11155	-1.0599	9	0.02654	T	1	.	15.0839	0.72135	0.0:0.0:0.0:1.0	.	261;227	F5H605;A4D1G6	.;.	L	261;243;243;227;227	ENSP00000352561:Q261L;ENSP00000353385:Q243L;ENSP00000399552:Q243L;ENSP00000377959:Q227L;ENSP00000389295:Q227L	ENSP00000352561:Q261L	Q	-	2	0	CALCR	92910974	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.051000	0.57412	2.223000	0.72356	0.455000	0.32223	CAG	.	.		0.453	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	
SULF1	23213	hgsc.bcm.edu	37	8	70551053	70551053	+	Silent	SNP	A	A	G			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr8:70551053A>G	ENST00000260128.4	+	21	3228	c.2511A>G	c.(2509-2511)ggA>ggG	p.G837G	SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000402687.4_Silent_p.G837G|SULF1_ENST00000458141.2_Silent_p.G837G|SULF1_ENST00000419716.3_Silent_p.G837G	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	837					apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			GCTGTCAAGGATATAAGCAGT	0.393																																					p.G837G		Atlas-SNP	.											.	SULF1	153	.	0			c.A2511G						.						93.0	81.0	85.0					8																	70551053		2203	4300	6503	SO:0001819	synonymous_variant	23213	exon21			TCAAGGATATAAG	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.2511A>G	chr8.hg19:g.70551053A>G		297.0	0.0		401.0	27.0	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Silent	SNP	ENST00000260128.4	hg19	CCDS6204.1																																																																																			.	.		0.393	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170	
ZFHX4	79776	hgsc.bcm.edu	37	8	77768190	77768190	+	Silent	SNP	C	C	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr8:77768190C>T	ENST00000521891.2	+	10	9481	c.9033C>T	c.(9031-9033)ctC>ctT	p.L3011L	ZFHX4_ENST00000455469.2_Silent_p.L2966L|ZFHX4_ENST00000050961.6_Silent_p.L2966L|ZFHX4_ENST00000518282.1_Silent_p.L2985L	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2966					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AGTGTACCCTCTGCGGGGTGA	0.463										HNSCC(33;0.089)																											p.L3011L		Atlas-SNP	.											.	ZFHX4	878	.	0			c.C9033T						.						48.0	47.0	48.0					8																	77768190		1928	4134	6062	SO:0001819	synonymous_variant	79776	exon10			TACCCTCTGCGGG		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.9033C>T	chr8.hg19:g.77768190C>T		162.0	0.0		215.0	83.0	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.		0.463	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
CSMD3	114788	hgsc.bcm.edu	37	8	113301744	113301744	+	Missense_Mutation	SNP	C	C	T	rs2193430	byFrequency	TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr8:113301744C>T	ENST00000297405.5	-	57	9242	c.8998G>A	c.(8998-9000)Gtt>Att	p.V3000I	CSMD3_ENST00000352409.3_Missense_Mutation_p.V2930I|CSMD3_ENST00000455883.2_Missense_Mutation_p.V2831I|CSMD3_ENST00000343508.3_Missense_Mutation_p.V2960I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3000	Sushi 21. {ECO:0000255|PROSITE- ProRule:PRU00302}.		V -> L (in dbSNP:rs2193430).			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						TTAGGAGGAACGCCAGGGTGT	0.393										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.V3000I		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G8998A						.						60.0	51.0	54.0					8																	113301744		2203	4300	6503	SO:0001583	missense	114788	exon57			GAGGAACGCCAGG	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.8998G>A	chr8.hg19:g.113301744C>T	ENSP00000297405:p.Val3000Ile	45.0	0.0		59.0	19.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	11.20	1.568966	0.28003	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12	6.01	3.23	0.37069	Complement control module (2);Sushi/SCR/CCP (3);	0.456519	0.21299	N	0.076830	T	0.50103	0.1596	L	0.41710	1.295	0.22446	N	0.999095	B;B;B	0.15141	0.005;0.001;0.012	B;B;B	0.12837	0.002;0.004;0.008	T	0.36841	-0.9731	10	0.33940	T	0.23	.	9.7625	0.40541	0.0:0.7215:0.0:0.2785	.	2831;3000;2960	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	I	2960;3000;2270;2831;2930	ENSP00000345799:V2960I;ENSP00000297405:V3000I;ENSP00000341558:V2270I;ENSP00000412263:V2831I;ENSP00000343124:V2930I	ENSP00000297405:V3000I	V	-	1	0	CSMD3	113370920	0.142000	0.22610	0.502000	0.27614	0.912000	0.54170	0.333000	0.19768	0.415000	0.25817	-0.150000	0.13652	GTT	.	C|0.991;G|0.009		0.393	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
ACO1	48	hgsc.bcm.edu	37	9	32434613	32434613	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr9:32434613G>T	ENST00000309951.6	+	17	2151	c.2013G>T	c.(2011-2013)ttG>ttT	p.L671F	ACO1_ENST00000379923.1_Missense_Mutation_p.L671F|ACO1_ENST00000541043.1_Missense_Mutation_p.L572F	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	671					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		TGCTAAATTTGGGAGATTCGG	0.438																																					p.L671F		Atlas-SNP	.											.	ACO1	149	.	0			c.G2013T						.						215.0	209.0	211.0					9																	32434613		2203	4300	6503	SO:0001583	missense	48	exon17			AAATTTGGGAGAT	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"""aconitate hydratase, cytoplasmic"""	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.2013G>T	chr9.hg19:g.32434613G>T	ENSP00000309477:p.Leu671Phe	130.0	0.0		114.0	5.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Missense_Mutation	SNP	ENST00000309951.6	hg19	CCDS6525.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.268171	0.23136	.	.	ENSG00000122729	ENST00000432017;ENST00000309951;ENST00000379923;ENST00000541043	T;T;T	0.45668	0.89;0.89;1.92	5.78	3.93	0.45458	Aconitase/3-isopropylmalate dehydratase, swivel (2);	0.067179	0.64402	D	0.000010	T	0.35624	0.0938	L	0.52206	1.635	0.58432	D	0.999999	P;B	0.50369	0.934;0.153	P;B	0.45660	0.489;0.064	T	0.12863	-1.0531	10	0.16420	T	0.52	-11.8682	6.6508	0.22961	0.1578:0.0:0.6978:0.1444	.	707;671	Q59FI0;P21399	.;ACOC_HUMAN	F	707;671;671;572	ENSP00000309477:L671F;ENSP00000369255:L671F;ENSP00000438733:L572F	ENSP00000309477:L671F	L	+	3	2	ACO1	32424613	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	0.971000	0.29396	0.787000	0.33731	0.655000	0.94253	TTG	.	.		0.438	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197	
TLR4	7099	hgsc.bcm.edu	37	9	120476829	120476829	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr9:120476829G>T	ENST00000355622.6	+	3	2524	c.2423G>T	c.(2422-2424)tGg>tTg	p.W808L	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.W768L	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	808	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.W808F(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	CACATCTTCTGGAGACGACTC	0.537																																					p.W808L		Atlas-SNP	.											.,1	TLR4	220	.	1	Substitution - Missense(1)	lung(1)	c.G2423T						.						95.0	98.0	97.0					9																	120476829		2203	4300	6503	SO:0001583	missense	7099	exon3			TCTTCTGGAGACG	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"""CD molecules"""	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.2423G>T	chr9.hg19:g.120476829G>T	ENSP00000363089:p.Trp808Leu	96.0	0.0		90.0	66.0	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	hg19	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.464376	0.84425	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.16073	2.37;2.37	6.03	6.03	0.97812	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.000000	0.64402	D	0.000004	T	0.41949	0.1181	M	0.80982	2.52	0.58432	D	0.999999	D	0.69078	0.997	D	0.63381	0.914	T	0.20605	-1.0270	10	0.56958	D	0.05	.	14.4478	0.67364	0.0:0.0:0.8533:0.1467	.	808	O00206	TLR4_HUMAN	L	768;808	ENSP00000377997:W768L;ENSP00000363089:W808L	ENSP00000363089:W808L	W	+	2	0	TLR4	119516650	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.199000	0.77831	2.861000	0.98227	0.655000	0.94253	TGG	.	.		0.537	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554	
GPR144	347088	hgsc.bcm.edu	37	9	127215648	127215648	+	Silent	SNP	G	G	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr9:127215648G>T	ENST00000334810.1	+	4	672	c.672G>T	c.(670-672)ctG>ctT	p.L224L				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	224	Pentaxin.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)	4						GCTGGGCGCTGTTCTCCGATG	0.771																																					p.L224L		Atlas-SNP	.											.	GPR144	33	.	0			c.G672T						.						1.0	1.0	1.0					9																	127215648		375	858	1233	SO:0001819	synonymous_variant	347088	exon4			GGCGCTGTTCTCC	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.672G>T	chr9.hg19:g.127215648G>T		31.0	0.0		14.0	10.0	NM_001161808	Q86SL4|Q8NH12	Silent	SNP	ENST00000334810.1	hg19	CCDS48016.1																																																																																			.	.		0.771	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
GPR158	57512	hgsc.bcm.edu	37	10	25887038	25887038	+	Missense_Mutation	SNP	C	C	T	rs143609365		TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr10:25887038C>T	ENST00000376351.3	+	11	2842	c.2483C>T	c.(2482-2484)aCg>aTg	p.T828M	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	828					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						AGAGACCAAACGGAAGAGTCC	0.468																																					p.T828M		Atlas-SNP	.											.	GPR158	255	.	0			c.C2483T						.						119.0	130.0	126.0					10																	25887038		2203	4300	6503	SO:0001583	missense	57512	exon11			ACCAAACGGAAGA	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"""GPCR / Class C : Orphans"""	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.2483C>T	chr10.hg19:g.25887038C>T	ENSP00000365529:p.Thr828Met	367.0	0.0		440.0	168.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.105543	0.77096	.	.	ENSG00000151025	ENST00000376351	T	0.61158	0.13	5.88	5.88	0.94601	.	0.548889	0.17149	N	0.185152	T	0.46502	0.1396	N	0.22421	0.69	0.09310	N	1	D	0.53151	0.958	B	0.41619	0.361	T	0.48536	-0.9027	10	0.49607	T	0.09	.	15.6895	0.77439	0.0:0.8638:0.1362:0.0	.	828	Q5T848	GP158_HUMAN	M	828	ENSP00000365529:T828M	ENSP00000365529:T828M	T	+	2	0	GPR158	25927044	0.003000	0.15002	0.007000	0.13788	0.831000	0.47069	1.575000	0.36493	2.779000	0.95612	0.650000	0.86243	ACG	.	C|1.000;G|0.000		0.468	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110	
P4HA1	5033	hgsc.bcm.edu	37	10	74810844	74810844	+	Nonsense_Mutation	SNP	G	G	T	rs200368222		TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr10:74810844G>T	ENST00000307116.2	-	7	983	c.867C>A	c.(865-867)taC>taA	p.Y289*	P4HA1_ENST00000412021.2_Nonsense_Mutation_p.Y289*|P4HA1_ENST00000440381.1_Nonsense_Mutation_p.Y289*|P4HA1_ENST00000373008.2_Nonsense_Mutation_p.Y289*|P4HA1_ENST00000394890.2_Nonsense_Mutation_p.Y289*|P4HA1_ENST00000263556.3_Nonsense_Mutation_p.Y289*			P13674	P4HA1_HUMAN	prolyl 4-hydroxylase, alpha polypeptide I	289					collagen fibril organization (GO:0030199)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|procollagen-proline 4-dioxygenase complex (GO:0016222)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	ACAGCATTTCGTACTTCTGTC	0.423																																					p.Y289X	Colon(147;367 2405 2662 52127)	Atlas-SNP	.											P4HA1_ENST00000412021,NS,carcinoma,0,3	P4HA1	86	.	0			c.C867A						.						300.0	283.0	289.0					10																	74810844		2203	4300	6503	SO:0001587	stop_gained	5033	exon7			CATTTCGTACTTC		CCDS7320.1, CCDS41537.1, CCDS44432.1	10q21.3-q23.1	2008-12-09	2008-12-09		ENSG00000122884	ENSG00000122884	1.14.11.2		8546	protein-coding gene	gene with protein product	"""collagen prolyl 4-hydroxylase alpha(I)"""	176710	"""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I"""	P4HA		2556027	Standard	NM_001017962		Approved	C-P4Halpha(I)	uc001jtg.3	P13674	OTTHUMG00000018449	ENST00000307116.2:c.867C>A	chr10.hg19:g.74810844G>T	ENSP00000307318:p.Tyr289*	102.0	0.0		124.0	5.0	NM_001142596	C9JL12|Q15082|Q15083|Q5VSQ5	Nonsense_Mutation	SNP	ENST00000307116.2	hg19		.	.	.	.	.	.	.	.	.	.	G	37	6.359858	0.97502	.	.	ENSG00000122884	ENST00000307116;ENST00000373008;ENST00000412021;ENST00000394890;ENST00000263556;ENST00000440381	.	.	.	5.67	0.0145	0.14100	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.1147	6.1825	0.20480	0.4442:0.1275:0.4283:0.0	.	.	.	.	X	289	.	ENSP00000263556:Y289X	Y	-	3	2	P4HA1	74480850	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.176000	0.31957	0.187000	0.20147	0.557000	0.71058	TAC	.	.		0.423	P4HA1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000048601.1	NM_000917	
SPTBN2	6712	hgsc.bcm.edu	37	11	66472298	66472298	+	Silent	SNP	G	G	A			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr11:66472298G>A	ENST00000533211.1	-	15	2780	c.2449C>T	c.(2449-2451)Ctg>Ttg	p.L817L	SPTBN2_ENST00000529997.1_Silent_p.L817L|SPTBN2_ENST00000309996.2_Silent_p.L817L			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	817					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GTGCGGCTCAGTGTGGGGGGC	0.721																																					p.L817L		Atlas-SNP	.											.	SPTBN2	188	.	0			c.C2449T						.						19.0	20.0	20.0					11																	66472298		2200	4292	6492	SO:0001819	synonymous_variant	6712	exon14			GGCTCAGTGTGGG	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.2449C>T	chr11.hg19:g.66472298G>A		51.0	0.0		53.0	22.0	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	hg19	CCDS8150.1																																																																																			.	.		0.721	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
SUV420H1	51111	hgsc.bcm.edu	37	11	67926442	67926442	+	Silent	SNP	A	A	G			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr11:67926442A>G	ENST00000304363.4	-	11	1724	c.1371T>C	c.(1369-1371)caT>caC	p.H457H		NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	457					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						GCCGCTTGCAATGATTTCTCA	0.358																																					p.H457H		Atlas-SNP	.											.	SUV420H1	125	.	0			c.T1371C						.						77.0	81.0	80.0					11																	67926442		2200	4294	6494	SO:0001819	synonymous_variant	51111	exon11			CTTGCAATGATTT	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"""Chromatin-modifying enzymes / K-methyltransferases"""	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.1371T>C	chr11.hg19:g.67926442A>G		110.0	0.0		134.0	61.0	NM_017635	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Silent	SNP	ENST00000304363.4	hg19	CCDS31623.1																																																																																			.	.		0.358	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635	
MMP7	4316	hgsc.bcm.edu	37	11	102395766	102395766	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr11:102395766G>A	ENST00000260227.4	-	4	566	c.514C>T	c.(514-516)Cca>Tca	p.P172S		NM_002423.3	NP_002414.1	P09237	MMP7_HUMAN	matrix metallopeptidase 7 (matrilysin, uterine)	172					antibacterial peptide secretion (GO:0002779)|collagen catabolic process (GO:0030574)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_cancers(8;2.04e-05)|all_epithelial(12;0.00053)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0105)|all cancers(10;0.0496)|Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0147)	Marimastat(DB00786)	GTGTTTCCTGGCCCATCAAAT	0.473																																					p.P172S		Atlas-SNP	.											.	MMP7	27	.	0			c.C514T						.						90.0	76.0	81.0					11																	102395766		2203	4299	6502	SO:0001583	missense	4316	exon4			TTCCTGGCCCATC	Z11887	CCDS8317.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000137673	ENSG00000137673	3.4.24.23		7174	protein-coding gene	gene with protein product		178990	"""matrix metalloproteinase 7 (matrilysin, uterine)"""	MPSL1		8978768	Standard	NM_002423		Approved	PUMP-1	uc001phb.3	P09237	OTTHUMG00000048193	ENST00000260227.4:c.514C>T	chr11.hg19:g.102395766G>A	ENSP00000260227:p.Pro172Ser	135.0	0.0		149.0	52.0	NM_002423	Q9BTK9	Missense_Mutation	SNP	ENST00000260227.4	hg19	CCDS8317.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.208178	0.58343	.	.	ENSG00000137673	ENST00000260227	T	0.20738	2.05	5.12	5.12	0.69794	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.123708	0.34133	N	0.004235	T	0.41903	0.1179	M	0.79011	2.435	0.09310	N	0.999999	D;D	0.65815	0.995;0.995	P;P	0.59487	0.858;0.746	T	0.36744	-0.9735	10	0.72032	D	0.01	-23.0146	11.6743	0.51422	0.0:0.1318:0.732:0.1362	.	172;172	Q53GF1;P09237	.;MMP7_HUMAN	S	172	ENSP00000260227:P172S	ENSP00000260227:P172S	P	-	1	0	MMP7	101900976	0.646000	0.27295	0.995000	0.50966	0.745000	0.42441	2.377000	0.44300	2.399000	0.81585	0.655000	0.94253	CCA	.	.		0.473	MMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109633.2		
PCSK7	9159	hgsc.bcm.edu	37	11	117097882	117097882	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr11:117097882G>A	ENST00000320934.3	-	5	1390	c.760C>T	c.(760-762)Cgc>Tgc	p.R254C	PCSK7_ENST00000540028.1_5'Flank	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	254	Peptidase S8.				peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CCTGCGATGCGGCTCCCGTAG	0.582			T	IGH@	MLCLS						OREG0021371	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R254C		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.C760T						.						80.0	65.0	70.0					11																	117097882		2201	4296	6497	SO:0001583	missense	9159	exon5			CGATGCGGCTCCC	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.760C>T	chr11.hg19:g.117097882G>A	ENSP00000325917:p.Arg254Cys	57.0	0.0	1478	70.0	20.0	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Missense_Mutation	SNP	ENST00000320934.3	hg19	CCDS8382.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.234474	0.79800	.	.	ENSG00000160613	ENST00000320934;ENST00000543900;ENST00000525027	D;T	0.82081	-1.57;0.85	5.61	4.61	0.57282	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.170822	0.48767	D	0.000170	D	0.90034	0.6888	M	0.82056	2.57	0.80722	D	1	D	0.76494	0.999	P	0.60886	0.88	D	0.91478	0.5202	10	0.87932	D	0	-27.6348	16.3613	0.83269	0.0:0.0:0.8594:0.1406	.	254	Q16549	PCSK7_HUMAN	C	254	ENSP00000325917:R254C;ENSP00000431181:R254C	ENSP00000325917:R254C	R	-	1	0	PCSK7	116603092	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.071000	0.57556	2.633000	0.89246	0.655000	0.94253	CGC	.	.		0.582	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
GLB1L3	112937	hgsc.bcm.edu	37	11	134179570	134179570	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr11:134179570G>A	ENST00000431683.2	+	11	1012	c.1012G>A	c.(1012-1014)Gta>Ata	p.V338I		NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	338					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		CTCCTTCAATGTATATATGTT	0.438																																					p.V338I		Atlas-SNP	.											.	GLB1L3	102	.	0			c.G1012A						.						89.0	84.0	86.0					11																	134179570		1889	4097	5986	SO:0001583	missense	112937	exon11			TTCAATGTATATA		CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.1012G>A	chr11.hg19:g.134179570G>A	ENSP00000396615:p.Val338Ile	102.0	0.0		109.0	47.0	NM_001080407	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Missense_Mutation	SNP	ENST00000431683.2	hg19	CCDS44780.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.977369	0.34848	.	.	ENSG00000166105	ENST00000431683	D	0.97850	-4.57	4.76	-2.19	0.07015	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	.	.	.	.	D	0.91012	0.7173	N	0.13098	0.295	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.82725	-0.0315	9	0.37606	T	0.19	.	1.0589	0.01596	0.3603:0.1474:0.3414:0.1509	.	338	Q8NCI6	GLBL3_HUMAN	I	338	ENSP00000396615:V338I	ENSP00000396615:V338I	V	+	1	0	GLB1L3	133684780	0.000000	0.05858	0.000000	0.03702	0.908000	0.53690	-0.110000	0.10824	-0.171000	0.10797	0.455000	0.32223	GTA	.	.		0.438	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416	
GALNT8	26290	hgsc.bcm.edu	37	12	4829970	4829970	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:4829970A>T	ENST00000252318.2	+	1	464	c.127A>T	c.(127-129)Agg>Tgg	p.R43W	RP11-234B24.2_ENST00000527518.1_lincRNA|RP11-234B24.6_ENST00000544741.2_Intron	NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	43					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						TGGTCTCCACAGGGAGCTTCC	0.473																																					p.R43W	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											.	GALNT8	89	.	0			c.A127T						.						100.0	102.0	101.0					12																	4829970		2203	4300	6503	SO:0001583	missense	26290	exon1			CTCCACAGGGAGC	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4130	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 8"""	606250	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"""			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.127A>T	chr12.hg19:g.4829970A>T	ENSP00000252318:p.Arg43Trp	156.0	0.0		227.0	91.0	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	hg19	CCDS8533.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.471916	0.43942	.	.	ENSG00000130035	ENST00000252318	T	0.55052	0.54	3.74	0.084	0.14436	.	119.586000	0.00166	N	0.000000	T	0.30572	0.0769	N	0.08118	0	0.09310	N	1	P	0.38788	0.647	B	0.32289	0.143	T	0.31943	-0.9925	10	0.66056	D	0.02	.	5.7037	0.17897	0.6194:0.0:0.3806:0.0	.	43	Q9NY28	GALT8_HUMAN	W	43	ENSP00000252318:R43W	ENSP00000252318:R43W	R	+	1	2	GALNT8	4700231	0.000000	0.05858	0.001000	0.08648	0.474000	0.32979	-0.094000	0.11094	0.147000	0.19030	0.374000	0.22700	AGG	.	.		0.473	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417	
PRB3	5544	hgsc.bcm.edu	37	12	11421025	11421025	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:11421025G>C	ENST00000279573.7	-	3	293	c.158C>G	c.(157-159)cCt>cGt	p.P53R	PRB3_ENST00000381842.3_Missense_Mutation_p.P53R|PRB3_ENST00000538488.1_Missense_Mutation_p.P53R|PRB3_ENST00000440870.3_5'UTR			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	53	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.		P -> C (in Gl-8; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:2171329}.	PQRTPPP -> SQGPPPR (in Ref. 1; CAA30728). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			CTTTCCTGGAGGAGGTGGGGT	0.607																																					p.P53R		Atlas-SNP	.											PRB3_ENST00000538488,NS,malignant_melanoma,0,4	PRB3	84	.	0			c.C158G						.						156.0	164.0	161.0					12																	11421025		2195	4297	6492	SO:0001583	missense	5544	exon3			CCTGGAGGAGGTG			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.158C>G	chr12.hg19:g.11421025G>C	ENSP00000279573:p.Pro53Arg	69.0	2.0		100.0	6.0	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Missense_Mutation	SNP	ENST00000279573.7	hg19		.	.	.	.	.	.	.	.	.	.	.	0.001	-3.726183	0.00005	.	.	ENSG00000197870	ENST00000381842;ENST00000538488	T;T	0.09630	2.96;2.96	0.522	-1.04	0.10068	.	0.000000	0.35677	U	0.003053	T	0.02455	0.0075	.	.	.	0.09310	N	1	P	0.41748	0.761	B	0.31869	0.137	T	0.50759	-0.8790	8	0.05959	T	0.93	.	.	.	.	.	53	Q04118	PRB3_HUMAN	R	53	ENSP00000371264:P53R;ENSP00000442626:P53R	ENSP00000279573:P53R	P	-	2	0	PRB3	11312292	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-2.740000	0.00799	-3.021000	0.00269	-4.297000	0.00007	CCT	.	.		0.607	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249	
NCKAP5L	57701	hgsc.bcm.edu	37	12	50190546	50190546	+	Missense_Mutation	SNP	G	G	A	rs369718554		TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:50190546G>A	ENST00000335999.6	-	8	1298	c.1097C>T	c.(1096-1098)gCg>gTg	p.A366V		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	362	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						CTGTGGGGGCGCCTGGTCTGG	0.657																																					p.A366V		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.C1097T						.	G	VAL/ALA	1,3805		0,1,1902	25.0	30.0	28.0		1097	2.7	0.9	12		28	0,8186		0,0,4093	no	missense	NCKAP5L	NM_001037806.3	64	0,1,5995	AA,AG,GG		0.0,0.0263,0.0083	benign	366/1335	50190546	1,11991	1903	4093	5996	SO:0001583	missense	57701	exon8			GGGGGCGCCTGGT	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"""KIAA1602"""	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.1097C>T	chr12.hg19:g.50190546G>A	ENSP00000337998:p.Ala366Val	84.0	0.0		87.0	26.0	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Missense_Mutation	SNP	ENST00000335999.6	hg19	CCDS41781.2	.	.	.	.	.	.	.	.	.	.	G	18.52	3.642759	0.67244	2.63E-4	0.0	ENSG00000167566	ENST00000335999;ENST00000354423	T	0.44881	0.91	3.6	2.71	0.32032	.	0.202420	0.24864	N	0.034983	T	0.22742	0.0549	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.16837	-1.0389	10	0.32370	T	0.25	-7.3521	12.1469	0.54028	0.0:0.8229:0.1771:0.0	.	362	E2QRB5	.	V	366;362	ENSP00000337998:A366V	ENSP00000337998:A366V	A	-	2	0	NCKAP5L	48476813	0.000000	0.05858	0.897000	0.35233	0.927000	0.56198	0.510000	0.22723	0.875000	0.35847	-0.384000	0.06662	GCG	.	.		0.657	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497	
SMARCC2	6601	hgsc.bcm.edu	37	12	56566407	56566407	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:56566407G>A	ENST00000267064.4	-	18	1818	c.1732C>T	c.(1732-1734)Cgc>Tgc	p.R578C	SMARCC2_ENST00000394023.3_Missense_Mutation_p.R609C|SMARCC2_ENST00000550164.1_Missense_Mutation_p.R609C|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000347471.4_Missense_Mutation_p.R609C	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	578					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)			ATGTCTGTGCGCAGCCCAAAG	0.498																																					p.R609C		Atlas-SNP	.											.	SMARCC2	212	.	0			c.C1825T						.						212.0	190.0	198.0					12																	56566407		2203	4300	6503	SO:0001583	missense	6601	exon19			CTGTGCGCAGCCC	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.1732C>T	chr12.hg19:g.56566407G>A	ENSP00000267064:p.Arg578Cys	104.0	0.0		133.0	23.0	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	hg19	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.568502	0.65651	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T	0.51574	0.76;0.79;0.7	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.73353	0.3576	M	0.88906	2.99	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.80764	0.985;0.994;0.985;0.985;0.994	T	0.74893	-0.3509	10	0.35671	T	0.21	-9.4038	17.8293	0.88676	0.0:0.0:1.0:0.0	.	498;609;613;578;609	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	C	609;609;609;578	ENSP00000449396:R609C;ENSP00000302919:R609C;ENSP00000267064:R578C	ENSP00000267064:R578C	R	-	1	0	SMARCC2	54852674	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.496000	0.66918	2.575000	0.86900	0.462000	0.41574	CGC	.	.		0.498	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		
LTA4H	4048	hgsc.bcm.edu	37	12	96394788	96394788	+	Silent	SNP	C	C	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:96394788C>T	ENST00000228740.2	-	19	1956	c.1815G>A	c.(1813-1815)ggG>ggA	p.G605G	LTA4H_ENST00000413268.2_3'UTR|LTA4H_ENST00000552789.1_Silent_p.G581G|RP11-256L6.3_ENST00000551849.1_RNA	NM_000895.2	NP_000886.1	P09960	LKHA4_HUMAN	leukotriene A4 hydrolase	605					arachidonic acid metabolic process (GO:0019369)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|peptide catabolic process (GO:0043171)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|leukotriene-A4 hydrolase activity (GO:0004463)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(3)|lung(4)|skin(2)|stomach(1)	12					Captopril(DB01197)	TTAAGTCTTTCCCCACCAGCA	0.408																																					p.G605G		Atlas-SNP	.											.	LTA4H	38	.	0			c.G1815A						.						130.0	120.0	123.0					12																	96394788		2203	4300	6503	SO:0001819	synonymous_variant	4048	exon19			GTCTTTCCCCACC	BC032528	CCDS9059.1, CCDS58266.1, CCDS58267.1	12q22	2005-10-06				ENSG00000111144	3.3.2.6		6710	protein-coding gene	gene with protein product		151570				7628486	Standard	NM_000895		Approved		uc001ten.2	P09960	OTTHUMG00000170355	ENST00000228740.2:c.1815G>A	chr12.hg19:g.96394788C>T		86.0	0.0		124.0	11.0	NM_000895	B4DNQ9|F8VV40|Q6IAT6|Q9UCT7	Silent	SNP	ENST00000228740.2	hg19	CCDS9059.1																																																																																			.	.		0.408	LTA4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408655.1	NM_000895	
DAO	1610	hgsc.bcm.edu	37	12	109288134	109288134	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:109288134G>T	ENST00000228476.3	+	7	807	c.603G>T	c.(601-603)caG>caT	p.Q201H	DAO_ENST00000551281.1_Missense_Mutation_p.Q135H	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	201					cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	GCCGGGGGCAGATCATGAAGG	0.537																																					p.Q201H		Atlas-SNP	.											.	DAO	58	.	0			c.G603T						.						50.0	40.0	43.0					12																	109288134		2203	4300	6503	SO:0001583	missense	1610	exon7			GGGGCAGATCATG	D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1.4.3.3		2671	protein-coding gene	gene with protein product		124050				1356107, 8182053	Standard	NM_001917		Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000228476.3:c.603G>T	chr12.hg19:g.109288134G>T	ENSP00000228476:p.Gln201His	126.0	0.0		129.0	55.0	NM_001917	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	hg19	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.740582	0.89573	.	.	ENSG00000110887	ENST00000551281;ENST00000228476;ENST00000547768	D;D;D	0.82433	-1.61;-1.61;-1.61	5.51	5.51	0.81932	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	D	0.92619	0.7655	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.93376	0.6739	10	0.62326	D	0.03	-14.4171	18.047	0.89335	0.0:0.0:1.0:0.0	.	201;184	P14920;Q7Z312	OXDA_HUMAN;.	H	135;201;78	ENSP00000446853:Q135H;ENSP00000228476:Q201H;ENSP00000449967:Q78H	ENSP00000228476:Q201H	Q	+	3	2	DAO	107812263	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.747000	0.47475	2.609000	0.88269	0.499000	0.49734	CAG	.	.		0.537	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1		
SBNO1	55206	hgsc.bcm.edu	37	12	123789129	123789129	+	Splice_Site	SNP	C	C	G			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:123789129C>G	ENST00000602398.1	-	29	3895	c.3768G>C	c.(3766-3768)aaG>aaC	p.K1256N	SBNO1_ENST00000602750.1_Splice_Site_p.K1255N|SBNO1_ENST00000267176.4_Splice_Site_p.K1255N|SBNO1_ENST00000420886.2_Splice_Site_p.K1256N			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1256					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		GAAAAAATACCTTCTTATATT	0.348																																					p.K1256N		Atlas-SNP	.											.	SBNO1	138	.	0			c.G3768C						.						25.0	27.0	26.0					12																	123789129		2194	4292	6486	SO:0001630	splice_region_variant	55206	exon28			AAATACCTTCTTA	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.3768+1G>C	chr12.hg19:g.123789129C>G		342.0	1.0		427.0	153.0	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	hg19	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.541803	0.85917	.	.	ENSG00000139697	ENST00000420886;ENST00000267176	D;D	0.83163	-1.69;-1.69	6.17	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.90724	0.7089	M	0.84219	2.685	0.80722	D	1	P;P;D	0.67145	0.455;0.59;0.996	B;B;D	0.64595	0.111;0.223;0.927	D	0.90685	0.4608	9	.	.	.	-21.7595	15.9972	0.80260	0.0:0.935:0.0:0.065	.	1256;1255;367	A3KN83;A3KN83-2;B3KUC1	SBNO1_HUMAN;.;.	N	1256;1255	ENSP00000387361:K1256N;ENSP00000267176:K1255N	.	K	-	3	2	SBNO1	122355082	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	5.704000	0.68347	2.941000	0.99782	0.655000	0.94253	AAG	.	.		0.348	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	Missense_Mutation
INO80	54617	hgsc.bcm.edu	37	15	41313209	41313209	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr15:41313209G>C	ENST00000361937.3	-	26	3587	c.3163C>G	c.(3163-3165)Cct>Gct	p.P1055A	INO80_ENST00000401393.3_Missense_Mutation_p.P1055A|RP11-540O11.4_ENST00000558967.1_RNA			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1055	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GCCAGTTCAGGGGCCCCATTC	0.507																																					p.P1055A		Atlas-SNP	.											INOC1,NS,malignant_melanoma,0,2	INO80	122	.	0			c.C3163G						.						81.0	74.0	76.0					15																	41313209		2203	4300	6503	SO:0001583	missense	54617	exon26			GTTCAGGGGCCCC	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"""INO80 complex subunits"""	26956	protein-coding gene	gene with protein product	"""INO80 complex subunit A"""	610169	"""INO80 complex homolog 1 (S. cerevisiae)"", ""INO80 homolog (S. cerevisiae)"""	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.3163C>G	chr15.hg19:g.41313209G>C	ENSP00000355205:p.Pro1055Ala	86.0	0.0		83.0	36.0	NM_017553	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	hg19	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.137486	0.77775	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.91407	-2.84;-2.84	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.93628	0.7965	L	0.49126	1.545	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.91614	0.5305	10	0.28530	T	0.3	.	19.0427	0.93008	0.0:0.0:1.0:0.0	.	1055	Q9ULG1	INO80_HUMAN	A	1055	ENSP00000355205:P1055A;ENSP00000384686:P1055A	ENSP00000355205:P1055A	P	-	1	0	INO80	39100501	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.669000	0.91163	2.722000	0.93159	0.655000	0.94253	CCT	.	.		0.507	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553	
ADAM10	102	hgsc.bcm.edu	37	15	58891888	58891888	+	Silent	SNP	A	A	C			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr15:58891888A>C	ENST00000260408.3	-	15	2504	c.2061T>G	c.(2059-2061)gcT>gcG	p.A687A	ADAM10_ENST00000402627.1_Intron|ADAM10_ENST00000396140.2_Silent_p.A386A|ADAM10_ENST00000561288.1_Intron|snoU13_ENST00000458913.1_RNA	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	687					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		GCATGATCAGAGCAATTCCCA	0.338																																					p.A687A		Atlas-SNP	.											.	ADAM10	59	.	0			c.T2061G						.						125.0	122.0	123.0					15																	58891888		2192	4292	6484	SO:0001819	synonymous_variant	102	exon15			GATCAGAGCAATT	AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	188	protein-coding gene	gene with protein product		602192	"""a disintegrin and metalloproteinase domain 10"""			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.2061T>G	chr15.hg19:g.58891888A>C		127.0	0.0		144.0	56.0	NM_001110	B4DU28|Q10742|Q92650	Silent	SNP	ENST00000260408.3	hg19	CCDS10167.1																																																																																			.	.		0.338	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2	NM_001110	
SNN	8303	hgsc.bcm.edu	37	16	11770176	11770176	+	Silent	SNP	C	C	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr16:11770176C>T	ENST00000329565.5	+	2	473	c.261C>T	c.(259-261)caC>caT	p.H87H	TXNDC11_ENST00000570917.1_5'Flank	NM_003498.5	NP_003489.1	O75324	SNN_HUMAN	stannin	87					response to abiotic stimulus (GO:0009628)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				endometrium(1)	1						CGGAAGTCCACGGCTGAGCCA	0.622																																					p.H87H		Atlas-SNP	.											.	SNN	7	.	0			c.C261T						.						58.0	39.0	46.0					16																	11770176		2197	4300	6497	SO:0001819	synonymous_variant	8303	exon2			AGTCCACGGCTGA	AF030196	CCDS10549.1	16p13	2008-02-05			ENSG00000184602	ENSG00000184602			11149	protein-coding gene	gene with protein product		603032				9657854	Standard	NM_003498		Approved		uc002dbf.3	O75324	OTTHUMG00000090535	ENST00000329565.5:c.261C>T	chr16.hg19:g.11770176C>T		133.0	0.0		154.0	60.0	NM_003498	D3DUG4|Q6FGI0	Silent	SNP	ENST00000329565.5	hg19	CCDS10549.1																																																																																			.	.		0.622	SNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207059.1	NM_003498	
KRT33A	3883	hgsc.bcm.edu	37	17	39506775	39506775	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr17:39506775G>A	ENST00000007735.3	-	1	289	c.245C>T	c.(244-246)gCg>gTg	p.A82V		NM_004138.3	NP_004129.2	O76009	KT33A_HUMAN	keratin 33A	82	Coil 1A.|Rod.			A -> T (in Ref. 3; BAG36784). {ECO:0000305}.		extracellular space (GO:0005615)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	21		Breast(137;0.000496)				CTCCAGCTCCGCGTTGTCCCG	0.607																																					p.A82V		Atlas-SNP	.											.	KRT33A	53	.	0			c.C245T						.						91.0	84.0	86.0					17																	39506775		2203	4300	6503	SO:0001583	missense	3883	exon1			AGCTCCGCGTTGT	Y16788	CCDS11388.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000006059	ENSG00000006059		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6450	protein-coding gene	gene with protein product	"""hard keratin type I 3I"""	602761	"""keratin, hair, acidic, 3A"""	KRTHA3A		7565656, 16831889	Standard	NM_004138		Approved	Ha-3I, Krt1-3	uc002hwk.2	O76009	OTTHUMG00000133432	ENST00000007735.3:c.245C>T	chr17.hg19:g.39506775G>A	ENSP00000007735:p.Ala82Val	148.0	0.0		212.0	81.0	NM_004138	B2RA87|Q6NTB9|Q6ZZB9	Missense_Mutation	SNP	ENST00000007735.3	hg19	CCDS11388.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.422370	0.62622	.	.	ENSG00000006059	ENST00000007735	D	0.89415	-2.51	5.22	4.24	0.50183	Filament (1);	0.000000	0.64402	D	0.000004	D	0.89904	0.6850	M	0.84082	2.675	0.23959	N	0.99635	P	0.37176	0.586	B	0.39152	0.292	D	0.84981	0.0888	10	0.66056	D	0.02	.	13.8543	0.63517	0.0:0.2917:0.7083:0.0	.	82	O76009	KT33A_HUMAN	V	82	ENSP00000007735:A82V	ENSP00000007735:A82V	A	-	2	0	KRT33A	36760301	0.068000	0.21057	0.973000	0.42090	0.981000	0.71138	2.440000	0.44855	1.554000	0.49487	0.650000	0.86243	GCG	.	.		0.607	KRT33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257295.1	NM_004138	
DSG3	1830	hgsc.bcm.edu	37	18	29039050	29039050	+	Silent	SNP	C	C	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr18:29039050C>T	ENST00000257189.4	+	5	510	c.427C>T	c.(427-429)Cta>Tta	p.L143L		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	143	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ACCACTTATACTAACGGTTAA	0.353																																					p.L143L		Atlas-SNP	.											.	DSG3	172	.	0			c.C427T						.						78.0	79.0	78.0					18																	29039050		2203	4300	6503	SO:0001819	synonymous_variant	1830	exon5			CTTATACTAACGG	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.427C>T	chr18.hg19:g.29039050C>T		317.0	1.0		429.0	156.0	NM_001944	A8K2V2	Silent	SNP	ENST00000257189.4	hg19	CCDS11898.1																																																																																			.	.		0.353	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
ZBTB7C	201501	hgsc.bcm.edu	37	18	45567333	45567333	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr18:45567333C>T	ENST00000588982.1	-	3	647	c.146G>A	c.(145-147)cGc>cAc	p.R49H	ZBTB7C_ENST00000535628.2_Missense_Mutation_p.R49H|ZBTB7C_ENST00000332053.2_Missense_Mutation_p.R49H|ZBTB7C_ENST00000590800.1_Missense_Mutation_p.R49H|ZBTB7C_ENST00000586438.1_Missense_Mutation_p.R49H			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	49	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						CAGGACGGAGCGGTGGGTCCG	0.597																																					p.R49H		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.G146A						.						80.0	74.0	76.0					18																	45567333		2203	4300	6503	SO:0001583	missense	201501	exon2			ACGGAGCGGTGGG	Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	31700	protein-coding gene	gene with protein product			"""zinc finger and BTB domain containing 36"""	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.146G>A	chr18.hg19:g.45567333C>T	ENSP00000468782:p.Arg49His	77.0	0.0		81.0	28.0	NM_001039360	O73453	Missense_Mutation	SNP	ENST00000588982.1	hg19	CCDS32830.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.098628	0.76870	.	.	ENSG00000184828	ENST00000535628;ENST00000332053	T;T	0.75367	-0.93;-0.93	5.04	5.04	0.67666	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.90988	0.7166	H	0.98351	4.21	0.54753	D	0.999984	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.99;0.945;0.945	D	0.93689	0.7005	10	0.87932	D	0	.	12.7794	0.57469	0.0:0.9201:0.0:0.0799	.	49;49;49	B4DKU0;B2RG49;A1YPR0	.;.;ZBT7C_HUMAN	H	49	ENSP00000439781:R49H;ENSP00000328732:R49H	ENSP00000328732:R49H	R	-	2	0	ZBTB7C	43821331	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.083000	0.71326	2.332000	0.79248	0.561000	0.74099	CGC	.	.		0.597	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360	
CPAMD8	27151	hgsc.bcm.edu	37	19	17100489	17100489	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr19:17100489G>T	ENST00000443236.1	-	13	1531	c.1500C>A	c.(1498-1500)tgC>tgA	p.C500*	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	453						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						GCTGCAGGTAGCACTGGCTGG	0.607																																					p.C500X		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C1500A						.						39.0	47.0	45.0					19																	17100489		1959	4136	6095	SO:0001587	stop_gained	27151	exon13			CAGGTAGCACTGG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1500C>A	chr19.hg19:g.17100489G>T	ENSP00000402505:p.Cys500*	131.0	0.0		137.0	71.0	NM_015692	Q8NC09|Q9ULD7	Nonsense_Mutation	SNP	ENST00000443236.1	hg19	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.185569|6.185569	0.97357|0.97357	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000443236|ENST00000291440	.|.	.|.	.|.	2.91|2.91	2.91|2.91	0.33838|0.33838	.|.	.|0.000000	.|0.64402	.|U	.|0.000001	T|.	0.55401|.	0.1918|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.49799|.	-0.8901|.	4|.	.|0.25106	.|T	.|0.35	.|.	10.1768|10.1768	0.42943|0.42943	0.1068:0.0:0.8932:0.0|0.1068:0.0:0.8932:0.0	.|.	.|.	.|.	.|.	D|X	511|500	.|.	.|ENSP00000291440:C500X	A|C	-|-	2|3	0|2	CPAMD8|CPAMD8	16961489|16961489	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.927000|0.927000	0.56198|0.56198	1.798000|1.798000	0.38814|0.38814	1.366000|1.366000	0.46076|0.46076	0.561000|0.561000	0.74099|0.74099	GCT|TGC	.	.		0.607	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
PAK4	10298	hgsc.bcm.edu	37	19	39663569	39663569	+	Silent	SNP	G	G	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr19:39663569G>T	ENST00000593690.1	+	5	643	c.216G>T	c.(214-216)cgG>cgT	p.R72R	PAK4_ENST00000321944.4_Silent_p.R72R|PAK4_ENST00000360442.3_Silent_p.R72R|PAK4_ENST00000599470.1_Intron|PAK4_ENST00000435673.2_Silent_p.R72R|PAK4_ENST00000358301.3_Silent_p.R72R|PAK4_ENST00000599386.1_Intron	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	72	Linker.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	13	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			CCATCGTGCGGGGCAGCAAAG	0.647																																					p.R72R		Atlas-SNP	.											.	PAK4	40	.	0			c.G216T						.						17.0	17.0	17.0					19																	39663569		2069	3996	6065	SO:0001819	synonymous_variant	10298	exon3			CGTGCGGGGCAGC	AJ011855	CCDS12528.1, CCDS33019.1	19p11-q11	2008-06-17	2008-06-17						16059	protein-coding gene	gene with protein product		605451	"""p21(CDKN1A)-activated kinase 4"""			9822598, 10461188	Standard	NM_001014831		Approved		uc002okn.1	O96013		ENST00000593690.1:c.216G>T	chr19.hg19:g.39663569G>T		129.0	0.0		202.0	82.0	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Silent	SNP	ENST00000593690.1	hg19	CCDS12528.1																																																																																			.	.		0.647	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1		
LRFN1	57622	hgsc.bcm.edu	37	19	39805727	39805727	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr19:39805727C>G	ENST00000248668.4	-	1	249	c.250G>C	c.(250-252)Gac>Cac	p.D84H	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	84						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			TTGGCGAAGTCTCGGCGGCGC	0.697																																					p.D84H		Atlas-SNP	.											.	LRFN1	59	.	0			c.G250C						.						10.0	13.0	12.0					19																	39805727		2167	4251	6418	SO:0001583	missense	57622	exon1			CGAAGTCTCGGCG	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.250G>C	chr19.hg19:g.39805727C>G	ENSP00000248668:p.Asp84His	56.0	0.0		58.0	18.0	NM_020862	Q8TBS9	Missense_Mutation	SNP	ENST00000248668.4	hg19	CCDS46071.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.177334	0.78564	.	.	ENSG00000128011	ENST00000248668	T	0.56941	0.43	4.43	4.43	0.53597	.	0.000000	0.41823	D	0.000801	T	0.77343	0.4116	M	0.91663	3.23	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82890	-0.0233	10	0.66056	D	0.02	.	14.5711	0.68210	0.0:1.0:0.0:0.0	.	84	Q9P244	LRFN1_HUMAN	H	84	ENSP00000248668:D84H	ENSP00000248668:D84H	D	-	1	0	LRFN1	44497567	1.000000	0.71417	0.991000	0.47740	0.994000	0.84299	7.541000	0.82084	2.288000	0.76882	0.557000	0.71058	GAC	.	.		0.697	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862	
SNAP25	6616	hgsc.bcm.edu	37	20	10273637	10273637	+	Intron	SNP	C	C	G			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr20:10273637C>G	ENST00000254976.2	+	5	374				SNAP25-AS1_ENST00000421143.2_RNA|SNAP25_ENST00000304886.2_Missense_Mutation_p.P91A|SNAP25-AS1_ENST00000453544.1_RNA	NM_130811.2	NP_570824.1	P60880	SNP25_HUMAN	synaptosomal-associated protein, 25kDa						energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long-term synaptic potentiation (GO:0060291)|neurotransmitter secretion (GO:0007269)|neurotransmitter uptake (GO:0001504)|regulation of establishment of protein localization (GO:0070201)|regulation of insulin secretion (GO:0050796)|regulation of neuron projection development (GO:0010975)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|SNARE complex (GO:0031201)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|trans-Golgi network (GO:0005802)	calcium-dependent protein binding (GO:0048306)			endometrium(1)|large_intestine(2)|lung(8)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	18					Botulinum Toxin Type A(DB00083)	TTTCATATGTCCTTGTAACAA	0.378																																					p.P91A		Atlas-SNP	.											.	SNAP25	79	.	0			c.C271G						.						100.0	99.0	100.0					20																	10273637		2203	4300	6503	SO:0001627	intron_variant	6616	exon5			ATATGTCCTTGTA		CCDS13109.1, CCDS13110.1	20p12-p11.2	2008-08-01	2002-08-29		ENSG00000132639	ENSG00000132639			11132	protein-coding gene	gene with protein product	"""resistance to inhibitors of cholinesterase 4 homolog"""	600322	"""synaptosomal-associated protein, 25kD"""	SNAP		8661740, 10692432	Standard	NM_003081		Approved	SNAP-25, RIC-4, RIC4, SEC9, bA416N4.2, dJ1068F16.2	uc002wnr.2	P60880	OTTHUMG00000031863	ENST00000254976.2:c.164-172C>G	chr20.hg19:g.10273637C>G		137.0	0.0		149.0	31.0	NM_003081	B2RAU4|D3DW16|D3DW17|P13795|P36974|P70557|P70558|Q53EM2|Q5U0B5|Q8IXK3|Q96FM2|Q9BR45	Missense_Mutation	SNP	ENST00000254976.2	hg19	CCDS13110.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.646403	0.67358	.	.	ENSG00000132639	ENST00000304886	.	.	.	6.16	6.16	0.99307	.	.	.	.	.	T	0.64821	0.2633	.	.	.	0.80722	D	1	B	0.21452	0.056	B	0.25140	0.058	T	0.57106	-0.7868	7	0.44086	T	0.13	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	91	P60880-2	.	A	91	.	ENSP00000307341:P91A	P	+	1	0	SNAP25	10221637	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	CCT	.	.		0.378	SNAP25-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077976.3	NM_130811	
SNAP25	6616	hgsc.bcm.edu	37	20	10273846	10273846	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr20:10273846C>G	ENST00000254976.2	+	5	412	c.201C>G	c.(199-201)atC>atG	p.I67M	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25_ENST00000304886.2_Intron|SNAP25-AS1_ENST00000453544.1_RNA	NM_130811.2	NP_570824.1	P60880	SNP25_HUMAN	synaptosomal-associated protein, 25kDa	67	Interaction with CENPF. {ECO:0000250}.|t-SNARE coiled-coil homology 1. {ECO:0000255|PROSITE-ProRule:PRU00202}.				energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long-term synaptic potentiation (GO:0060291)|neurotransmitter secretion (GO:0007269)|neurotransmitter uptake (GO:0001504)|regulation of establishment of protein localization (GO:0070201)|regulation of insulin secretion (GO:0050796)|regulation of neuron projection development (GO:0010975)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|SNARE complex (GO:0031201)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|trans-Golgi network (GO:0005802)	calcium-dependent protein binding (GO:0048306)			endometrium(1)|large_intestine(2)|lung(8)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	18					Botulinum Toxin Type A(DB00083)	TGGACCAAATCAATAAGGACA	0.428																																					p.I67M		Atlas-SNP	.											.	SNAP25	79	.	0			c.C201G						.						150.0	160.0	157.0					20																	10273846		2203	4300	6503	SO:0001583	missense	6616	exon5			CCAAATCAATAAG		CCDS13109.1, CCDS13110.1	20p12-p11.2	2008-08-01	2002-08-29		ENSG00000132639	ENSG00000132639			11132	protein-coding gene	gene with protein product	"""resistance to inhibitors of cholinesterase 4 homolog"""	600322	"""synaptosomal-associated protein, 25kD"""	SNAP		8661740, 10692432	Standard	NM_003081		Approved	SNAP-25, RIC-4, RIC4, SEC9, bA416N4.2, dJ1068F16.2	uc002wnr.2	P60880	OTTHUMG00000031863	ENST00000254976.2:c.201C>G	chr20.hg19:g.10273846C>G	ENSP00000254976:p.Ile67Met	212.0	0.0		236.0	88.0	NM_130811	B2RAU4|D3DW16|D3DW17|P13795|P36974|P70557|P70558|Q53EM2|Q5U0B5|Q8IXK3|Q96FM2|Q9BR45	Missense_Mutation	SNP	ENST00000254976.2	hg19	CCDS13110.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.400937	0.62177	.	.	ENSG00000132639	ENST00000254976;ENST00000430336	.	.	.	5.9	5.9	0.94986	Target SNARE coiled-coil domain (2);	0.000000	0.85682	D	0.000000	T	0.76385	0.3980	M	0.83312	2.635	0.80722	D	1	D	0.55605	0.972	P	0.53006	0.715	T	0.74746	-0.3561	9	0.33141	T	0.24	-7.9478	20.2789	0.98501	0.0:1.0:0.0:0.0	.	67	P60880	SNP25_HUMAN	M	67	.	ENSP00000254976:I67M	I	+	3	3	SNAP25	10221846	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.788000	0.95919	0.650000	0.86243	ATC	.	.		0.428	SNAP25-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077976.3	NM_130811	
SPAG4	6676	hgsc.bcm.edu	37	20	34204001	34204001	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr20:34204001T>G	ENST00000374273.3	+	1	188	c.76T>G	c.(76-78)Tca>Gca	p.S26A		NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	26					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|motile cilium (GO:0031514)	structural molecule activity (GO:0005198)			NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			CGAGAACAGCTCAATGAGCAT	0.682																																					p.S26A		Atlas-SNP	.											.	SPAG4	36	.	0			c.T76G						.						22.0	24.0	23.0					20																	34204001		2201	4295	6496	SO:0001583	missense	6676	exon1			AACAGCTCAATGA	AF043344	CCDS13259.1	20q11.2	2010-04-23			ENSG00000061656	ENSG00000061656			11214	protein-coding gene	gene with protein product	"""acrosomal protein ACR55"", ""Sad1 and UNC84 domain containing 4"", ""cancer/testis antigen 127"""	603038				9691178, 10373309	Standard	NM_003116		Approved	SUN4, CT127	uc002xdb.1	Q9NPE6	OTTHUMG00000032352	ENST00000374273.3:c.76T>G	chr20.hg19:g.34204001T>G	ENSP00000363391:p.Ser26Ala	131.0	0.0		151.0	34.0	NM_003116	O43648	Missense_Mutation	SNP	ENST00000374273.3	hg19	CCDS13259.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.643051	0.87859	.	.	ENSG00000061656	ENST00000374273	T	0.15017	2.46	4.72	4.72	0.59763	.	0.105204	0.40385	N	0.001110	T	0.27559	0.0677	L	0.34521	1.04	0.31538	N	0.660258	D	0.58268	0.982	D	0.67548	0.952	T	0.14035	-1.0487	10	0.72032	D	0.01	-17.5121	10.5157	0.44887	0.0:0.0:0.0:1.0	.	26	Q9NPE6	SPAG4_HUMAN	A	26	ENSP00000363391:S26A	ENSP00000363391:S26A	S	+	1	0	SPAG4	33667415	0.993000	0.37304	0.938000	0.37757	0.927000	0.56198	1.365000	0.34182	1.991000	0.58162	0.459000	0.35465	TCA	.	.		0.682	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116	
COL20A1	57642	hgsc.bcm.edu	37	20	61943320	61943320	+	Silent	SNP	G	G	A	rs374496650		TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr20:61943320G>A	ENST00000358894.6	+	14	1816	c.1716G>A	c.(1714-1716)gcG>gcA	p.A572A	COL20A1_ENST00000435874.1_Silent_p.A579A|COL20A1_ENST00000422202.1_Silent_p.A579A|COL20A1_ENST00000326996.6_Silent_p.A572A	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	572	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GCCACGACGCGGCACGAGTGT	0.677																																					p.A572A		Atlas-SNP	.											.	COL20A1	137	.	0			c.G1716A						.	G		0,4030		0,0,2015	20.0	24.0	23.0		1716	-7.2	0.0	20		23	6,8320		0,6,4157	no	coding-synonymous	COL20A1	NM_020882.2		0,6,6172	AA,AG,GG		0.0721,0.0,0.0486		572/1285	61943320	6,12350	2015	4163	6178	SO:0001819	synonymous_variant	57642	exon14			CGACGCGGCACGA	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.1716G>A	chr20.hg19:g.61943320G>A		85.0	0.0		100.0	35.0	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Silent	SNP	ENST00000358894.6	hg19	CCDS46628.1																																																																																			.	.		0.677	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
DYRK1A	1859	hgsc.bcm.edu	37	21	38845103	38845103	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr21:38845103G>A	ENST00000398960.2	+	2	203	c.128G>A	c.(127-129)cGt>cAt	p.R43H	DYRK1A_ENST00000398956.2_Missense_Mutation_p.R43H|DYRK1A_ENST00000339659.4_Missense_Mutation_p.R43H|DYRK1A_ENST00000462274.1_3'UTR|DYRK1A_ENST00000338785.3_Missense_Mutation_p.R43H|DYRK1A_ENST00000321219.8_Missense_Mutation_p.R43H|DYRK1A_ENST00000451934.1_Missense_Mutation_p.R43H	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	43					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TACAGTGACCGTCGCCAGCCA	0.473																																					p.R43H	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											.	DYRK1A	85	.	0			c.G128A						.						151.0	129.0	137.0					21																	38845103		2203	4300	6503	SO:0001583	missense	1859	exon2			GTGACCGTCGCCA	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.128G>A	chr21.hg19:g.38845103G>A	ENSP00000381932:p.Arg43His	103.0	0.0		58.0	42.0	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	hg19	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	G	36	5.933585	0.97122	.	.	ENSG00000157540	ENST00000338785;ENST00000455097;ENST00000426672;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956	T;T;T;T;T;T;T	0.57273	0.46;0.77;0.41;0.47;0.46;0.43;0.47	6.16	6.16	0.99307	.	0.050757	0.85682	D	0.000000	T	0.42698	0.1214	N	0.14661	0.345	0.80722	D	1	D;D;P;D;D	0.60575	0.979;0.979;0.955;0.988;0.979	B;P;B;P;P	0.45474	0.361;0.482;0.212;0.482;0.482	T	0.18871	-1.0323	10	0.17832	T	0.49	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	43;43;43;43;43	Q13627-3;Q13627-4;Q13627;Q13627-2;Q13627-5	.;.;DYR1A_HUMAN;.;.	H	43	ENSP00000342690:R43H;ENSP00000412269:R43H;ENSP00000340373:R43H;ENSP00000319032:R43H;ENSP00000416089:R43H;ENSP00000381932:R43H;ENSP00000381929:R43H	ENSP00000319032:R43H	R	+	2	0	DYRK1A	37766973	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.937000	0.99478	0.650000	0.86243	CGT	.	.		0.473	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396	
NOL12	79159	hgsc.bcm.edu	37	22	38083917	38083917	+	Splice_Site	SNP	G	G	T			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr22:38083917G>T	ENST00000359114.4	+	2	154	c.84G>T	c.(82-84)cgG>cgT	p.R28R	NOL12_ENST00000493862.1_3'UTR	NM_024313.2	NP_077289.1	Q9UGY1	NOL12_HUMAN	nucleolar protein 12	28						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	8	Melanoma(58;0.0574)					CTTCCTGTAGGGAGTACCTGA	0.537																																					p.R28R		Atlas-SNP	.											.	NOL12	22	.	0			c.G84T						.						23.0	21.0	22.0					22																	38083917		2195	4285	6480	SO:0001630	splice_region_variant	79159	exon2			CTGTAGGGAGTAC	Z83844	CCDS13955.1	22q13.1	2012-05-02			ENSG00000256872	ENSG00000273899			28585	protein-coding gene	gene with protein product						12477932	Standard	NM_024313		Approved	MGC3731, Nop25, RRP17	uc003atp.3	Q9UGY1	OTTHUMG00000150660	ENST00000359114.4:c.84-1G>T	chr22.hg19:g.38083917G>T		295.0	0.0		325.0	22.0	NM_024313		Silent	SNP	ENST00000359114.4	hg19	CCDS13955.1																																																																																			.	.		0.537	NOL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319476.1	NM_024313	Silent
WDR45	11152	hgsc.bcm.edu	37	X	48934306	48934306	+	Silent	SNP	G	G	A			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chrX:48934306G>A	ENST00000376372.3	-	5	520	c.339C>T	c.(337-339)gaC>gaT	p.D113D	WDR45_ENST00000376368.2_Silent_p.D114D|WDR45_ENST00000473974.1_Silent_p.D113D|WDR45_ENST00000553851.1_Intron|WDR45_ENST00000485908.1_Silent_p.D78D|WDR45_ENST00000465431.1_5'Flank|WDR45_ENST00000322995.8_Silent_p.D113D|WDR45_ENST00000396681.4_Silent_p.D113D|PRAF2_ENST00000491199.1_5'Flank|PRAF2_ENST00000376386.3_5'Flank|AF196779.12_ENST00000376358.3_Intron|WDR45_ENST00000356463.3_Silent_p.D114D|PRAF2_ENST00000376390.4_5'Flank	NM_001029896.1	NP_001025067.1	Q9Y484	WIPI4_HUMAN	WD repeat domain 45	113					autophagy (GO:0006914)|cell death (GO:0008219)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	19						AGGCTCACTTGTCATGGCGCA	0.622																																					p.D114D		Atlas-SNP	.											.	WDR45	40	.	0			c.C342T						.						69.0	54.0	59.0					X																	48934306		2203	4300	6503	SO:0001819	synonymous_variant	11152	exon6			TCACTTGTCATGG	BC003037	CCDS14318.1, CCDS35250.1	Xp11.23	2013-06-06	2004-09-02	2004-09-03	ENSG00000196998	ENSG00000196998		"""WD repeat domain containing"""	28912	protein-coding gene	gene with protein product	"""neurodegeneration with brain iron accumulation 5"""	300526	"""WD repeat domain, X-linked 1"""	WDRX1		12477932	Standard	NM_007075		Approved	JM5, WIPI4, NBIA5	uc004dmk.1	Q9Y484	OTTHUMG00000034500	ENST00000376372.3:c.339C>T	chrX.hg19:g.48934306G>A		214.0	0.0		271.0	120.0	NM_007075	A6NGH5|B7WPI2|Q5MNZ5|Q6IBS7|Q6NT94|Q96H03	Silent	SNP	ENST00000376372.3	hg19	CCDS35250.1	.	.	.	.	.	.	.	.	.	.	G	13.25	2.179685	0.38511	.	.	ENSG00000196998	ENST00000367375	.	.	.	3.87	3.87	0.44632	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.6696	14.6194	0.68574	0.0:0.0:1.0:0.0	.	.	.	.	X	70	.	.	Q	-	1	0	WDR45	48821250	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.994000	0.70623	2.182000	0.69389	0.529000	0.55759	CAA	.	.		0.622	WDR45-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083418.2	NM_007075	
MAGIX	79917	hgsc.bcm.edu	37	X	49020204	49020204	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chrX:49020204G>C	ENST00000412696.2	+	2	133	c.133G>C	c.(133-135)Gcg>Ccg	p.A45P	MAGIX_ENST00000376339.1_5'UTR|MAGIX_ENST00000425661.2_Missense_Mutation_p.A45P|MAGIX_ENST00000376338.3_5'Flank	NM_024859.2	NP_079135.3	Q9H6Y5	MAGIX_HUMAN	MAGI family member, X-linked	45																	GGCGCGAGCTGCGGTCGACGT	0.781																																					p.A45P		Atlas-SNP	.											.	MAGIX	25	.	0			c.G133C						.						1.0	1.0	1.0					X																	49020204		736	1642	2378	SO:0001583	missense	79917	exon2			CGAGCTGCGGTCG	AK025340	CCDS48106.1, CCDS48107.1, CCDS75976.1	Xp11.23	2014-05-06			ENSG00000017621	ENSG00000269313			30006	protein-coding gene	gene with protein product							Standard	XM_005278065		Approved	PDZX, JM10, FLJ21687	uc010nin.1	Q9H6Y5	OTTHUMG00000188218	ENST00000412696.2:c.133G>C	chrX.hg19:g.49020204G>C	ENSP00000387928:p.Ala45Pro	62.0	0.0		105.0	55.0	NM_001099681	A6XND4|A8MSX9|B7WP26|Q14C81	Missense_Mutation	SNP	ENST00000412696.2	hg19	CCDS48106.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	13.23|13.23	2.175406|2.175406	0.38413|0.38413	.|.	.|.	ENSG00000017621|ENSG00000017621	ENST00000425661;ENST00000412696|ENST00000458388	T;T|.	0.26957|.	1.92;1.7|.	3.37|3.37	2.5|2.5	0.30297|0.30297	.|.	.|.	.|.	.|.	.|.	T|T	0.30823|0.30823	0.0777|0.0777	L|L	0.29908|0.29908	0.895|0.895	0.26836|0.26836	N|N	0.96847|0.96847	D;D|.	0.67145|.	0.996;0.994|.	P;P|.	0.61132|.	0.884;0.854|.	T|T	0.20438|0.20438	-1.0275|-1.0275	9|5	0.37606|.	T|.	0.19|.	-5.4914|-5.4914	6.1176|6.1176	0.20136|0.20136	0.1442:0.0:0.8558:0.0|0.1442:0.0:0.8558:0.0	.|.	45;45|.	F8WCY7;Q9H6Y5|.	.;MAGIX_HUMAN|.	P|S	45|50	ENSP00000403515:A45P;ENSP00000387928:A45P|.	ENSP00000387928:A45P|.	A|C	+|+	1|2	0|0	MAGIX|MAGIX	48907148|48907148	0.347000|0.347000	0.24853|0.24853	0.430000|0.430000	0.26722|0.26722	0.009000|0.009000	0.06853|0.06853	1.088000|1.088000	0.30877|0.30877	0.822000|0.822000	0.34565|0.34565	0.284000|0.284000	0.19432|0.19432	GCG|TGC	.	.		0.781	MAGIX-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378832.1	NM_024859	
MT-ND5	4540	hgsc.bcm.edu	37	M	13337	13337	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chrM:13337T>C	ENST00000361567.2	+	1	1001	c.1001T>C	c.(1000-1002)tTc>tCc	p.F334S	MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TR_ENST00000387439.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	334					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TACCCACGCCTTCTTCAAAGC	0.428																																					p.F334S		Atlas-SNP	.											.	.	.	.	0			c.T1001C						.																																			SO:0001583	missense	0	exon1			ACGCCTTCTTCAA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1001T>C	chrM.hg19:g.13337T>C	ENSP00000354813:p.Phe334Ser	20.0	0.0		70.0	55.0	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.428	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
KRT2	3849	hgsc.bcm.edu	37	12	53045631	53045632	+	In_Frame_Ins	INS	-	-	CGCCTCCAAAGCCGCTGC			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr12:53045631_53045632insCGCCTCCAAAGCCGCTGC	ENST00000309680.3	-	1	316_317	c.295_296insGCAGCGGCTTTGGAGGCG	c.(295-297)ggc>gGCAGCGGCTTTGGAGGCGgc	p.99_99G>GSGFGGG		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	99	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		aaagctgctgccgcctccaaaa	0.619																																					p.G99delinsGSGFGGG		Atlas-INDEL	.											.	KRT2	94	.	0			c.296_297insGCAGCGGCTTTGGAGGCG						.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6439	protein-coding gene	gene with protein product	"""epidermal ichthyosis bullosa of Siemens"""	600194	"""keratin 2A (epidermal ichthyosis bullosa of Siemens)"""	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.295_296insGCAGCGGCTTTGGAGGCG	chr12.hg19:g.53045631_53045632insCGCCTCCAAAGCCGCTGC	Exception_encountered	165.0	0.0		196.0	43.0	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.		0.619	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423	
BAP1	8314	hgsc.bcm.edu	37	3	52437901	52437901	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:52437901delC	ENST00000460680.1	-	13	1731	c.1260delG	c.(1258-1260)gggfs	p.G420fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.G402fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K421fs*11(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CTGTTCCCTTCCCCTTATACC	0.562			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															p.K421fs	GBM(101;493 1458 7992 21037 25532)	Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	1	Insertion - Frameshift(1)	kidney(1)	c.1261delA						.						76.0	80.0	78.0					3																	52437901		2203	4300	6503	SO:0001589	frameshift_variant	8314	exon13			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1260delG	chr3.hg19:g.52437901delC	ENSP00000417132:p.Gly420fs	54.0	0.0		24.0	16.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.562	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		
PRLHR	2834	hgsc.bcm.edu	37	10	120354129	120354142	+	Frame_Shift_Del	DEL	GGCGCACGTCGTGC	GGCGCACGTCGTGC	-	rs34269354|rs143477537|rs369106208	byFrequency	TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	GGCGCACGTCGTGC	GGCGCACGTCGTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr10:120354129_120354142delGGCGCACGTCGTGC	ENST00000369169.1	-	1	614_627	c.615_628delGCACGACGTGCGCC	c.(613-630)ccgcacgacgtgcgcctcfs	p.HDVRL206fs	PRLHR_ENST00000239032.2_Frame_Shift_Del_p.HDVRL206fs			P49683	PRLHR_HUMAN	prolactin releasing hormone receptor	206					feeding behavior (GO:0007631)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|hormone metabolic process (GO:0042445)|neuropeptide signaling pathway (GO:0007218)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)|neuropeptide Y receptor activity (GO:0004983)			large_intestine(2)|lung(8)|ovary(1)|skin(1)	12		Colorectal(252;0.0429)|Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0166)		TCCTCGCAGAGGCGCACGTCGTGCGGCTTGAGCT	0.701																																					p.206_210del		Atlas-Indel,Pindel	.											.	PRLHR	41	.	0			c.616_629del						.																																			SO:0001589	frameshift_variant	2834	exon2			.	AB048946	CCDS7606.1	10q25.3-q26	2014-02-21	2005-11-24	2005-11-24	ENSG00000119973	ENSG00000119973		"""GPCR / Class A : RF amide peptide receptors"""	4464	protein-coding gene	gene with protein product		600895	"""G protein-coupled receptor 10"""	GPR10		8666380, 15885496	Standard	NM_004248		Approved	PrRPR	uc001ldp.1	P49683	OTTHUMG00000019136	ENST00000369169.1:c.615_628delGCACGACGTGCGCC	chr10.hg19:g.120354129_120354142delGGCGCACGTCGTGC	ENSP00000358167:p.His206fs	68.0	0.0		72.0	16.0	NM_004248	O75194|Q502U8|Q5VXR9	Frame_Shift_Del	DEL	ENST00000369169.1	hg19	CCDS7606.1																																																																																			.	.		0.701	PRLHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050610.1	NM_004248	
CHID1	66005	hgsc.bcm.edu	37	11	870164	870179	+	Splice_Site	DEL	CTGCAAGACAAAGGGA	CTGCAAGACAAAGGGA	-			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	CTGCAAGACAAAGGGA	CTGCAAGACAAAGGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr11:870164_870179delCTGCAAGACAAAGGGA	ENST00000449825.1	-	12	1397		c.e12-1		CHID1_ENST00000436108.2_Splice_Site|CHID1_ENST00000323578.8_Splice_Site|CHID1_ENST00000526714.1_5'Flank|CHID1_ENST00000528581.1_Splice_Site|CHID1_ENST00000454838.2_Splice_Site|CHID1_ENST00000429789.2_Splice_Site|CHID1_ENST00000336845.5_Splice_Site|CHID1_ENST00000323541.7_Splice_Site	NM_001142675.1	NP_001136147.1	Q9BWS9	CHID1_HUMAN	chitinase domain containing 1						carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|innate immune response (GO:0045087)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	chitinase activity (GO:0004568)|oligosaccharide binding (GO:0070492)			endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	13		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.48e-25)|Epithelial(43;3.75e-24)|BRCA - Breast invasive adenocarcinoma(625;4.65e-05)|Lung(200;0.0624)|LUSC - Lung squamous cell carcinoma(625;0.0735)		ACTGCGGCTCCTGCAAGACAAAGGGACTGTCAGCCC	0.667																																					p.372_372del	Pancreas(117;992 2327 5172 41921)	Atlas-Indel,Pindel	.											.	CHID1	29	.	0			c.1116_1116del						.																																			SO:0001630	splice_region_variant	66005	exon13			.	AK124697	CCDS7722.1, CCDS44510.1, CCDS44511.1	11p15.5	2005-10-27			ENSG00000177830	ENSG00000177830			28474	protein-coding gene	gene with protein product		615692					Standard	NM_023947		Approved	MGC3234, FLJ42707	uc001lsm.3	Q9BWS9	OTTHUMG00000133314	ENST00000449825.1:c.1041-1TCCCTTTGTCTTGCAG>-	chr11.hg19:g.870164_870179delCTGCAAGACAAAGGGA		115.0	0.0		125.0	17.0	NM_001142676	B3KWB0|Q8NBM9|Q96CZ3|Q96S93|Q96SK0|Q9BY52	Frame_Shift_Del	DEL	ENST00000449825.1	hg19	CCDS7722.1																																																																																			.	.		0.667	CHID1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257112.1	NM_023947	Intron
ENOSF1	55556	hgsc.bcm.edu	37	18	712566	712566	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr18:712566delG	ENST00000251101.7	-	1	110	c.22delC	c.(22-24)cggfs	p.R8fs	ENOSF1_ENST00000383578.3_5'UTR|ENOSF1_ENST00000340116.7_5'Flank|ENOSF1_ENST00000539164.1_Frame_Shift_Del_p.R8fs|ENOSF1_ENST00000580982.1_Frame_Shift_Del_p.R8fs	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	8					cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						ACCGAGAGCCGGGAGATCCTG	0.761																																					p.R8fs		Atlas-Indel,Pindel	.											.	ENOSF1	44	.	0			c.23delG						.						5.0	5.0	5.0					18																	712566		1632	3121	4753	SO:0001589	frameshift_variant	55556	exon1			.	X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199			30365	protein-coding gene	gene with protein product		607427				14508106	Standard	NM_001126123		Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.22delC	chr18.hg19:g.712566delG	ENSP00000251101:p.Arg8fs	153.0	0.0		197.0	71.0	NM_017512	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Frame_Shift_Del	DEL	ENST00000251101.7	hg19	CCDS11822.1																																																																																			.	.		0.761	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512	
LRFN1	57622	hgsc.bcm.edu	37	19	39805729	39805729	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr19:39805729delC	ENST00000248668.4	-	1	247	c.248delG	c.(247-249)cgafs	p.R83fs	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	83						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GGCGAAGTCTCGGCGGCGCAC	0.692																																					p.R83fs		Atlas-INDEL	.											.	LRFN1	59	.	0			c.249delA						.						10.0	13.0	12.0					19																	39805729		2160	4246	6406	SO:0001589	frameshift_variant	57622	exon1			.	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.248delG	chr19.hg19:g.39805729delC	ENSP00000248668:p.Arg83fs	55.0	0.0		58.0	18.0	NM_020862	Q8TBS9	Frame_Shift_Del	DEL	ENST00000248668.4	hg19	CCDS46071.1																																																																																			.	.		0.692	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862	
XRN1	54464	hgsc.bcm.edu	37	3	142030539	142030542	+	Frame_Shift_Del	DEL	ACTT	ACTT	-			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	ACTT	ACTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr3:142030539_142030542delACTT	ENST00000264951.4	-	42	5049_5052	c.4932_4935delAAGT	c.(4930-4935)gtaagtfs	p.VS1644fs	XRN1_ENST00000392981.2_Frame_Shift_Del_p.VS1632fs	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	1644					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						TCTCCCGTGGACTTACTTTGACAA	0.451																																					p.1645_1646del		Atlas-Indel,Pindel	.											.	XRN1	138	.	0			c.4933_4936del						.																																			SO:0001589	frameshift_variant	54464	exon42			.	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.4932_4935delAAGT	chr3.hg19:g.142030543_142030546delACTT	ENSP00000264951:p.Val1644fs	205.0	0.0		192.0	146.0	NM_019001	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Frame_Shift_Del	DEL	ENST00000264951.4	hg19	CCDS3123.1																																																																																			.	.		0.451	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001	
CLEC16A	23274	hgsc.bcm.edu	37	16	11214572	11214670	+	Splice_Site	DEL	TGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	TGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	-	rs3217121|rs200560039|rs201962167|rs555596086|rs374910952|rs201061352|rs199864914|rs397699050|rs58648897|rs56282757|rs12925474|rs113276201|rs201455904|rs544295262|rs201350159|rs557770599|rs112965500|rs369310040|rs199582436|rs200624127|rs201460026	byFrequency	TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	TGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	TGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr16:11214572_11214670delTGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	ENST00000409790.1	+	20	2447_2498	c.2217_2268delTGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC	c.(2215-2268)cctgatgtgtccaggcttggctggggagtggtcaagtttgcaggcctattgcag>cc	p.PDVSRLGWGVVKFAGLLQ739del	CLEC16A_ENST00000409552.3_Splice_Site_p.PDVSRLGWGVVKFAGLLQ721del|CLEC16A_ENST00000465491.1_3'UTR	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TGGTGGAGCCTGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTacaaacacacacacac	0.462																																					p.739_756del		Pindel	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.2216_2268del						.																																			SO:0001630	splice_region_variant	23274	exon19			.	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2268+1TGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC>-	chr16.hg19:g.11214572_11214670delTGATGTGTCCAGGCTTGGCTGGGGAGTGGTCAAGTTTGCAGGCCTATTGCAGGTAAGATGGCCAGGAGCTCTGGGATCTGTTCTCAGTTGGCTACAAAC		42.0	0.0		48.0	10.0	NM_015226		Frame_Shift_Del	DEL	ENST00000409790.1	hg19	CCDS45409.1																																																																																			.	.		0.462	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	In_Frame_Del
LRFN1	57622	hgsc.bcm.edu	37	19	39805727	39805729	+	In_Frame_Del	DEL	CTC	CTC	-			TCGA-DD-AA3A-01A-11D-A36X-10	TCGA-DD-AA3A-10A-01D-A370-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a17ef437-5859-4b97-b7a4-dfb5d1d1e83e	fa7c6f30-8c06-492f-b010-88d415e47d00	g.chr19:39805727_39805729delCTC	ENST00000248668.4	-	1	247_249	c.248_250delGAG	c.(247-252)cgagac>cac	p.83_84RD>H	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	83						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			TTGGCGAAGTCTCGGCGGCGCAC	0.695																																					p.83_84del		Pindel	.											.	LRFN1	59	.	0			c.249_251del						.																																			SO:0001651	inframe_deletion	57622	exon1			.	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.248_250delGAG	chr19.hg19:g.39805727_39805729delCTC	ENSP00000248668:p.Arg83_Asp84delinsHis	56.0	0.0		58.0	12.0	NM_020862	Q8TBS9	In_Frame_Del	DEL	ENST00000248668.4	hg19	CCDS46071.1																																																																																			.	.		0.695	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862	
