#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
NRD1	4898	hgsc.bcm.edu	37	1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	rs62648104		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:52306079T>A	ENST00000354831.7	-	2	638	c.449A>T	c.(448-450)gAg>gTg	p.E150V	NRD1_ENST00000539524.1_Missense_Mutation_p.E18V|NRD1_ENST00000544028.1_Missense_Mutation_p.E18V|NRD1_ENST00000352171.7_Missense_Mutation_p.E150V|NRD1_ENST00000485608.1_5'UTR	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0	Asp/Glu-rich (highly acidic).|Poly-Glu.				cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						ttcttcttcctccacctcctc	0.378																																					p.E150V		Atlas-SNP	.											.	NRD1	89	.	0			c.A449T						.						163.0	138.0	146.0					1																	52306079		2203	4300	6503	SO:0001583	missense	4898	exon2			TCTTCCTCCACCT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.449A>T	chr1.hg19:g.52306079T>A	ENSP00000346890:p.Glu150Val	111.0	0.0		298.0	18.0	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.	.	.	.	.	.	.	.	.	.	T	3.056	-0.194350	0.06259	.	.	ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000546169;ENST00000544028	T;T;T;T	0.38240	1.31;3.15;1.15;1.22	5.25	2.92	0.33932	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.525899	0.19688	N	0.108344	T	0.18341	0.0440	N	0.14661	0.345	0.09310	N	1	B;B;B	0.23650	0.062;0.089;0.01	B;B;B	0.17098	0.017;0.007;0.007	T	0.14755	-1.0461	10	0.38643	T	0.18	-0.0317	5.1939	0.15225	0.0:0.1704:0.2022:0.6274	rs62648104	150;150;150	F5H6R2;O43847;B1AKJ5	.;NRDC_HUMAN;.	V	150;150;18;150;18	ENSP00000262679:E150V;ENSP00000346890:E150V;ENSP00000444416:E18V;ENSP00000442262:E18V	ENSP00000262679:E150V	E	-	2	0	NRD1	52078667	0.129000	0.22400	0.012000	0.15200	0.145000	0.21501	0.870000	0.28010	0.317000	0.23160	0.454000	0.30748	GAG	.	T|0.024;A|0.976		0.378	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525	
PTPN22	26191	hgsc.bcm.edu	37	1	114380291	114380291	+	Silent	SNP	A	A	G			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:114380291A>G	ENST00000359785.5	-	13	1866	c.1731T>C	c.(1729-1731)taT>taC	p.Y577Y	PTPN22_ENST00000525799.1_Silent_p.Y450Y|PTPN22_ENST00000528414.1_Silent_p.Y522Y|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000420377.2_Silent_p.Y577Y|PTPN22_ENST00000538253.1_Silent_p.Y333Y	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	577					negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTGAATTGTAATAAGAGAAGA	0.363																																					p.Y577Y		Atlas-SNP	.											.	PTPN22	90	.	0			c.T1731C						.						97.0	98.0	98.0					1																	114380291		2203	4300	6503	SO:0001819	synonymous_variant	26191	exon13			ATTGTAATAAGAG	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9652	protein-coding gene	gene with protein product		600716	"""protein tyrosine phosphatase, non-receptor type 8"""	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.1731T>C	chr1.hg19:g.114380291A>G		63.0	0.0		162.0	60.0	NM_015967	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Silent	SNP	ENST00000359785.5	hg19	CCDS863.1																																																																																			.	.		0.363	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967	
SYCP1	6847	hgsc.bcm.edu	37	1	115524051	115524051	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:115524051C>T	ENST00000369522.3	+	29	2717	c.2477C>T	c.(2476-2478)tCa>tTa	p.S826L	SYCP1_ENST00000477590.1_3'UTR|SYCP1_ENST00000369518.1_Missense_Mutation_p.S826L	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	826					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AATTTCACATCAGTTGATCAT	0.333																																					p.S826L		Atlas-SNP	.											.	SYCP1	149	.	0			c.C2477T						.						92.0	92.0	92.0					1																	115524051		2203	4297	6500	SO:0001583	missense	6847	exon29			TCACATCAGTTGA	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"""cancer/testis antigen 8"""	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2477C>T	chr1.hg19:g.115524051C>T	ENSP00000358535:p.Ser826Leu	74.0	0.0		215.0	96.0	NM_003176	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	hg19	CCDS879.1	.	.	.	.	.	.	.	.	.	.	C	11.12	1.545076	0.27652	.	.	ENSG00000198765	ENST00000369522;ENST00000369518	T;T	0.34072	1.38;1.38	5.52	5.52	0.82312	.	0.552403	0.19046	N	0.124171	T	0.30727	0.0774	M	0.62723	1.935	0.32710	N	0.511757	D;D	0.54047	0.964;0.964	P;P	0.45310	0.476;0.476	T	0.34725	-0.9817	10	0.72032	D	0.01	-3.8726	14.9278	0.70893	0.0:1.0:0.0:0.0	.	826;826	B7ZLS9;Q15431	.;SYCP1_HUMAN	L	826	ENSP00000358535:S826L;ENSP00000358531:S826L	ENSP00000358531:S826L	S	+	2	0	SYCP1	115325574	0.949000	0.32298	0.813000	0.32504	0.039000	0.13416	2.043000	0.41231	2.609000	0.88269	0.591000	0.81541	TCA	.	.		0.333	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176	
FCGR3A	2214	hgsc.bcm.edu	37	1	161596059	161596059	+	Intron	SNP	A	A	C			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:161596059A>C	ENST00000540048.1	-	2	94				FCGR3B_ENST00000367964.2_Missense_Mutation_p.F151L|FCGR3B_ENST00000531221.1_Missense_Mutation_p.F187L|FCGR2B_ENST00000367962.4_Intron|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367960.5_Intron|FCGR3B_ENST00000294800.3_Missense_Mutation_p.F151L|FCGR2B_ENST00000403078.3_Intron			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AATTATGATGAAAATACTTCC	0.443																																					p.F187L		Atlas-SNP	.											.	FCGR3B	35	.	0			c.T561G						.						152.0	151.0	151.0					1																	161596059		2191	4299	6490	SO:0001627	intron_variant	2215	exon4			ATGATGAAAATAC	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000540048.1:c.61+4098T>G	chr1.hg19:g.161596059A>C		100.0	0.0		199.0	160.0	NM_001244753	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000540048.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	7.898|7.898	0.733772|0.733772	0.15574|0.15574	.|.	.|.	ENSG00000162747|ENSG00000162747	ENST00000367964;ENST00000294800;ENST00000531221|ENST00000421702	T;T;T|.	0.11821|.	2.74;2.74;2.74|.	2.35|2.35	-2.11|-2.11	0.07187|0.07187	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);|.	0.778704|.	0.10279|.	U|.	0.693741|.	T|T	0.10766|0.10766	0.0263|0.0263	L|L	0.39898|0.39898	1.24|1.24	0.09310|0.09310	N|N	1|1	D|.	0.56287|.	0.975|.	P|.	0.48677|.	0.586|.	T|T	0.34477|0.34477	-0.9827|-0.9827	10|5	0.25106|.	T|.	0.35|.	.|.	2.9454|2.9454	0.05845|0.05845	0.3664:0.2608:0.3728:0.0|0.3664:0.2608:0.3728:0.0	.|.	151|.	O75015|.	FCG3B_HUMAN|.	L|A	151;151;187|172	ENSP00000356941:F151L;ENSP00000294800:F151L;ENSP00000433642:F187L|.	ENSP00000294800:F151L|.	F|S	-|-	3|1	2|0	FCGR3B|FCGR3B	159862683|159862683	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.098000|0.098000	0.18820|0.18820	-0.432000|-0.432000	0.06956|0.06956	-0.170000|-0.170000	0.10816|0.10816	0.155000|0.155000	0.16302|0.16302	TTT|TCA	.	.		0.443	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569	
GPR137B	7107	hgsc.bcm.edu	37	1	236368456	236368456	+	Missense_Mutation	SNP	T	T	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:236368456T>A	ENST00000366592.3	+	6	1088	c.997T>A	c.(997-999)Ttc>Atc	p.F333I	GPR137B_ENST00000477559.1_3'UTR	NM_003272.3	NP_003263.1	O60478	G137B_HUMAN	G protein-coupled receptor 137B	333						integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|membrane (GO:0016020)				endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			CAGCCATGGATTCAGTCCCAG	0.463																																					p.F333I		Atlas-SNP	.											.	GPR137B	57	.	0			c.T997A						.						181.0	179.0	180.0					1																	236368456		2203	4300	6503	SO:0001583	missense	7107	exon6			CATGGATTCAGTC	AF027826	CCDS1609.1	1q42-q43	2012-08-10	2006-01-26	2006-01-26	ENSG00000077585	ENSG00000077585			11862	protein-coding gene	gene with protein product		604658	"""transmembrane 7 superfamily member 1 (upregulated in kidney)"""	TM7SF1		9521871	Standard	NM_003272		Approved		uc001hxq.3	O60478	OTTHUMG00000037994	ENST00000366592.3:c.997T>A	chr1.hg19:g.236368456T>A	ENSP00000355551:p.Phe333Ile	47.0	0.0		151.0	56.0	NM_003272	Q53EK7|Q5TAE6|Q6FHI3	Missense_Mutation	SNP	ENST00000366592.3	hg19	CCDS1609.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.128649|5.128649	0.94473|0.94473	.|.	.|.	ENSG00000077585|ENSG00000077585	ENST00000454895|ENST00000366592;ENST00000391852;ENST00000419162	.|T;T	.|0.48836	.|0.8;0.82	5.9|5.9	5.9|5.9	0.94986|0.94986	.|.	.|0.049214	.|0.85682	.|D	.|0.000000	T|T	0.59729|0.59729	0.2215|0.2215	M|M	0.78049|0.78049	2.395|2.395	0.80722|0.80722	D|D	1|1	.|P;P	.|0.51537	.|0.775;0.946	.|B;P	.|0.48840	.|0.225;0.592	T|T	0.65672|0.65672	-0.6111|-0.6111	5|10	.|0.62326	.|D	.|0.03	-35.2765|-35.2765	15.9906|15.9906	0.80202|0.80202	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|196;333	.|Q5TAF1;O60478	.|.;G137B_HUMAN	E|I	196|333;332;115	.|ENSP00000355551:F333I;ENSP00000401841:F115I	.|ENSP00000355551:F333I	D|F	+|+	3|1	2|0	GPR137B|GPR137B	234435079|234435079	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	3.697000|3.697000	0.54764|0.54764	2.257000|2.257000	0.74773|0.74773	0.528000|0.528000	0.53228|0.53228	GAT|TTC	.	.		0.463	GPR137B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092761.1	NM_003272	
RYR2	6262	hgsc.bcm.edu	37	1	237774079	237774079	+	Silent	SNP	G	G	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:237774079G>T	ENST00000366574.2	+	36	5018	c.4701G>T	c.(4699-4701)tcG>tcT	p.S1567S	RYR2_ENST00000542537.1_Silent_p.S1551S|RYR2_ENST00000360064.6_Silent_p.S1565S	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1567	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGCCTCTCTCGGCGGGATTAT	0.532																																					p.S1567S		Atlas-SNP	.											.	RYR2	1273	.	0			c.G4701T						.						34.0	34.0	34.0					1																	237774079		1897	4104	6001	SO:0001819	synonymous_variant	6262	exon36			TCTCTCGGCGGGA	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.4701G>T	chr1.hg19:g.237774079G>T		67.0	0.0		181.0	52.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.532	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
OR2L13	284521	hgsc.bcm.edu	37	1	248263611	248263611	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:248263611G>T	ENST00000358120.2	+	2	1079	c.934G>T	c.(934-936)Gaa>Taa	p.E312*	OR2L13_ENST00000366478.2_Nonsense_Mutation_p.E312*			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	312						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			TTTCCTGAAAGAATAATCATG	0.433																																					p.E312X		Atlas-SNP	.											.	OR2L13	261	.	0			c.G934T						.						29.0	31.0	30.0					1																	248263611		2203	4300	6503	SO:0001587	stop_gained	284521	exon3			CTGAAAGAATAAT	BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"""GPCR / Class A : Olfactory receptors"""	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.934G>T	chr1.hg19:g.248263611G>T	ENSP00000350836:p.Glu312*	32.0	0.0		110.0	27.0	NM_175911	Q5VUR5	Nonsense_Mutation	SNP	ENST00000358120.2	hg19	CCDS1637.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.032243	0.54790	.	.	ENSG00000196071	ENST00000366478;ENST00000358120	.	.	.	4.12	-8.23	0.01033	.	1.716890	0.03777	N	0.260790	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	1.9389	0.03342	0.1185:0.2183:0.185:0.4783	.	.	.	.	X	312	.	ENSP00000350836:E312X	E	+	1	0	OR2L13	246330234	0.001000	0.12720	0.000000	0.03702	0.011000	0.07611	0.013000	0.13310	-2.305000	0.00654	-1.036000	0.02392	GAA	.	.		0.433	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911	
OR2T4	127074	hgsc.bcm.edu	37	1	248525404	248525404	+	Silent	SNP	C	C	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:248525404C>T	ENST00000366475.1	+	1	522	c.522C>T	c.(520-522)ctC>ctT	p.L174L		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	174						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGGTGTGTCTCTTCCTGTCAT	0.542																																					p.L174L		Atlas-SNP	.											.	OR2T4	126	.	0			c.C522T						.						270.0	235.0	247.0					1																	248525404		2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			GTGTCTCTTCCTG	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.522C>T	chr1.hg19:g.248525404C>T		172.0	0.0		1540.0	69.0	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	hg19	CCDS31113.1																																																																																			.	.		0.542	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
OR2T4	127074	hgsc.bcm.edu	37	1	248525411	248525411	+	Missense_Mutation	SNP	T	T	G			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:248525411T>G	ENST00000366475.1	+	1	529	c.529T>G	c.(529-531)Tca>Gca	p.S177A		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCTCTTCCTGTCATCAGGCTG	0.532																																					p.S177A		Atlas-SNP	.											.	OR2T4	126	.	0			c.T529G						.						266.0	232.0	243.0					1																	248525411		2203	4300	6503	SO:0001583	missense	127074	exon1			TTCCTGTCATCAG	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.529T>G	chr1.hg19:g.248525411T>G	ENSP00000355431:p.Ser177Ala	174.0	0.0		1529.0	62.0	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	hg19	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.746146	0.00087	.	.	ENSG00000196944	ENST00000366475	T	0.36699	1.24	3.48	0.418	0.16429	GPCR, rhodopsin-like superfamily (1);	1.058640	0.07443	N	0.897735	T	0.07503	0.0189	N	0.00321	-1.65	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33599	-0.9862	10	0.05959	T	0.93	.	2.6302	0.04941	0.3488:0.0:0.4402:0.2111	.	177	Q8NH00	OR2T4_HUMAN	A	177	ENSP00000355431:S177A	ENSP00000355431:S177A	S	+	1	0	OR2T4	246592034	0.197000	0.23362	0.009000	0.14445	0.004000	0.04260	0.693000	0.25497	0.026000	0.15269	-0.359000	0.07587	TCA	.	.		0.532	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
CLEC4F	165530	hgsc.bcm.edu	37	2	71047619	71047619	+	Missense_Mutation	SNP	G	G	T	rs575554427		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr2:71047619G>T	ENST00000272367.2	-	1	113	c.37C>A	c.(37-39)Cag>Aag	p.Q13K	CLEC4F_ENST00000426626.1_Missense_Mutation_p.Q13K	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	13					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						GAGACACACTGGTTATCTGTG	0.617																																					p.Q13K	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.C37A						.						109.0	78.0	89.0					2																	71047619		2203	4299	6502	SO:0001583	missense	165530	exon1			CACACTGGTTATC	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"""C-type lectin domain containing"""	25357	protein-coding gene	gene with protein product			"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"""	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.37C>A	chr2.hg19:g.71047619G>T	ENSP00000272367:p.Gln13Lys	54.0	0.0		100.0	49.0	NM_173535	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	hg19	CCDS1910.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.734209	0.48939	.	.	ENSG00000152672	ENST00000272367;ENST00000426626	T;T	0.03330	3.99;3.97	3.36	2.44	0.29823	.	.	.	.	.	T	0.05547	0.0146	L	0.52573	1.65	0.09310	N	0.999999	P;P	0.51057	0.941;0.941	B;B	0.44224	0.444;0.444	T	0.33650	-0.9860	9	0.87932	D	0	.	8.4551	0.32895	0.0:0.2405:0.7595:0.0	.	13;13	B7ZMM1;Q8N1N0	.;CLC4F_HUMAN	K	13	ENSP00000272367:Q13K;ENSP00000390581:Q13K	ENSP00000272367:Q13K	Q	-	1	0	CLEC4F	70901127	0.418000	0.25440	0.167000	0.22817	0.294000	0.27393	2.075000	0.41538	0.954000	0.37851	0.467000	0.42956	CAG	.	.		0.617	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
DNAH6	1768	hgsc.bcm.edu	37	2	85043137	85043137	+	Silent	SNP	G	G	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr2:85043137G>A	ENST00000237449.6	+	75	12311	c.12303G>A	c.(12301-12303)aaG>aaA	p.K4101K	DNAH6_ENST00000389394.3_Silent_p.K4101K			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	4101					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						AAAACTATAAGCCAAGCCCAA	0.458																																					p.K4101K		Atlas-SNP	.											.	DNAH6	194	.	0			c.G12303A						.						163.0	143.0	149.0					2																	85043137		692	1591	2283	SO:0001819	synonymous_variant	1768	exon76			CTATAAGCCAAGC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.12303G>A	chr2.hg19:g.85043137G>A		75.0	0.0		228.0	85.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.		0.458	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
CHL1	10752	hgsc.bcm.edu	37	3	440785	440785	+	Missense_Mutation	SNP	A	A	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr3:440785A>T	ENST00000256509.2	+	26	3981	c.3339A>T	c.(3337-3339)ttA>ttT	p.L1113F	CHL1_ENST00000397491.2_Missense_Mutation_p.L1097F	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		CACTACTATTATTAACTGTTT	0.358																																					p.L1113F		Atlas-SNP	.											.	CHL1	242	.	0			c.A3339T						.						196.0	188.0	190.0					3																	440785		2203	4300	6503	SO:0001583	missense	10752	exon26			ACTATTATTAACT	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.3339A>T	chr3.hg19:g.440785A>T	ENSP00000256509:p.Leu1113Phe	120.0	0.0		456.0	196.0	NM_006614	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	hg19	CCDS2556.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.92|17.92	3.505650|3.505650	0.64410|0.64410	.|.	.|.	ENSG00000134121|ENSG00000134121	ENST00000256509;ENST00000397491|ENST00000445697	T;T|.	0.70631|.	-0.5;-0.47|.	5.45|5.45	2.24|2.24	0.28232|0.28232	.|.	0.081995|.	0.51477|.	D|.	0.000098|.	T|T	0.63486|0.63486	0.2515|0.2515	M|M	0.63428|0.63428	1.95|1.95	0.39107|0.39107	D|D	0.961404|0.961404	D;D;D|.	0.89917|.	1.0;1.0;0.996|.	D;D;D|.	0.87578|.	0.998;0.993;0.974|.	T|T	0.63976|0.63976	-0.6515|-0.6515	10|5	0.87932|.	D|.	0|.	.|.	12.3397|12.3397	0.55087|0.55087	0.2175:0.0:0.7825:0.0|0.2175:0.0:0.7825:0.0	.|.	1097;1097;1113|.	B3KX75;O00533;O00533-2|.	.;CHL1_HUMAN;.|.	F|F	1113;1097|247	ENSP00000256509:L1113F;ENSP00000380628:L1097F|.	ENSP00000256509:L1113F|.	L|Y	+|+	3|2	2|0	CHL1|CHL1	415785|415785	1.000000|1.000000	0.71417|0.71417	0.160000|0.160000	0.22671|0.22671	0.875000|0.875000	0.50365|0.50365	1.949000|1.949000	0.40313|0.40313	0.672000|0.672000	0.31204|0.31204	-0.146000|-0.146000	0.13790|0.13790	TTA|TAT	.	.		0.358	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266100	41266100	+	Missense_Mutation	SNP	T	T	G	rs121913416		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr3:41266100T>G	ENST00000349496.5	+	3	377	c.97T>G	c.(97-99)Tct>Gct	p.S33A	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26A|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33A|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33A|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.S33P(47)|p.S33A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.W25_D32del(4)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.D32_S33insS(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.S33T(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TTACCTGGACTCTGGAATCCA	0.488		15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												p.S33A	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	CTNNB1,gallbladder,other,-1,1	CTNNB1	4904	.	212	Deletion - In frame(115)|Substitution - Missense(70)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)|Insertion - In frame(1)	liver(130)|large_intestine(20)|endometrium(14)|stomach(10)|pituitary(9)|pancreas(9)|central_nervous_system(8)|adrenal_gland(2)|small_intestine(2)|biliary_tract(2)|skin(2)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|breast(1)	c.T97G						.						93.0	77.0	82.0					3																	41266100		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CTGGACTCTGGAA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.97T>G	chr3.hg19:g.41266100T>G	ENSP00000344456:p.Ser33Ala	89.0	0.0		238.0	105.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.317386	0.81469	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.70281	0.3206	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74509	-0.3642	10	0.87932	D	0	-10.7796	16.0677	0.80897	0.0:0.0:0.0:1.0	.	33	P35222	CTNB1_HUMAN	A	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26A;ENSP00000385604:S33A;ENSP00000412219:S33A;ENSP00000379486:S33A;ENSP00000344456:S33A;ENSP00000411226:S26A;ENSP00000379488:S33A;ENSP00000409302:S33A;ENSP00000401599:S33A	ENSP00000344456:S33A	S	+	1	0	CTNNB1	41241104	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.201000	0.70794	0.533000	0.62120	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
PLXNA1	5361	hgsc.bcm.edu	37	3	126733602	126733602	+	Silent	SNP	C	C	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr3:126733602C>A	ENST00000393409.2	+	13	2805	c.2805C>A	c.(2803-2805)gcC>gcA	p.A935A	PLXNA1_ENST00000251772.4_Silent_p.A912A	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	935	IPT/TIG 1.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		CCCATGACGCCCTGGTGGAGG	0.692																																					p.A935A		Atlas-SNP	.											.	PLXNA1	185	.	0			c.C2805A						.						62.0	47.0	52.0					3																	126733602		2202	4299	6501	SO:0001819	synonymous_variant	5361	exon13			TGACGCCCTGGTG	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.2805C>A	chr3.hg19:g.126733602C>A		31.0	0.0		87.0	37.0	NM_032242		Silent	SNP	ENST00000393409.2	hg19	CCDS33847.2																																																																																			.	.		0.692	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
TSC22D2	9819	hgsc.bcm.edu	37	3	150128513	150128513	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr3:150128513C>T	ENST00000361875.3	+	1	2392	c.1376C>T	c.(1375-1377)cCg>cTg	p.P459L	TSC22D2_ENST00000361136.2_Missense_Mutation_p.P459L	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	459					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GGAGTGCCCCCGGCTACTGTG	0.736																																					p.P459L		Atlas-SNP	.											.	TSC22D2	42	.	0			c.C1376T						.						8.0	10.0	9.0					3																	150128513		2174	4252	6426	SO:0001583	missense	9819	exon1			TGCCCCCGGCTAC	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.1376C>T	chr3.hg19:g.150128513C>T	ENSP00000354543:p.Pro459Leu	7.0	0.0		40.0	19.0	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Missense_Mutation	SNP	ENST00000361875.3	hg19	CCDS3149.1	.	.	.	.	.	.	.	.	.	.	C	6.916	0.538699	0.13250	.	.	ENSG00000196428	ENST00000361875;ENST00000361136	T;T	0.35048	1.37;1.33	3.01	-0.242	0.13039	.	1.000620	0.08065	N	0.998965	T	0.19485	0.0468	N	0.12182	0.205	0.09310	N	0.999993	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.24512	-1.0158	10	0.46703	T	0.11	.	6.0063	0.19549	0.3438:0.5554:0.0:0.1008	.	459;459	O75157-2;O75157	.;T22D2_HUMAN	L	459	ENSP00000354543:P459L;ENSP00000354893:P459L	ENSP00000354893:P459L	P	+	2	0	TSC22D2	151611203	0.000000	0.05858	0.170000	0.22879	0.812000	0.45895	0.083000	0.14871	-0.060000	0.13132	0.557000	0.71058	CCG	.	.		0.736	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779	
FNDC3B	64778	hgsc.bcm.edu	37	3	172098773	172098773	+	Silent	SNP	T	T	C			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr3:172098773T>C	ENST00000336824.4	+	25	3292	c.3193T>C	c.(3193-3195)Tta>Cta	p.L1065L	FNDC3B_ENST00000415807.2_Silent_p.L1065L|FNDC3B_ENST00000416957.1_Silent_p.L1065L	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	1065	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		AGTAACACAGTTAGAAGGAAA	0.378																																					p.L1065L		Atlas-SNP	.											.	FNDC3B	118	.	0			c.T3193C						.						168.0	161.0	163.0					3																	172098773		2203	4300	6503	SO:0001819	synonymous_variant	64778	exon25			ACACAGTTAGAAG	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.3193T>C	chr3.hg19:g.172098773T>C		51.0	0.0		101.0	31.0	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	hg19	CCDS3217.1																																																																																			.	.		0.378	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
RFC1	5981	hgsc.bcm.edu	37	4	39310299	39310299	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr4:39310299C>A	ENST00000381897.1	-	13	1975	c.1842G>T	c.(1840-1842)tgG>tgT	p.W614C	RFC1_ENST00000349703.2_Missense_Mutation_p.W614C	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	614					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						AGTTTCGGAGCCAGCGTAGGA	0.428																																					p.W614C	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.G1842T						.						159.0	166.0	164.0					4																	39310299		2203	4300	6503	SO:0001583	missense	5981	exon13			TCGGAGCCAGCGT	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"""ATPases / AAA-type"""	9969	protein-coding gene	gene with protein product		102579	"""replication factor C (activator 1) 1 (145kD)"""			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.1842G>T	chr4.hg19:g.39310299C>A	ENSP00000371321:p.Trp614Cys	141.0	0.0		563.0	248.0	NM_002913	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Missense_Mutation	SNP	ENST00000381897.1	hg19	CCDS56329.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.611366	0.87258	.	.	ENSG00000035928	ENST00000381897;ENST00000349703	T;T	0.17854	2.25;2.25	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.54398	0.1856	M	0.90922	3.16	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.62548	-0.6831	10	0.87932	D	0	-6.9473	20.3053	0.98627	0.0:1.0:0.0:0.0	.	614;614	P35251;P35251-2	RFC1_HUMAN;.	C	614	ENSP00000371321:W614C;ENSP00000261424:W614C	ENSP00000261424:W614C	W	-	3	0	RFC1	38986694	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.502000	0.81614	2.808000	0.96608	0.655000	0.94253	TGG	.	.		0.428	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913	
PABPC4L	132430	hgsc.bcm.edu	37	4	135121534	135121534	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr4:135121534C>A	ENST00000421491.3	-	2	897	c.641G>T	c.(640-642)gGc>gTc	p.G214V	PABPC4L_ENST00000529122.2_Missense_Mutation_p.G272V			P0CB38	PAB4L_HUMAN	poly(A) binding protein, cytoplasmic 4-like	214	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)	3						CAGAGTTTTGCCATATTTGCT	0.413																																					p.G272V		Atlas-SNP	.											.	PABPC4L	60	.	0			c.G815T						.						85.0	70.0	74.0					4																	135121534		692	1591	2283	SO:0001583	missense	132430	exon2			GTTTTGCCATATT	AY672099		4q28.3	2013-02-12				ENSG00000254535		"""RNA binding motif (RRM) containing"""	31955	protein-coding gene	gene with protein product							Standard	NM_001114734		Approved		uc010ioe.3	P0CB38		ENST00000421491.3:c.641G>T	chr4.hg19:g.135121534C>A	ENSP00000463233:p.Gly214Val	62.0	0.0		195.0	87.0	NM_001114734		Missense_Mutation	SNP	ENST00000421491.3	hg19																																																																																				.	.		0.413	PABPC4L-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364399.2	NM_001114734	
EDNRA	1909	hgsc.bcm.edu	37	4	148457097	148457097	+	Silent	SNP	G	G	A	rs200693894		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr4:148457097G>A	ENST00000324300.5	+	5	1331	c.816G>A	c.(814-816)gcG>gcA	p.A272A	EDNRA_ENST00000503721.1_3'UTR|EDNRA_ENST00000511804.1_Silent_p.A47A|EDNRA_ENST00000358556.4_Silent_p.A163A|EDNRA_ENST00000506066.1_Silent_p.A163A|EDNRA_ENST00000339690.5_3'UTR	NM_001957.3	NP_001948.1	P25101	EDNRA_HUMAN	endothelin receptor type A	272					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|glomerular filtration (GO:0003094)|glucose transport (GO:0015758)|head development (GO:0060322)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|maternal process involved in parturition (GO:0060137)|metabolic process (GO:0008152)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP biosynthetic process (GO:0030818)|neural crest cell development (GO:0014032)|patterning of blood vessels (GO:0001569)|penile erection (GO:0043084)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of kidney development (GO:0090184)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of odontogenesis (GO:0042482)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|smooth muscle cell proliferation (GO:0048659)|smooth muscle contraction (GO:0006939)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	endothelin receptor activity (GO:0004962)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)	17	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Acetylsalicylic acid(DB00945)|Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TGTGCACTGCGATCTTCTACA	0.418																																					p.A272A		Atlas-SNP	.											.	EDNRA	48	.	0			c.G816A						.						220.0	205.0	210.0					4																	148457097		2203	4300	6503	SO:0001819	synonymous_variant	1909	exon5			CACTGCGATCTTC	D90348	CCDS3769.1, CCDS54810.1, CCDS58927.1	4q31.22	2013-09-20			ENSG00000151617	ENSG00000151617		"""GPCR / Class A : Endothelin receptors"""	3179	protein-coding gene	gene with protein product		131243				1659806	Standard	NM_001957		Approved		uc003iky.3	P25101	OTTHUMG00000161354	ENST00000324300.5:c.816G>A	chr4.hg19:g.148457097G>A		109.0	0.0		297.0	127.0	NM_001957	B2R723|B4E2V6|B7Z9G6|D3DP03|E7ER36|O43441|Q16432|Q16433|Q8TBH2	Silent	SNP	ENST00000324300.5	hg19	CCDS3769.1																																																																																			.	.		0.418	EDNRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364635.1		
TNPO1	3842	hgsc.bcm.edu	37	5	72168474	72168474	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:72168474C>T	ENST00000337273.5	+	7	1031	c.605C>T	c.(604-606)gCt>gTt	p.A202V	TNPO1_ENST00000447967.2_Silent_p.L114L|TNPO1_ENST00000454282.1_Missense_Mutation_p.A152V|TNPO1_ENST00000523768.1_Missense_Mutation_p.A152V|TNPO1_ENST00000506351.2_Missense_Mutation_p.A194V	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	202					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		AGGTCTCACGCTGTTGCATGT	0.328																																					p.A202V		Atlas-SNP	.											TNPO1,colon,carcinoma,0,1	TNPO1	90	.	0			c.C605T						.						145.0	127.0	133.0					5																	72168474		2203	4300	6503	SO:0001583	missense	3842	exon7			CTCACGCTGTTGC	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"""Importins"""	6401	protein-coding gene	gene with protein product	"""importin 2"""	602901	"""karyopherin (importin) beta 2"""	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.605C>T	chr5.hg19:g.72168474C>T	ENSP00000336712:p.Ala202Val	96.0	0.0		223.0	100.0	NM_002270	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	C	34	5.336982	0.95758	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351	T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72	5.25	5.25	0.73442	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.89114	0.6623	H	0.95780	3.72	0.80722	D	1	D;D	0.67145	0.996;0.992	D;P	0.70487	0.969;0.808	D	0.92131	0.5712	10	0.87932	D	0	-14.3056	19.1933	0.93675	0.0:1.0:0.0:0.0	.	152;202	Q92973-3;Q92973	.;TNPO1_HUMAN	V	202;152;152;194	ENSP00000336712:A202V;ENSP00000398524:A152V;ENSP00000428899:A152V;ENSP00000425118:A194V	ENSP00000336712:A202V	A	+	2	0	TNPO1	72204230	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	5.756000	0.68757	2.626000	0.88956	0.591000	0.81541	GCT	.	.		0.328	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270	
TTC37	9652	hgsc.bcm.edu	37	5	94839530	94839530	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:94839530C>T	ENST00000358746.2	-	31	3503	c.3205G>A	c.(3205-3207)Gag>Aag	p.E1069K		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	1069						cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						TTGCTGCTCTCTTTATAAAGC	0.363																																					p.E1069K		Atlas-SNP	.											.	TTC37	128	.	0			c.G3205A						.						122.0	121.0	121.0					5																	94839530		2203	4300	6503	SO:0001583	missense	9652	exon31			TGCTCTCTTTATA	AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"""Tetratricopeptide (TTC) repeat domain containing"""	23639	protein-coding gene	gene with protein product		614589	"""KIAA0372"""	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.3205G>A	chr5.hg19:g.94839530C>T	ENSP00000351596:p.Glu1069Lys	86.0	0.0		154.0	63.0	NM_014639	O15077|Q6PJI3	Missense_Mutation	SNP	ENST00000358746.2	hg19	CCDS4072.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496049	0.85069	.	.	ENSG00000198677	ENST00000358746	T	0.54675	0.56	5.7	5.7	0.88788	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.56187	0.1968	M	0.77616	2.38	0.80722	D	1	P	0.40731	0.728	B	0.36092	0.217	T	0.57768	-0.7754	10	0.29301	T	0.29	.	20.2096	0.98287	0.0:1.0:0.0:0.0	.	1069	Q6PGP7	TTC37_HUMAN	K	1069	ENSP00000351596:E1069K	ENSP00000351596:E1069K	E	-	1	0	TTC37	94865286	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	6.497000	0.73674	2.841000	0.97950	0.637000	0.83480	GAG	.	.		0.363	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639	
CDO1	1036	hgsc.bcm.edu	37	5	115146946	115146946	+	Silent	SNP	T	T	C			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:115146946T>C	ENST00000250535.4	-	3	871	c.315A>G	c.(313-315)acA>acG	p.T105T	CDO1_ENST00000502631.1_5'UTR	NM_001801.2	NP_001792.2	Q16878	CDO1_HUMAN	cysteine dioxygenase type 1	105					cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|inflammatory response (GO:0006954)|L-cysteine catabolic process (GO:0019448)|lactation (GO:0007595)|oxidation-reduction process (GO:0055114)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to ethanol (GO:0045471)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|sulfur amino acid biosynthetic process (GO:0000097)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)	cytosol (GO:0005829)	cysteine dioxygenase activity (GO:0017172)|ferrous iron binding (GO:0008198)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|skin(5)	11		all_cancers(142;0.0046)|all_epithelial(76;0.000161)|Prostate(80;0.0132)|Ovarian(225;0.0776)		OV - Ovarian serous cystadenocarcinoma(64;7.8e-08)|Epithelial(69;7.32e-07)|all cancers(49;3.24e-05)	L-Cysteine(DB00151)	AGGCAAATAATGTCTCCTTTA	0.393																																					p.T105T		Atlas-SNP	.											CDO1,NS,carcinoma,0,1	CDO1	29	.	0			c.A315G						.						218.0	209.0	212.0					5																	115146946		2202	4300	6502	SO:0001819	synonymous_variant	1036	exon3			AAATAATGTCTCC		CCDS4121.1	5q23.2	2013-06-11	2013-06-11		ENSG00000129596	ENSG00000129596	1.13.11.20		1795	protein-coding gene	gene with protein product		603943	"""cysteine dioxygenase, type I"""			7524679	Standard	NM_001801		Approved		uc003krg.3	Q16878	OTTHUMG00000128891	ENST00000250535.4:c.315A>G	chr5.hg19:g.115146946T>C		106.0	0.0		302.0	120.0	NM_001801	B2RAK4|P78513|Q6FHZ8|Q8TB64	Silent	SNP	ENST00000250535.4	hg19	CCDS4121.1																																																																																			.	.		0.393	CDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250853.2	NM_001801	
PCDHA3	56145	hgsc.bcm.edu	37	5	140182753	140182753	+	Silent	SNP	C	C	G			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:140182753C>G	ENST00000522353.2	+	1	1971	c.1971C>G	c.(1969-1971)ccC>ccG	p.P657P	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA3_ENST00000532566.2_Silent_p.P657P	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	657	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGGTGAACCCTCATTGACCG	0.692																																					p.P657P		Atlas-SNP	.											.	PCDHA3	396	.	0			c.C1971G						.						60.0	61.0	61.0					5																	140182753		2203	4300	6503	SO:0001819	synonymous_variant	56145	exon1			TGAACCCTCATTG	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1971C>G	chr5.hg19:g.140182753C>G		50.0	0.0		106.0	48.0	NM_031497	O75286	Silent	SNP	ENST00000522353.2	hg19	CCDS54915.1																																																																																			.	.		0.692	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
LCP2	3937	hgsc.bcm.edu	37	5	169685155	169685155	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:169685155A>G	ENST00000046794.5	-	16	1601	c.986T>C	c.(985-987)tTg>tCg	p.L329S	LCP2_ENST00000521416.1_Missense_Mutation_p.L124S	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	329					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		TGGCTGGGGCAAAGGTCTCTG	0.498																																					p.L329S		Atlas-SNP	.											.	LCP2	133	.	0			c.T986C						.						175.0	173.0	174.0					5																	169685155		1945	4144	6089	SO:0001583	missense	3937	exon16			TGGGGCAAAGGTC		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"""SH2 domain containing"""	6529	protein-coding gene	gene with protein product	"""76 kDa tyrosine phosphoprotein"", ""SH2 domain-containing leukocyte protein of 76kD"""	601603	"""lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"""	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.986T>C	chr5.hg19:g.169685155A>G	ENSP00000046794:p.Leu329Ser	75.0	0.0		154.0	63.0	NM_005565	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	hg19	CCDS47339.1	.	.	.	.	.	.	.	.	.	.	A	14.72	2.620395	0.46736	.	.	ENSG00000043462	ENST00000046794;ENST00000521416;ENST00000520344	T;T	0.48836	0.82;0.8	5.72	4.56	0.56223	.	0.301944	0.29073	N	0.013231	T	0.42494	0.1205	L	0.50333	1.59	0.36232	D	0.852709	P;P	0.44776	0.843;0.469	B;B	0.42653	0.394;0.209	T	0.50988	-0.8762	9	.	.	.	-5.6214	9.5973	0.39582	0.92:0.0:0.08:0.0	.	124;329	E7ESF6;Q13094	.;LCP2_HUMAN	S	329;124;96	ENSP00000046794:L329S;ENSP00000428871:L124S	.	L	-	2	0	LCP2	169617733	0.999000	0.42202	0.984000	0.44739	0.744000	0.42396	2.971000	0.49248	1.108000	0.41662	0.533000	0.62120	TTG	.	.		0.498	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565	
SIMC1	375484	hgsc.bcm.edu	37	5	175772304	175772305	+	Missense_Mutation	DNP	CC	CC	AA			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:175772304_175772305CC>AA	ENST00000443967.1	+	12	2882_2883	c.2475_2476CC>AA	c.(2473-2478)ttCCgc>ttAAgc	p.825_826FR>LS	KIAA1191_ENST00000393728.2_5'Flank|SIMC1_ENST00000341199.6_Missense_Mutation_p.410_411FR>LS|SIMC1_ENST00000332772.4_Missense_Mutation_p.286_287FR>LS|SIMC1_ENST00000430704.2_Missense_Mutation_p.410_411FR>LS|RP11-843P14.2_ENST00000508187.1_RNA			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	825							SUMO polymer binding (GO:0032184)										TTGAGGCCTTCCGCAGCCGCCT	0.51																																					p.F410L|p.R411S		Atlas-SNP	.											.	.	.	.	0			c.C1230A|c.C1231A						.																																			SO:0001583	missense	375484	exon9			GGCCTTCCGCAGC|GCCTTCCGCAGCC	BC037298	CCDS4398.2	5q35.2	2013-08-14	2012-11-14	2012-11-14	ENSG00000170085	ENSG00000170085			24779	protein-coding gene	gene with protein product	"""oocyte maturation associated 1"", ""platform element for inhibition of autolytic degradation"""		"""chromosome 5 open reading frame 25"""	C5orf25		23086935, 23707407	Standard	NM_198567		Approved	FLJ44216, OOMA1, PLEIAD	uc003mds.4	Q8NDZ2	OTTHUMG00000130663	Exception_encountered	chr5.hg19:g.175772304_175772305delinsAA	ENSP00000406571:p.F825_R826delinsLS	73.0|72.0	0.0		191.0|193.0	81.0|80.0	NM_198567	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	Missense_Mutation	SNP	ENST00000443967.1	hg19																																																																																				.	.		0.510	SIMC1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000253155.2	NM_198567	
TRIM52	84851	hgsc.bcm.edu	37	5	180687428	180687428	+	Silent	SNP	C	C	T	rs200454506|rs3073543|rs33972170	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr5:180687428C>T	ENST00000327767.4	-	1	691	c.387G>A	c.(385-387)gaG>gaA	p.E129E	TRIM52-AS1_ENST00000507434.1_RNA|TRIM52_ENST00000514805.1_5'UTR|CTC-338M12.4_ENST00000511331.1_RNA|CTC-338M12.4_ENST00000505151.1_RNA|TRIM52-AS1_ENST00000509252.1_RNA|TRIM52-AS1_ENST00000514146.1_RNA|CTC-338M12.4_ENST00000417281.2_RNA	NM_032765.2	NP_116154.1	Q96A61	TRI52_HUMAN	tripartite motif containing 52	129	Glu-rich.				positive regulation of NF-kappaB transcription factor activity (GO:0051092)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.0106)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0588)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.232)		CCTGATCTTCCTCTTCTTCTT	0.458																																					p.E129E		Atlas-SNP	.											.	TRIM52	20	.	0			c.G387A						.						187.0	165.0	173.0					5																	180687428		2203	4300	6503	SO:0001819	synonymous_variant	84851	exon1			ATCTTCCTCTTCT		CCDS4467.1	5q35.3	2013-01-09	2011-01-25		ENSG00000183718	ENSG00000183718		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19024	protein-coding gene	gene with protein product			"""tripartite motif-containing 52"""				Standard	NM_032765		Approved	RNF102	uc003mnp.3	Q96A61	OTTHUMG00000130964	ENST00000327767.4:c.387G>A	chr5.hg19:g.180687428C>T		59.0	0.0		184.0	18.0	NM_032765		Silent	SNP	ENST00000327767.4	hg19	CCDS4467.1																																																																																			.	.		0.458	TRIM52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253572.3	NM_032765	
ITPR3	3710	hgsc.bcm.edu	37	6	33657110	33657110	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr6:33657110C>A	ENST00000374316.5	+	51	7850	c.6790C>A	c.(6790-6792)Ctc>Atc	p.L2264I	ITPR3_ENST00000605930.1_Missense_Mutation_p.L2264I			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2264					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	CATCCGCCCCCTCATCGTGGC	0.612																																					p.L2264I		Atlas-SNP	.											.	ITPR3	409	.	0			c.C6790A						.						133.0	112.0	119.0					6																	33657110		2203	4300	6503	SO:0001583	missense	3710	exon50			CGCCCCCTCATCG	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.6790C>A	chr6.hg19:g.33657110C>A	ENSP00000363435:p.Leu2264Ile	57.0	0.0		75.0	32.0	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.060027	0.55325	.	.	ENSG00000096433	ENST00000374316	D	0.92249	-3.0	5.07	4.17	0.49024	.	0.201739	0.42821	D	0.000658	D	0.87708	0.6245	L	0.58669	1.825	0.45464	D	0.998435	B;B	0.22346	0.028;0.068	B;B	0.35312	0.2;0.132	D	0.86469	0.1784	10	0.52906	T	0.07	-35.9732	10.4156	0.44320	0.0:0.7737:0.1477:0.0786	.	2264;1934	Q14573;Q59ES2	ITPR3_HUMAN;.	I	2264	ENSP00000363435:L2264I	ENSP00000363435:L2264I	L	+	1	0	ITPR3	33765088	0.978000	0.34361	1.000000	0.80357	0.960000	0.62799	2.274000	0.43390	2.653000	0.90120	0.561000	0.74099	CTC	.	.		0.612	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
CYP39A1	51302	hgsc.bcm.edu	37	6	46607278	46607278	+	Silent	SNP	C	C	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr6:46607278C>T	ENST00000275016.2	-	3	644	c.441G>A	c.(439-441)ctG>ctA	p.L147L		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	147					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						CTAAATTCTCCAGTTGTTCAT	0.353																																					p.L147L		Atlas-SNP	.											.	CYP39A1	41	.	0			c.G441A						.						139.0	131.0	134.0					6																	46607278		2203	4300	6503	SO:0001819	synonymous_variant	51302	exon3			ATTCTCCAGTTGT	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.441G>A	chr6.hg19:g.46607278C>T		108.0	0.0		336.0	138.0	NM_016593	Q5VTT0|Q96FW5	Silent	SNP	ENST00000275016.2	hg19	CCDS4916.1																																																																																			.	.		0.353	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
CDK13	8621	hgsc.bcm.edu	37	7	40085553	40085553	+	Silent	SNP	T	T	C			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:40085553T>C	ENST00000181839.4	+	6	3077	c.2472T>C	c.(2470-2472)ggT>ggC	p.G824G	CDK13_ENST00000340829.5_Silent_p.G824G|CDK13_ENST00000484589.1_3'UTR	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	824	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						TCATGGAGGGTCTGGATTATT	0.313																																					p.G824G		Atlas-SNP	.											.	CDK13	114	.	0			c.T2472C						.						131.0	139.0	136.0					7																	40085553		2203	4300	6503	SO:0001819	synonymous_variant	8621	exon6			GGAGGGTCTGGAT	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"""Cyclin-dependent kinases"""	1733	protein-coding gene	gene with protein product	"""cholinesterase-related cell division controller"""	603309	"""cell division cycle 2-like 5 (cholinesterase-related cell division controller)"""	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.2472T>C	chr7.hg19:g.40085553T>C		60.0	0.0		154.0	74.0	NM_003718	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Silent	SNP	ENST00000181839.4	hg19	CCDS5461.1																																																																																			.	.		0.313	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718	
PHTF2	57157	hgsc.bcm.edu	37	7	77569480	77569480	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:77569480C>A	ENST00000248550.7	+	13	1677	c.1601C>A	c.(1600-1602)tCa>tAa	p.S534*	PHTF2_ENST00000307305.8_Nonsense_Mutation_p.S496*|PHTF2_ENST00000422959.2_Nonsense_Mutation_p.S500*|PHTF2_ENST00000424760.1_Nonsense_Mutation_p.S496*|PHTF2_ENST00000275575.7_Nonsense_Mutation_p.S496*|PHTF2_ENST00000416283.2_Nonsense_Mutation_p.S500*			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	534					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						CATTCTGCTTCAGAACTTTAT	0.373																																					p.S500X		Atlas-SNP	.											.	PHTF2	104	.	0			c.C1499A						.						126.0	116.0	119.0					7																	77569480		1862	4106	5968	SO:0001587	stop_gained	57157	exon12			CTGCTTCAGAACT	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.1601C>A	chr7.hg19:g.77569480C>A	ENSP00000248550:p.Ser534*	126.0	0.0		495.0	183.0	NM_001127357	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Nonsense_Mutation	SNP	ENST00000248550.7	hg19		.	.	.	.	.	.	.	.	.	.	C	38	6.899107	0.97920	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000424760;ENST00000275575;ENST00000416283;ENST00000248550	.	.	.	5.67	5.67	0.87782	.	0.344882	0.27482	N	0.019166	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.3448	13.9903	0.64362	0.0:0.9275:0.0:0.0725	.	.	.	.	X	500;500;496;496;496;500;534	.	ENSP00000248550:S534X	S	+	2	0	PHTF2	77407416	0.990000	0.36364	0.995000	0.50966	0.969000	0.65631	1.485000	0.35519	2.665000	0.90641	0.557000	0.71058	TCA	.	.		0.373	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432	
MUC17	140453	hgsc.bcm.edu	37	7	100678724	100678724	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:100678724C>A	ENST00000306151.4	+	3	4091	c.4027C>A	c.(4027-4029)Cct>Act	p.P1343T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1343	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AACAAGTATACCTGTCAACAC	0.463																																					p.P1343T		Atlas-SNP	.											.	MUC17	804	.	0			c.C4027A						.						231.0	226.0	228.0					7																	100678724		2203	4300	6503	SO:0001583	missense	140453	exon3			AGTATACCTGTCA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.4027C>A	chr7.hg19:g.100678724C>A	ENSP00000302716:p.Pro1343Thr	66.0	0.0		198.0	10.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	c	0.046	-1.266293	0.01433	.	.	ENSG00000169876	ENST00000306151	T	0.03212	4.01	0.656	-0.414	0.12359	.	.	.	.	.	T	0.02342	0.0072	L	0.29908	0.895	0.09310	N	1	B	0.24576	0.106	B	0.16722	0.016	T	0.48758	-0.9007	8	0.08381	T	0.77	.	.	.	.	.	1343	Q685J3	MUC17_HUMAN	T	1343	ENSP00000302716:P1343T	ENSP00000302716:P1343T	P	+	1	0	MUC17	100465444	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.852000	0.00350	-0.128000	0.11641	-1.404000	0.01136	CCT	.	.		0.463	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
NRCAM	4897	hgsc.bcm.edu	37	7	107824934	107824934	+	Silent	SNP	G	G	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:107824934G>A	ENST00000425651.2	-	18	2159	c.2160C>T	c.(2158-2160)cgC>cgT	p.R720R	NRCAM_ENST00000379024.4_Silent_p.R701R|NRCAM_ENST00000351718.4_Silent_p.R704R|NRCAM_ENST00000379028.3_Silent_p.R720R|NRCAM_ENST00000413765.2_Silent_p.R701R|NRCAM_ENST00000379022.4_Silent_p.R720R	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	720	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						CTGCCATCACGCGGAAGGAGT	0.547																																					p.R720R		Atlas-SNP	.											.	NRCAM	267	.	0			c.C2160T						.						99.0	91.0	94.0					7																	107824934		2203	4300	6503	SO:0001819	synonymous_variant	4897	exon18			CATCACGCGGAAG		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.2160C>T	chr7.hg19:g.107824934G>A		42.0	0.0		106.0	39.0	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	hg19	CCDS47686.1																																																																																			.	.		0.547	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
HYAL4	23553	hgsc.bcm.edu	37	7	123508467	123508467	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:123508467C>A	ENST00000223026.4	+	3	778	c.140C>A	c.(139-141)cCt>cAt	p.P47H	HYAL4_ENST00000476325.1_Missense_Mutation_p.P47H	NM_012269.2	NP_036401.2	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	47					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|glycosaminoglycan catabolic process (GO:0006027)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	hyalurononglucosaminidase activity (GO:0004415)	p.P47L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	23						CAAAGGAAACCTTTTATAGCT	0.353																																					p.P47H		Atlas-SNP	.											HYAL4,NS,carcinoma,0,1	HYAL4	65	.	1	Substitution - Missense(1)	endometrium(1)	c.C140A						.						72.0	77.0	75.0					7																	123508467		2203	4300	6503	SO:0001583	missense	23553	exon3			GGAAACCTTTTAT	AF009010	CCDS5789.1	7q31.3	2010-01-14			ENSG00000106302	ENSG00000106302			5323	protein-coding gene	gene with protein product	"""hyaluronidase 4"""	604510				10493834	Standard	NM_012269		Approved		uc003vlc.3	Q2M3T9	OTTHUMG00000157349	ENST00000223026.4:c.140C>A	chr7.hg19:g.123508467C>A	ENSP00000223026:p.Pro47His	60.0	0.0		162.0	70.0	NM_012269	D0VXG1|Q9UL99|Q9Y6T9	Missense_Mutation	SNP	ENST00000223026.4	hg19	CCDS5789.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.090318	0.76756	.	.	ENSG00000106302	ENST00000489978;ENST00000223026;ENST00000476325	T;T	0.55052	0.54;0.54	5.73	5.73	0.89815	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.71324	0.3326	M	0.83483	2.645	0.47621	D	0.999479	P;D	0.56746	0.887;0.977	P;P	0.59546	0.657;0.859	T	0.75593	-0.3264	10	0.87932	D	0	-0.4856	14.5749	0.68238	0.1453:0.8547:0.0:0.0	.	47;47	F8WDH9;Q2M3T9	.;HYAL4_HUMAN	H	47	ENSP00000223026:P47H;ENSP00000417186:P47H	ENSP00000223026:P47H	P	+	2	0	HYAL4	123295703	1.000000	0.71417	0.979000	0.43373	0.964000	0.63967	4.591000	0.61019	2.698000	0.92095	0.655000	0.94253	CCT	.	.		0.353	HYAL4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348545.1	NM_012269	
KMT2C	58508	hgsc.bcm.edu	37	7	151962169	151962169	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:151962169G>A	ENST00000262189.6	-	8	1356	c.1138C>T	c.(1138-1140)Cgt>Tgt	p.R380C	KMT2C_ENST00000355193.2_Missense_Mutation_p.R380C	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	380					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R380C(2)									CAACCTGCACGTTTTAATGGA	0.448																																					p.R380C		Atlas-SNP	.											MLL3_ENST00000355193,extremity,malignant_melanoma,+1,2	MLL3	1564	.	2	Substitution - Missense(2)	central_nervous_system(2)	c.C1138T						.						418.0	376.0	390.0					7																	151962169		2203	4300	6503	SO:0001583	missense	58508	exon8			CTGCACGTTTTAA	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1138C>T	chr7.hg19:g.151962169G>A	ENSP00000262189:p.Arg380Cys	134.0	0.0		367.0	16.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.858881	0.32884	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98926	-5.24;-5.24	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.38548	U	0.001645	D	0.99039	0.9671	M	0.83223	2.63	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.99437	1.0937	10	0.87932	D	0	.	14.4119	0.67119	0.0:0.0:0.852:0.148	.	380	Q8NEZ4	MLL3_HUMAN	C	380	ENSP00000262189:R380C;ENSP00000347325:R380C	ENSP00000262189:R380C	R	-	1	0	MLL3	151593102	1.000000	0.71417	1.000000	0.80357	0.490000	0.33462	3.895000	0.56258	2.271000	0.75665	0.557000	0.71058	CGT	.	.		0.448	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
CDHR1	92211	hgsc.bcm.edu	37	10	85960359	85960359	+	Silent	SNP	C	C	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr10:85960359C>T	ENST00000372117.3	+	6	544	c.441C>T	c.(439-441)gaC>gaT	p.D147D	CDHR1_ENST00000440770.2_5'Flank|CDHR1_ENST00000332904.3_Silent_p.D147D	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	147	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						CCCCTCAGGACATACCTGCTG	0.592																																					p.D147D		Atlas-SNP	.											.	CDHR1	122	.	0			c.C441T						.						79.0	58.0	65.0					10																	85960359		2203	4300	6503	SO:0001819	synonymous_variant	92211	exon6			TCAGGACATACCT	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.441C>T	chr10.hg19:g.85960359C>T		76.0	0.0		123.0	62.0	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	hg19	CCDS7372.1																																																																																			.	.		0.592	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
CUTC	51076	hgsc.bcm.edu	37	10	101503802	101503802	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr10:101503802C>T	ENST00000370476.5	+	5	541	c.412C>T	c.(412-414)Cgc>Tgc	p.R138C		NM_015960.2	NP_057044.2	Q9NTM9	CUTC_HUMAN	cutC copper transporter	138					copper ion homeostasis (GO:0055070)|copper ion transport (GO:0006825)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	copper ion binding (GO:0005507)	p.R138G(1)|p.R138C(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Colorectal(252;0.234)		Epithelial(162;3e-10)|all cancers(201;2.37e-08)		AGCTATTTGCCGCCCTCTGCC	0.338																																					p.R138C		Atlas-SNP	.											CUTC,NS,carcinoma,0,2	CUTC	32	.	2	Substitution - Missense(2)	prostate(1)|lung(1)	c.C412T						.						130.0	123.0	126.0					10																	101503802		2203	4300	6503	SO:0001583	missense	51076	exon5			ATTTGCCGCCCTC	AF132966	CCDS7483.1	10q24.31	2013-07-31	2013-07-31		ENSG00000119929	ENSG00000119929			24271	protein-coding gene	gene with protein product		610101	"""cutC copper transporter homolog (E. coli)"""			16182249	Standard	NM_015960		Approved	CGI-32	uc001kqd.4	Q9NTM9	OTTHUMG00000018889	ENST00000370476.5:c.412C>T	chr10.hg19:g.101503802C>T	ENSP00000359507:p.Arg138Cys	62.0	0.0		174.0	85.0	NM_015960	Q5TCZ8|Q9Y321	Missense_Mutation	SNP	ENST00000370476.5	hg19	CCDS7483.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.828442	0.50845	.	.	ENSG00000119929	ENST00000370476;ENST00000370472	.	.	.	4.97	4.97	0.65823	Copper homeostasis CutC domain (2);	0.051997	0.85682	D	0.000000	T	0.63780	0.2540	M	0.83223	2.63	0.80722	D	1	P;B	0.36027	0.533;0.101	B;B	0.24269	0.052;0.03	T	0.70092	-0.4967	9	0.48119	T	0.1	-9.0535	18.7716	0.91894	0.0:1.0:0.0:0.0	.	138;138	B4DYM2;Q9NTM9	.;CUTC_HUMAN	C	138;75	.	ENSP00000359503:R75C	R	+	1	0	CUTC	101493792	1.000000	0.71417	1.000000	0.80357	0.569000	0.35902	6.643000	0.74334	2.727000	0.93392	0.591000	0.81541	CGC	.	.		0.338	CUTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049811.1	NM_015960	
MUC6	4588	hgsc.bcm.edu	37	11	1016851	1016851	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr11:1016851T>C	ENST00000421673.2	-	31	6000	c.5950A>G	c.(5950-5952)Atg>Gtg	p.M1984V		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1984	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTTGCAGTCATAGGACCTGTG	0.582																																					p.M1984V		Atlas-SNP	.											.	MUC6	408	.	0			c.A5950G						.						1531.0	1522.0	1525.0					11																	1016851		2203	4298	6501	SO:0001583	missense	4588	exon31			CAGTCATAGGACC	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5950A>G	chr11.hg19:g.1016851T>C	ENSP00000406861:p.Met1984Val	186.0	0.0		1978.0	89.0	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	1.757	-0.487796	0.04352	.	.	ENSG00000184956	ENST00000421673	T	0.17370	2.28	2.75	-1.23	0.09465	.	.	.	.	.	T	0.10809	0.0264	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45205	-0.9277	9	0.06365	T	0.9	.	7.0983	0.25321	0.0:0.1589:0.2688:0.5723	.	1984	Q6W4X9	MUC6_HUMAN	V	1984	ENSP00000406861:M1984V	ENSP00000406861:M1984V	M	-	1	0	MUC6	1006851	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.137000	0.00588	-0.732000	0.04856	-2.319000	0.00253	ATG	.	.		0.582	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
EFEMP2	30008	hgsc.bcm.edu	37	11	65638628	65638628	+	Splice_Site	SNP	C	C	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr11:65638628C>A	ENST00000307998.6	-	4	597	c.367G>T	c.(367-369)Gat>Tat	p.D123Y	EFEMP2_ENST00000528176.1_Splice_Site_p.D123Y	NM_016938.4	NP_058634.4	O95967	FBLN4_HUMAN	EGF containing fibulin-like extracellular matrix protein 2	123	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				blood coagulation (GO:0007596)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21				READ - Rectum adenocarcinoma(159;0.169)		CCCCACTCACCCACACAGCTG	0.632																																					p.D123Y		Atlas-SNP	.											.	EFEMP2	42	.	0			c.G367T						.						58.0	56.0	57.0					11																	65638628		2201	4296	6497	SO:0001630	splice_region_variant	30008	exon4			ACTCACCCACACA	AF109121	CCDS8116.1	11q13	2011-06-17	2011-01-25		ENSG00000172638	ENSG00000172638		"""Fibulins"""	3219	protein-coding gene	gene with protein product	"""fibulin 4"""	604633	"""EGF-containing fibulin-like extracellular matrix protein 2"""			10601734, 10982184	Standard	NR_037718		Approved	FBLN4, UPH1	uc001ofy.4	O95967	OTTHUMG00000166664	ENST00000307998.6:c.367+1G>T	chr11.hg19:g.65638628C>A		23.0	0.0		58.0	20.0	NM_016938	A8K7R4|B3KM31|B3KQT1|O75967	Missense_Mutation	SNP	ENST00000307998.6	hg19	CCDS8116.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.308672	0.81247	.	.	ENSG00000172638	ENST00000528176;ENST00000307998;ENST00000526624;ENST00000527378	D;D;D;D	0.99080	-5.4;-5.4;-5.4;-5.4	4.58	4.58	0.56647	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.39834	N	0.001260	D	0.99408	0.9791	M	0.93241	3.395	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.70487	0.969;0.966	D	0.98440	1.0586	9	.	.	.	.	14.88	0.70525	0.0:1.0:0.0:0.0	.	123;123	E9PRU1;O95967	.;FBLN4_HUMAN	Y	123	ENSP00000434151:D123Y;ENSP00000309953:D123Y;ENSP00000435419:D123Y;ENSP00000435963:D123Y	.	D	-	1	0	EFEMP2	65395204	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	5.096000	0.64535	2.361000	0.80049	0.655000	0.94253	GAT	.	.		0.632	EFEMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391047.4	NM_016938	Missense_Mutation
DDX11	1663	hgsc.bcm.edu	37	12	31255209	31255209	+	Silent	SNP	G	G	A	rs571690896	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr12:31255209G>A	ENST00000407793.2	+	22	2486	c.2235G>A	c.(2233-2235)gtG>gtA	p.V745V	DDX11_ENST00000545668.1_Silent_p.V745V|DDX11_ENST00000542838.1_Silent_p.V745V|DDX11_ENST00000228264.6_Silent_p.V719V|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000350437.4_Silent_p.V695V	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	745					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					CACACCAGGTGGAGCAGGTGC	0.587										Multiple Myeloma(12;0.14)			G|||	11	0.00219649	0.0008	0.0014	5008	,	,		21388	0.003		0.002	False		,,,				2504	0.0041				p.V745V		Atlas-SNP	.											.	DDX11	188	.	0			c.G2235A						.						80.0	87.0	85.0					12																	31255209		2203	4300	6503	SO:0001819	synonymous_variant	1663	exon22			CCAGGTGGAGCAG	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.2235G>A	chr12.hg19:g.31255209G>A		105.0	0.0		236.0	12.0	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	hg19	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	G	7.213	0.595897	0.13875	.	.	ENSG00000013573	ENST00000539702	.	.	.	3.85	2.93	0.34026	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.3677	0.44035	0.0:0.0:0.8026:0.1974	.	.	.	.	X	3	.	.	W	+	2	0	DDX11	31146476	1.000000	0.71417	1.000000	0.80357	0.636000	0.38137	3.612000	0.54142	0.793000	0.33875	0.603000	0.83216	TGG	.	G|0.500;A|0.500		0.587	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
TMTC2	160335	hgsc.bcm.edu	37	12	83358835	83358835	+	Missense_Mutation	SNP	C	C	G			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr12:83358835C>G	ENST00000321196.3	+	5	2338	c.1631C>G	c.(1630-1632)gCa>gGa	p.A544G	TMTC2_ENST00000548305.1_Missense_Mutation_p.A544G|TMTC2_ENST00000549919.1_Missense_Mutation_p.A538G	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	544					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						AGCAGGTTTGCAGAAGCACTA	0.348																																					p.A544G		Atlas-SNP	.											.	TMTC2	100	.	0			c.C1631G						.						95.0	103.0	101.0					12																	83358835		2203	4300	6503	SO:0001583	missense	160335	exon5			GGTTTGCAGAAGC	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"""Tetratricopeptide (TTC) repeat domain containing"""	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.1631C>G	chr12.hg19:g.83358835C>G	ENSP00000322300:p.Ala544Gly	131.0	0.0		498.0	193.0	NM_152588	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	hg19	CCDS9025.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737144	0.69304	.	.	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919;ENST00000546590	T;T;T	0.76578	-1.03;-0.04;-1.03	5.92	5.92	0.95590	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.275758	0.43416	D	0.000577	T	0.74718	0.3753	L	0.45581	1.43	0.40649	D	0.982014	B;B;B	0.17038	0.003;0.006;0.02	B;B;B	0.18871	0.014;0.016;0.023	T	0.67554	-0.5641	10	0.30854	T	0.27	-4.1126	20.3343	0.98733	0.0:1.0:0.0:0.0	.	544;299;544	Q8N394;F8VRQ2;F8VSH2	TMTC2_HUMAN;.;.	G	544;544;538;299	ENSP00000322300:A544G;ENSP00000448292:A544G;ENSP00000447609:A538G	ENSP00000322300:A544G	A	+	2	0	TMTC2	81882966	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.727000	0.68523	2.822000	0.97130	0.650000	0.86243	GCA	.	.		0.348	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588	
GALNT4	8693	hgsc.bcm.edu	37	12	89916794	89916794	+	Missense_Mutation	SNP	A	A	C			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr12:89916794A>C	ENST00000529983.2	-	1	1789	c.1533T>G	c.(1531-1533)aaT>aaG	p.N511K	POC1B_ENST00000541909.1_Intron|POC1B_ENST00000393179.4_Intron|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.N508K|POC1B-GALNT4_ENST00000547474.1_3'UTR|GALNT4_ENST00000413530.1_Missense_Mutation_p.N339K|POC1B_ENST00000549504.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000549035.1_Intron|POC1B_ENST00000313546.3_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	511	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						TTCCCACATAATTTTTTTGCT	0.363																																					p.N511K		Atlas-SNP	.											.	GALNT4	38	.	0			c.T1533G						.						65.0	62.0	63.0					12																	89916794		1832	4085	5917	SO:0001583	missense	8693	exon1			CACATAATTTTTT	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4126	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 4"""	603565	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"""			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.1533T>G	chr12.hg19:g.89916794A>C	ENSP00000436604:p.Asn511Lys	59.0	0.0		169.0	85.0	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	hg19	CCDS53817.1	.	.	.	.	.	.	.	.	.	.	A	8.561	0.877726	0.17395	.	.	ENSG00000259075;ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000413530;ENST00000529983	T;T;T	0.32023	1.47;1.47;1.47	5.93	-0.841	0.10752	Ricin B-related lectin (1);Ricin B lectin (3);	.	.	.	.	T	0.09730	0.0239	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.29305	-1.0016	9	0.21014	T	0.42	.	0.3181	0.00298	0.3187:0.265:0.1911:0.2253	.	508;511	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	K	508;339;511	ENSP00000447852:N508K;ENSP00000389686:N339K;ENSP00000436604:N511K	ENSP00000436604:N511K	N	-	3	2	GALNT4;RP11-1109F11.4	88440925	0.000000	0.05858	0.000000	0.03702	0.954000	0.61252	-0.508000	0.06344	-0.144000	0.11314	0.482000	0.46254	AAT	.	.		0.363	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
NOS1	4842	hgsc.bcm.edu	37	12	117768410	117768410	+	Silent	SNP	G	G	A	rs369224010		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr12:117768410G>A	ENST00000338101.4	-	1	469	c.465C>T	c.(463-465)ccC>ccT	p.P155P	NOS1_ENST00000317775.6_Silent_p.P155P|NOS1_ENST00000344089.3_Silent_p.P155P|NOS1_ENST00000549189.1_5'Flank			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0	Ala-rich.				cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GCCCATTCCCGGGACCCGAGG	0.701																																					p.P155P	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C465T						.	G	,	1,3821		0,1,1910	39.0	44.0	42.0		465,465	-9.5	0.0	12		42	1,8233		0,1,4116	no	coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204218.1	,	0,2,6026	AA,AG,GG		0.0121,0.0262,0.0166	,	155/1435,155/1469	117768410	2,12054	1911	4117	6028	SO:0001819	synonymous_variant	4842	exon2			ATTCCCGGGACCC		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.465C>T	chr12.hg19:g.117768410G>A		25.0	0.0		55.0	22.0	NM_000620		Silent	SNP	ENST00000338101.4	hg19	CCDS55890.1																																																																																			.	.		0.701	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
DHX37	57647	hgsc.bcm.edu	37	12	125453127	125453127	+	Missense_Mutation	SNP	C	C	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr12:125453127C>A	ENST00000308736.2	-	10	1459	c.1361G>T	c.(1360-1362)gGc>gTc	p.G454V	DHX37_ENST00000544745.1_Missense_Mutation_p.G241V	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	454							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		GAAGCACTCGCCACTGTAGTC	0.612																																					p.G454V		Atlas-SNP	.											.	DHX37	114	.	0			c.G1361T						.						133.0	133.0	133.0					12																	125453127		2203	4300	6503	SO:0001583	missense	57647	exon10			CACTCGCCACTGT	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"""DEAH-boxes"""	17210	protein-coding gene	gene with protein product			"""DEAD/DEAH box helicase DDX37"""	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.1361G>T	chr12.hg19:g.125453127C>A	ENSP00000311135:p.Gly454Val	19.0	0.0		32.0	16.0	NM_032656	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	hg19	CCDS9261.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.756702	0.31137	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.03831	3.79;3.79	4.6	4.6	0.57074	.	0.104012	0.64402	D	0.000003	T	0.07773	0.0195	M	0.63428	1.95	0.80722	D	1	B	0.14438	0.01	B	0.17098	0.017	T	0.12372	-1.0550	10	0.32370	T	0.25	-27.7653	13.9708	0.64240	0.0:0.847:0.153:0.0	.	454	Q8IY37	DHX37_HUMAN	V	454;241	ENSP00000311135:G454V;ENSP00000439009:G241V	ENSP00000311135:G454V	G	-	2	0	DHX37	124019080	0.998000	0.40836	0.770000	0.31555	0.759000	0.43091	3.530000	0.53539	2.263000	0.75096	0.561000	0.74099	GGC	.	.		0.612	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
CCDC168	643677	hgsc.bcm.edu	37	13	103390332	103390332	+	5'Flank	SNP	C	C	T	rs200872789	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr13:103390332C>T	ENST00000322527.2	-	0	0					NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168																		tcttcaacttcgtgatccatt	0.448													C|||	18	0.00359425	0.0008	0.0014	5008	,	,		21577	0.003		0.0	False		,,,				2504	0.0133				p.E4239K		Atlas-SNP	.											.	.	.	.	0			c.G12715A						.	C	LYS/GLU	2,1382		0,2,690	140.0	111.0	120.0		12715	-0.3	0.0	13		120	1,3181		0,1,1590	yes	missense	CCDC168	NM_001146197.1	56	0,3,2280	TT,TC,CC		0.0314,0.1445,0.0657		4239/7082	103390332	3,4563	692	1591	2283	SO:0001631	upstream_gene_variant	643677	exon4			CAACTTCGTGATC		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287		chr13.hg19:g.103390332C>T	Exception_encountered	166.0	0.0		924.0	375.0	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	hg19																																																																																				.	.		0.448	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
SYNDIG1L	646658	hgsc.bcm.edu	37	14	74876039	74876039	+	Missense_Mutation	SNP	C	C	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr14:74876039C>T	ENST00000554823.1	-	1	470	c.409G>A	c.(409-411)Gaa>Aaa	p.E137K	SYNDIG1L_ENST00000331628.3_Missense_Mutation_p.E137K			A6NDD5	SYN1L_HUMAN	synapse differentiation inducing 1-like	137					response to biotic stimulus (GO:0009607)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(8)|pancreas(1)|prostate(1)|skin(1)	14						ACCTCCTCTTCCTCCTGGTCA	0.512																																					p.E137K		Atlas-SNP	.											.	SYNDIG1L	24	.	0			c.G409A						.						88.0	94.0	92.0					14																	74876039		2055	4180	6235	SO:0001583	missense	646658	exon2			CCTCTTCCTCCTG		CCDS41970.1	14q24.3	2011-06-30	2011-06-30	2011-06-30		ENSG00000183379			32388	protein-coding gene	gene with protein product	"""caudate-and putamen-enriched sequence"", ""interferon induced transmembrane protein domain containing 4"""	609999	"""transmembrane protein 90A"""	TMEM90A		16359841	Standard	NM_001105579		Approved	capucin, IFITMD4	uc001xpx.2	A6NDD5		ENST00000554823.1:c.409G>A	chr14.hg19:g.74876039C>T	ENSP00000450439:p.Glu137Lys	72.0	0.0		88.0	54.0	NM_001105579		Missense_Mutation	SNP	ENST00000554823.1	hg19	CCDS41970.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348504	0.41599	.	.	ENSG00000183379	ENST00000331628;ENST00000554823	D;D	0.95821	-3.82;-3.82	4.63	2.81	0.32909	.	0.406089	0.25857	N	0.027842	D	0.90181	0.6931	L	0.38175	1.15	0.22001	N	0.999422	B	0.18310	0.027	B	0.14023	0.01	T	0.80236	-0.1466	10	0.35671	T	0.21	-10.8241	6.4673	0.21990	0.0:0.7047:0.0:0.2953	.	137	A6NDD5	SYN1L_HUMAN	K	137	ENSP00000331474:E137K;ENSP00000450439:E137K	ENSP00000331474:E137K	E	-	1	0	SYNDIG1L	73945792	.	.	0.957000	0.39632	0.148000	0.21650	.	.	0.578000	0.29487	-0.373000	0.07131	GAA	.	.		0.512	SYNDIG1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412341.1	XM_938515	
CTU2	348180	hgsc.bcm.edu	37	16	88776355	88776355	+	Silent	SNP	C	C	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr16:88776355C>T	ENST00000453996.2	+	3	221	c.153C>T	c.(151-153)ttC>ttT	p.F51F	CTU2_ENST00000312060.5_Silent_p.F51F|CTU2_ENST00000378384.3_Intron|CTU2_ENST00000567949.1_Silent_p.F51F	NM_001012759.1	NP_001012777.1			cytosolic thiouridylase subunit 2 homolog (S. pombe)											NS(1)|breast(1)|endometrium(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11						GGGACTGTTTCAAGGCCTTCT	0.597																																					p.F51F		Atlas-SNP	.											.	CTU2	66	.	0			c.C153T						.						170.0	166.0	167.0					16																	88776355		2198	4300	6498	SO:0001819	synonymous_variant	348180	exon3			CTGTTTCAAGGCC	BC021056	CCDS32506.1, CCDS45545.1	16q24.3	2013-10-11	2009-08-19	2009-08-19		ENSG00000174177			28005	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 84"""	C16orf84		19017811	Standard	NM_001012759		Approved	NCS2	uc002flm.3	Q2VPK5		ENST00000453996.2:c.153C>T	chr16.hg19:g.88776355C>T		62.0	0.0		102.0	44.0	NM_001012759		Silent	SNP	ENST00000453996.2	hg19	CCDS45545.1																																																																																			.	.		0.597	CTU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423025.1	NM_001012762	
DLG4	1742	hgsc.bcm.edu	37	17	7097812	7097812	+	Missense_Mutation	SNP	G	G	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr17:7097812G>A	ENST00000399506.2	-	12	1495	c.1304C>T	c.(1303-1305)gCc>gTc	p.A435V	DLG4_ENST00000399510.2_Missense_Mutation_p.A478V|DLG4_ENST00000302955.6_Missense_Mutation_p.A432V			P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	435	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	ATCAAACAGGGCCCTGGAGGG	0.597																																					p.A478V		Atlas-SNP	.											.	DLG4	110	.	0			c.C1433T						.						28.0	32.0	31.0					17																	7097812		2041	4198	6239	SO:0001583	missense	1742	exon14			AACAGGGCCCTGG	U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535			2903	protein-coding gene	gene with protein product		602887				9286702	Standard	NM_001128827		Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000399506.2:c.1304C>T	chr17.hg19:g.7097812G>A	ENSP00000382425:p.Ala435Val	35.0	0.0		45.0	30.0	NM_001365	B7Z1S1|G5E939|Q92941|Q9UKK8	Missense_Mutation	SNP	ENST00000399506.2	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.555178	0.96514	.	.	ENSG00000132535	ENST00000399506;ENST00000302955;ENST00000399510;ENST00000293813;ENST00000380912;ENST00000539674	T;T;T	0.80304	-1.36;-1.36;-1.36	5.3	5.3	0.74995	Src homology-3 domain (4);	.	.	.	.	D	0.91358	0.7274	M	0.90309	3.105	0.80722	D	1	D;D;D;D	0.76494	0.995;0.999;0.998;0.989	D;D;D;D	0.79784	0.953;0.972;0.985;0.993	D	0.92680	0.6157	9	0.87932	D	0	.	16.5016	0.84259	0.0:0.0:1.0:0.0	.	475;435;432;478	B9EGL1;P78352;G5E939;P78352-2	.;DLG4_HUMAN;.;.	V	435;432;478;478;375;478	ENSP00000382425:A435V;ENSP00000307471:A432V;ENSP00000382428:A478V	ENSP00000293813:A478V	A	-	2	0	DLG4	7038536	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.601000	0.98297	2.769000	0.95229	0.655000	0.94253	GCC	.	.		0.597	DLG4-002	KNOWN	non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000259419.2	NM_001365	
KRT33B	3884	hgsc.bcm.edu	37	17	39525703	39525703	+	Silent	SNP	G	G	A	rs386797081|rs532358097	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr17:39525703G>A	ENST00000251646.3	-	1	349	c.300C>T	c.(298-300)tgC>tgT	p.C100C		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	100	Linker 1.|Rod.				aging (GO:0007568)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(6)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000496)				GGTAGCTGGGGCACAGCAAGG	0.572													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18426	0.0		0.0	False		,,,				2504	0.0				p.C100C		Atlas-SNP	.											.	KRT33B	46	.	0			c.C300T						.						69.0	68.0	68.0					17																	39525703		2191	4300	6491	SO:0001819	synonymous_variant	3884	exon1			GCTGGGGCACAGC	X82634	CCDS11389.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131738	ENSG00000131738		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6451	protein-coding gene	gene with protein product	"""hard keratin type I 3II"""	602762	"""keratin, hair, acidic, 3B"""	KRTHA3B		7565656, 16831889	Standard	NM_002279		Approved	Ha-3II	uc002hwl.4	Q14525	OTTHUMG00000133429	ENST00000251646.3:c.300C>T	chr17.hg19:g.39525703G>A		40.0	0.0		112.0	10.0	NM_002279	O76010	Silent	SNP	ENST00000251646.3	hg19	CCDS11389.1																																																																																			.	.		0.572	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
CCDC57	284001	hgsc.bcm.edu	37	17	80115731	80115731	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr17:80115731G>A	ENST00000389641.4	-	14	2170	c.2134C>T	c.(2134-2136)Cag>Tag	p.Q712*	CCDC57_ENST00000392343.3_Nonsense_Mutation_p.Q712*|RP11-1376P16.1_ENST00000582774.1_RNA|CCDC57_ENST00000327026.3_5'UTR|CCDC57_ENST00000392347.1_Nonsense_Mutation_p.Q712*			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	712										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			TCAGCCACCTGCTTCCGCAGC	0.682																																					p.Q712X		Atlas-SNP	.											.	CCDC57	102	.	0			c.C2134T						.						25.0	29.0	27.0					17																	80115731		1989	4159	6148	SO:0001587	stop_gained	284001	exon14			CCACCTGCTTCCG	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.2134C>T	chr17.hg19:g.80115731G>A	ENSP00000374292:p.Gln712*	25.0	0.0		49.0	28.0	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Nonsense_Mutation	SNP	ENST00000389641.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.540187|5.540187	0.96474|0.96474	.|.	.|.	ENSG00000176155|ENSG00000176155	ENST00000419322|ENST00000389641;ENST00000392347;ENST00000327026;ENST00000392343	.|.	.|.	.|.	3.19|3.19	2.15|2.15	0.27550|0.27550	.|.	.|0.000000	.|0.38959	.|N	.|0.001517	T|.	0.60932|.	0.2307|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.58918|.	-0.7551|.	4|.	.|0.49607	.|T	.|0.09	-22.0135|-22.0135	8.1007|8.1007	0.30854|0.30854	0.0:0.2506:0.7494:0.0|0.0:0.2506:0.7494:0.0	.|.	.|.	.|.	.|.	V|X	57|712;712;220;712	.|.	.|ENSP00000315967:Q220X	A|Q	-|-	2|1	0|0	CCDC57|CCDC57	77709020|77709020	0.988000|0.988000	0.35896|0.35896	0.645000|0.645000	0.29479|0.29479	0.176000|0.176000	0.22953|0.22953	2.236000|2.236000	0.43052|0.43052	0.612000|0.612000	0.30071|0.30071	0.462000|0.462000	0.41574|0.41574	GCA|CAG	.	.		0.682	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082	
APCDD1	147495	hgsc.bcm.edu	37	18	10471887	10471887	+	Silent	SNP	C	C	T	rs145453912		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr18:10471887C>T	ENST00000355285.5	+	3	957	c.603C>T	c.(601-603)gcC>gcT	p.A201A	APCDD1_ENST00000578882.1_Intron	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		GCACCAAGGCCGTGAACTTTG	0.607																																					p.A201A		Atlas-SNP	.											APCDD1,NS,carcinoma,0,1	APCDD1	57	.	0			c.C603T						.						144.0	132.0	136.0					18																	10471887		2203	4300	6503	SO:0001819	synonymous_variant	147495	exon3			CAAGGCCGTGAAC	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.603C>T	chr18.hg19:g.10471887C>T		30.0	0.0		69.0	26.0	NM_153000		Silent	SNP	ENST00000355285.5	hg19	CCDS11849.1																																																																																			.	C|1.000;G|0.000		0.607	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000	
ZNF527	84503	hgsc.bcm.edu	37	19	37879212	37879212	+	Missense_Mutation	SNP	G	G	T			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr19:37879212G>T	ENST00000436120.2	+	5	368	c.261G>T	c.(259-261)tgG>tgT	p.W87C	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	87	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTTCAGACTGGGAGTCTTGGT	0.383																																					p.W87C		Atlas-SNP	.											.	ZNF527	78	.	0			c.G261T						.						44.0	42.0	42.0					19																	37879212		1822	4086	5908	SO:0001583	missense	84503	exon5			AGACTGGGAGTCT	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"""Zinc fingers, C2H2-type"", ""-"""	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.261G>T	chr19.hg19:g.37879212G>T	ENSP00000390179:p.Trp87Cys	88.0	0.0		240.0	92.0	NM_032453	B4DVL5	Missense_Mutation	SNP	ENST00000436120.2	hg19	CCDS42559.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.413878	0.42817	.	.	ENSG00000189164	ENST00000356178;ENST00000317566;ENST00000436120	.	.	.	4.72	3.62	0.41486	.	0.000000	0.30501	N	0.009483	T	0.39306	0.1073	N	0.16862	0.45	0.80722	D	1	B;B	0.20988	0.03;0.05	B;B	0.21151	0.015;0.033	T	0.35226	-0.9797	9	0.51188	T	0.08	.	10.1897	0.43019	0.0:0.0:0.8027:0.1973	.	87;55	Q8NB42;Q8NB42-2	ZN527_HUMAN;.	C	87;55;35	.	ENSP00000325231:W55C	W	+	3	0	ZNF527	42571052	0.786000	0.28738	1.000000	0.80357	0.991000	0.79684	0.462000	0.21956	2.455000	0.83008	0.655000	0.94253	TGG	.	.		0.383	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453	
HNRNPL	3191	hgsc.bcm.edu	37	19	39328060	39328060	+	Missense_Mutation	SNP	G	G	C			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr19:39328060G>C	ENST00000221419.5	-	12	2041	c.1675C>G	c.(1675-1677)Ctg>Gtg	p.L559V	AC104534.3_ENST00000594769.1_Silent_p.L175L|HNRNPL_ENST00000600873.1_Missense_Mutation_p.L426V	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	559	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			AGGAAGCCCAGAGTCTCCAGG	0.522																																					p.L559V		Atlas-SNP	.											.	HNRNPL	67	.	0			c.C1675G						.						86.0	82.0	83.0					19																	39328060		2203	4300	6503	SO:0001583	missense	3191	exon12			AGCCCAGAGTCTC	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"""RNA binding motif (RRM) containing"""	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.1675C>G	chr19.hg19:g.39328060G>C	ENSP00000221419:p.Leu559Val	69.0	0.0		172.0	68.0	NM_001533	A6ND69|A6NIT8|Q9H3P3	Missense_Mutation	SNP	ENST00000221419.5	hg19	CCDS33015.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.390924	0.42410	.	.	ENSG00000104824	ENST00000221419;ENST00000388749;ENST00000388750	.	.	.	6.06	-3.63	0.04529	Nucleotide-binding, alpha-beta plait (1);	0.129890	0.52532	D	0.000079	T	0.75206	0.3818	M	0.68593	2.085	0.45261	D	0.998266	P;P;D	0.62365	0.869;0.951;0.991	P;P;D	0.72625	0.775;0.701;0.978	T	0.78378	-0.2227	9	0.87932	D	0	.	20.3926	0.98949	0.1295:0.0:0.8705:0.0	.	559;528;542	P14866;B2R959;Q6NTA2	HNRPL_HUMAN;.;.	V	559;426;426	.	ENSP00000221419:L559V	L	-	1	2	HNRNPL	44019900	0.981000	0.34729	0.133000	0.22050	0.921000	0.55340	1.881000	0.39638	-0.563000	0.06078	-0.302000	0.09304	CTG	.	.		0.522	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1		
OSCAR	126014	hgsc.bcm.edu	37	19	54602893	54602893	+	Intron	SNP	C	C	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr19:54602893C>A	ENST00000284648.6	-	3	268				OSCAR_ENST00000359649.4_Splice_Site|OSCAR_ENST00000351806.4_Intron|OSCAR_ENST00000391761.1_Intron|OSCAR_ENST00000356532.3_Splice_Site|OSCAR_ENST00000358375.4_Intron|OSCAR_ENST00000391760.1_Intron			Q8IYS5	OSCAR_HUMAN	osteoclast associated, immunoglobulin-like receptor							extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|skin(1)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)					ataatgGCCACTAAGgggaat	0.428																																					.		Atlas-SNP	.											.	OSCAR	22	.	0			c.71-1G>T						.						86.0	81.0	83.0					19																	54602893		2203	4300	6503	SO:0001627	intron_variant	126014	exon4			TGGCCACTAAGGG	AK130199	CCDS12873.1, CCDS12874.1, CCDS12875.1, CCDS12876.1, CCDS62789.1, CCDS74444.1	19q13.42	2013-01-29			ENSG00000170909	ENSG00000170909		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29960	protein-coding gene	gene with protein product		606862				11805147	Standard	NM_206818		Approved		uc002qda.3	Q8IYS5	OTTHUMG00000064966	ENST00000284648.6:c.70+145G>T	chr19.hg19:g.54602893C>A		44.0	0.0		117.0	50.0	NM_130771	B7WNS2|Q5GRG5|Q8N763|Q8NHL4|Q8WXQ0|Q8WXQ1|Q8WXQ2	Splice_Site	SNP	ENST00000284648.6	hg19		.	.	.	.	.	.	.	.	.	.	C	5.864	0.343657	0.11126	.	.	ENSG00000170909	ENST00000356532;ENST00000359649	.	.	.	2.17	2.17	0.27698	.	.	.	.	.	.	.	.	.	.	.	0.20403	N	0.99991	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.9473	0.29993	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	OSCAR	59294705	0.015000	0.18098	0.013000	0.15412	0.087000	0.18053	0.337000	0.19841	1.558000	0.49541	0.456000	0.33151	.	.	.		0.428	OSCAR-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000139493.4	NM_133169	
COX4I2	84701	hgsc.bcm.edu	37	20	30227827	30227827	+	Silent	SNP	C	C	T	rs539460095		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr20:30227827C>T	ENST00000376075.3	+	3	249	c.174C>T	c.(172-174)aaC>aaT	p.N58N	COX4I2_ENST00000490030.1_3'UTR	NM_032609.2	NP_115998.2	Q96KJ9	COX42_HUMAN	cytochrome c oxidase subunit IV isoform 2 (lung)	58					cellular respiration (GO:0045333)|generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)	mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	11	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.01e-05)|all cancers(5;9.46e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00121)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			CAGAACTCAACGCTGAGGAGC	0.612													C|||	1	0.000199681	0.0	0.0	5008	,	,		16861	0.001		0.0	False		,,,				2504	0.0				p.N58N		Atlas-SNP	.											.	COX4I2	18	.	0			c.C174T						.						61.0	51.0	54.0					20																	30227827		2203	4300	6503	SO:0001819	synonymous_variant	84701	exon3			ACTCAACGCTGAG	AF257180	CCDS13187.1	20q11.21	2011-07-04	2004-08-11		ENSG00000131055	ENSG00000131055		"""Mitochondrial respiratory chain complex / Complex IV"""	16232	protein-coding gene	gene with protein product	"""cytochrome c oxidase subunit IV-like 2"""	607976	"""cytochrome c oxidase subunit IV isoform 2"""	COX4L2		11311561, 17937768	Standard	NM_032609		Approved	COXIV-2, COX4B, dJ857M17.2, COX4-2	uc002wwj.1	Q96KJ9	OTTHUMG00000032180	ENST00000376075.3:c.174C>T	chr20.hg19:g.30227827C>T		15.0	0.0		22.0	11.0	NM_032609	Q6GTF4|Q9H0Z4	Silent	SNP	ENST00000376075.3	hg19	CCDS13187.1																																																																																			.	.		0.612	COX4I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078548.1	NM_032609	
TRPC4AP	26133	hgsc.bcm.edu	37	20	33598060	33598060	+	Missense_Mutation	SNP	G	G	C			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr20:33598060G>C	ENST00000252015.2	-	12	1530	c.1441C>G	c.(1441-1443)Ctg>Gtg	p.L481V	TRPC4AP_ENST00000432634.2_Missense_Mutation_p.L442V|TRPC4AP_ENST00000451813.2_Missense_Mutation_p.L473V|TRPC4AP_ENST00000539834.1_Missense_Mutation_p.L83V			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	481					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			AGTTCATTCAGCTCCTGGTTG	0.532																																					p.L481V		Atlas-SNP	.											.	TRPC4AP	64	.	0			c.C1441G						.						234.0	162.0	186.0					20																	33598060		2203	4300	6503	SO:0001583	missense	26133	exon12			CATTCAGCTCCTG	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 158"""	608430	"""chromosome 20 open reading frame 188"""	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.1441C>G	chr20.hg19:g.33598060G>C	ENSP00000252015:p.Leu481Val	106.0	0.0		277.0	107.0	NM_015638	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	hg19	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.155652	0.57259	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000539834;ENST00000432634;ENST00000541994	.	.	.	5.67	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.62539	0.2436	M	0.62723	1.935	0.53688	D	0.999975	B;B;B	0.29481	0.245;0.201;0.201	B;B;B	0.35182	0.197;0.138;0.138	T	0.63497	-0.6624	9	0.52906	T	0.07	.	12.8124	0.57647	0.0758:0.0:0.9242:0.0	.	442;473;481	B4E0Q1;E1P5Q0;Q8TEL6	.;.;TP4AP_HUMAN	V	481;473;83;442;466	.	ENSP00000252015:L481V	L	-	1	2	TRPC4AP	33061721	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.846000	0.62860	1.399000	0.46721	0.555000	0.69702	CTG	.	.		0.532	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
LCA5L	150082	hgsc.bcm.edu	37	21	40800132	40800132	+	Silent	SNP	T	T	C			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr21:40800132T>C	ENST00000358268.2	-	4	816	c.288A>G	c.(286-288)aaA>aaG	p.K96K	LCA5L_ENST00000485895.2_Silent_p.K96K|LCA5L_ENST00000288350.3_Silent_p.K96K|LCA5L_ENST00000380671.2_Silent_p.K96K			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	96										breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				CATTATACTTTTTCTTCTCCT	0.313																																					p.K96K		Atlas-SNP	.											.	LCA5L	57	.	0			c.A288G						.						57.0	63.0	61.0					21																	40800132		2201	4297	6498	SO:0001819	synonymous_variant	150082	exon4			ATACTTTTTCTTC	AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 13"""	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.288A>G	chr21.hg19:g.40800132T>C		109.0	0.0		303.0	123.0	NM_152505	D3DSI0|Q3ZCT0	Silent	SNP	ENST00000358268.2	hg19	CCDS13665.1																																																																																			.	.		0.313	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505	
PCNT	5116	hgsc.bcm.edu	37	21	47773060	47773060	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr21:47773060A>G	ENST00000359568.5	+	10	1606	c.1499A>G	c.(1498-1500)gAt>gGt	p.D500G	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	500	Glu-rich.				brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CGTGTGGAAGATTTAGAACAG	0.473																																					p.D500G		Atlas-SNP	.											.	PCNT	283	.	0			c.A1499G						.						56.0	60.0	59.0					21																	47773060		2203	4300	6503	SO:0001583	missense	5116	exon10			TGGAAGATTTAGA	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.1499A>G	chr21.hg19:g.47773060A>G	ENSP00000352572:p.Asp500Gly	56.0	0.0		92.0	25.0	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	A	12.10	1.836279	0.32421	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.02709	4.19	4.68	4.68	0.58851	.	.	.	.	.	T	0.03564	0.0102	L	0.43152	1.355	0.32642	N	0.520569	P;P	0.38978	0.531;0.652	B;B	0.32762	0.152;0.073	T	0.18116	-1.0347	9	0.56958	D	0.05	.	13.3185	0.60421	1.0:0.0:0.0:0.0	.	382;500	O95613-2;O95613	.;PCNT_HUMAN	G	500;487	ENSP00000352572:D500G	ENSP00000338675:D487G	D	+	2	0	PCNT	46597488	0.999000	0.42202	0.024000	0.17045	0.011000	0.07611	4.493000	0.60341	1.732000	0.51606	0.460000	0.39030	GAT	.	.		0.473	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
PRR14L	253143	hgsc.bcm.edu	37	22	32111160	32111160	+	Missense_Mutation	SNP	T	T	G			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr22:32111160T>G	ENST00000327423.6	-	4	2854	c.2665A>C	c.(2665-2667)Acc>Ccc	p.T889P	PRR14L_ENST00000461722.1_5'Flank|PRR14L_ENST00000397493.2_Missense_Mutation_p.T889P|PRR14L_ENST00000434485.1_Missense_Mutation_p.T889P	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	889										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						GTGTGAATGGTTTTGTTTGAA	0.408																																					p.T889P		Atlas-SNP	.											.	PRR14L	198	.	0			c.A2665C						.						199.0	149.0	164.0					22																	32111160		692	1591	2283	SO:0001583	missense	253143	exon4			GAATGGTTTTGTT	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.2665A>C	chr22.hg19:g.32111160T>G	ENSP00000331845:p.Thr889Pro	123.0	0.0		438.0	208.0	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	hg19	CCDS13900.2	.	.	.	.	.	.	.	.	.	.	T	11.09	1.536073	0.27475	.	.	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.06849	3.25;3.26;3.25	5.36	-1.29	0.09288	.	0.425905	0.19729	N	0.107386	T	0.06188	0.0160	L	0.47716	1.5	0.09310	N	1	P;B;P	0.35656	0.514;0.226;0.514	B;B;B	0.34138	0.176;0.176;0.176	T	0.29397	-1.0013	9	.	.	.	1.1631	4.9926	0.14222	0.1423:0.3861:0.0:0.4716	.	889;889;889	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	P	889	ENSP00000380630:T889P;ENSP00000331845:T889P;ENSP00000388314:T889P	.	T	-	1	0	PRR14L	30441160	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.068000	0.11561	-0.326000	0.08564	-0.263000	0.10527	ACC	.	.		0.408	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	
PNMA3	29944	hgsc.bcm.edu	37	X	152225435	152225435	+	Missense_Mutation	SNP	A	A	G			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chrX:152225435A>G	ENST00000370264.4	+	1	49	c.23A>G	c.(22-24)gAc>gGc	p.D8G	PNMA3_ENST00000447306.1_Missense_Mutation_p.D8G|PNMA3_ENST00000370265.4_Missense_Mutation_p.D8G			Q9UL41	PNMA3_HUMAN	paraneoplastic Ma antigen 3	8					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	16	Acute lymphoblastic leukemia(192;6.56e-05)					ttgttacaggactggtgtcgg	0.567																																					p.D8G		Atlas-SNP	.											.	PNMA3	81	.	0			c.A23G						.						111.0	87.0	95.0					X																	152225435		2203	4300	6503	SO:0001583	missense	29944	exon2			TACAGGACTGGTG	AF083116	CCDS35435.2, CCDS65344.1	Xq28	2012-02-09	2012-02-09		ENSG00000183837	ENSG00000183837		"""Paraneoplastic Ma antigens"""	18742	protein-coding gene	gene with protein product	"""paraneoplastic cancer-testis-brain antigen"""	300675	"""paraneoplastic antigen MA3"""			11558790	Standard	NM_013364		Approved	MA5, MA3, MGC132756, MGC132758	uc004fhc.2	Q9UL41	OTTHUMG00000024195	ENST00000370264.4:c.23A>G	chrX.hg19:g.152225435A>G	ENSP00000359286:p.Asp8Gly	40.0	0.0		117.0	104.0	NM_013364	D3DWT7|Q9H0A4	Missense_Mutation	SNP	ENST00000370264.4	hg19	CCDS35435.2	.	.	.	.	.	.	.	.	.	.	a	14.75	2.627457	0.46944	.	.	ENSG00000183837	ENST00000370265;ENST00000447306;ENST00000370264	T;T;T	0.31769	1.48;1.48;1.48	1.93	1.93	0.25924	.	.	.	.	.	T	0.49660	0.1570	M	0.75085	2.285	0.20703	N	0.999864	D	0.89917	1.0	D	0.91635	0.999	T	0.22730	-1.0208	9	0.72032	D	0.01	.	5.3241	0.15896	1.0:0.0:0.0:0.0	.	8	Q9UL41	PNMA3_HUMAN	G	8	ENSP00000359288:D8G;ENSP00000407642:D8G;ENSP00000359286:D8G	ENSP00000359286:D8G	D	+	2	0	PNMA3	151976091	0.998000	0.40836	0.468000	0.27192	0.004000	0.04260	1.432000	0.34936	1.028000	0.39785	0.336000	0.21669	GAC	.	.		0.567	PNMA3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060946.2	NM_013364	
MT-CO3	4514	hgsc.bcm.edu	37	M	9329	9329	+	Silent	SNP	G	G	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chrM:9329G>A	ENST00000362079.2	+	1	123	c.123G>A	c.(121-123)acG>acA	p.T41T	MT-TR_ENST00000387439.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TS1_ENST00000387416.2_RNA			P00414	COX3_HUMAN	mitochondrially encoded cytochrome c oxidase III	41					aerobic electron transport chain (GO:0019646)|cellular metabolic process (GO:0044237)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(10)|kidney(14)|lung(1)|urinary_tract(1)	27						CACTCCATAACGCTCCTCATA	0.507																																					p.T41T		Atlas-SNP	.											.	.	.	.	0			c.G123A						.																																			SO:0001819	synonymous_variant	5742	exon1			CATAACGCTCCTC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198938	ENSG00000198938		"""Mitochondrial respiratory chain complex / Complex IV"""	7422	protein-coding gene	gene with protein product		516050	"""cytochrome c oxidase III"""	MTCO3			Standard			Approved	COX3, COIII, CO3		P00414		ENST00000362079.2:c.123G>A	chrM.hg19:g.9329G>A		24.0	0.0		243.0	17.0	ENST00000362079	Q14Y83	Silent	SNP	ENST00000362079.2	hg19																																																																																				.	.		0.507	MT-CO3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024032	
MT-ND4	4538	hgsc.bcm.edu	37	M	11120	11120	+	Missense_Mutation	SNP	T	T	C			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chrM:11120T>C	ENST00000361381.2	+	1	361	c.361T>C	c.(361-363)Ttc>Ctc	p.F121L	MT-TR_ENST00000387439.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-ND5_ENST00000361567.2_5'Flank			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	121					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(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						TATTTTATATCTTCTTCGAAA	0.418																																					p.F121L		Atlas-SNP	.											.	.	.	.	0			c.T361C						.																																			SO:0001583	missense	0	exon1			TATATCTTCTTCG			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.361T>C	chrM.hg19:g.11120T>C	ENSP00000354961:p.Phe121Leu	20.0	0.0		226.0	10.0	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	hg19																																																																																				.	.		0.418	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
NEFH	4744	hgsc.bcm.edu	37	22	29885573	29885574	+	In_Frame_Ins	INS	-	-	CCTGAGAAGGCCAAGTCC	rs541596221		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr22:29885573_29885574insCCTGAGAAGGCCAAGTCC	ENST00000310624.6	+	4	1977_1978	c.1944_1945insCCTGAGAAGGCCAAGTCC	c.(1945-1947)cct>CCTGAGAAGGCCAAGTCCcct	p.649_649P>PEKAKSP		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	655	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AAGCAAAGTCCCCTGAGAAGGC	0.569																																					p.S648delinsSPEKAKS		Atlas-INDEL	.											.	NEFH	178	.	0			c.1944_1945insCCTGAGAAGGCCAAGTCC						.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1945_1962dupCCTGAGAAGGCCAAGTCC	chr22.hg19:g.29885573_29885574insCCTGAGAAGGCCAAGTCC	Exception_encountered	46.0	0.0		152.0	19.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
MYH11	4629	hgsc.bcm.edu	37	16	15808930	15808930	+	Frame_Shift_Del	DEL	T	T	-			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr16:15808930delT	ENST00000300036.5	-	40	5731	c.5622delA	c.(5620-5622)aaafs	p.K1874fs	MYH11_ENST00000576790.2_Frame_Shift_Del_p.K1874fs|NDE1_ENST00000396354.1_Intron|NDE1_ENST00000342673.5_Intron|MYH11_ENST00000452625.2_Frame_Shift_Del_p.K1881fs|NDE1_ENST00000396355.1_Intron|MYH11_ENST00000396324.3_Frame_Shift_Del_p.K1881fs	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1874					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TGGCATTGCCTTTCTCTGCCT	0.672			T	CBFB	AML																																p.G1882fs		Atlas-Indel,Pindel	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.5644delG						.						105.0	101.0	102.0					16																	15808930		2197	4300	6497	SO:0001589	frameshift_variant	4629	exon41			.	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5622delA	chr16.hg19:g.15808930delT	ENSP00000300036:p.Lys1874fs	49.0	0.0		92.0	39.0	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Frame_Shift_Del	DEL	ENST00000300036.5	hg19	CCDS10565.1																																																																																			.	.		0.672	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
CATIP	375307	hgsc.bcm.edu	37	2	219222268	219222286	+	Frame_Shift_Del	DEL	CTACAGATGCTGTTCTTCT	CTACAGATGCTGTTCTTCT	-	rs376076590		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CTACAGATGCTGTTCTTCT	CTACAGATGCTGTTCTTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr2:219222268_219222286delCTACAGATGCTGTTCTTCT	ENST00000289388.3	+	3	159_177	c.130_148delCTACAGATGCTGTTCTTCT	c.(130-150)ctacagatgctgttcttctctfs	p.LQMLFFS44fs	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		44					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L44L(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAAGGAGGAGCTACAGATGCTGTTCTTCTCTGAGACGCT	0.589																																					p.43_49del		Atlas-INDEL	.											.	C2orf62	28	.	1	Substitution - coding silent(1)	endometrium(1)	c.129_147del						.																																			SO:0001589	frameshift_variant	375307	exon3			.																												ENST00000289388.3:c.130_148delCTACAGATGCTGTTCTTCT	chr2.hg19:g.219222268_219222286delCTACAGATGCTGTTCTTCT	ENSP00000289388:p.Leu44fs	37.0	0.0		41.0	16.0	NM_198559		Frame_Shift_Del	DEL	ENST00000289388.3	hg19	CCDS2414.1																																																																																			.	.		0.589	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1		
METTL2B	55798	hgsc.bcm.edu	37	7	128140983	128140984	+	Frame_Shift_Ins	INS	-	-	T	rs139332186	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:128140983_128140984insT	ENST00000262432.8	+	8	980_981	c.943_944insT	c.(943-945)gtgfs	p.V315fs	METTL2B_ENST00000480046.1_Frame_Shift_Ins_p.V250fs	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	315					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						AAATTTCTATGTGAGAGGTGAT	0.396																																					p.V315fs		Atlas-INDEL	.											.	METTL2B	34	.	0			c.943_944insT						.																																			SO:0001589	frameshift_variant	55798	exon8			.	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"""methyltransferase like 2"""	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.944dupT	chr7.hg19:g.128140984_128140984dupT	ENSP00000262432:p.Val315fs	79.0	0.0		254.0	41.0	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Frame_Shift_Ins	INS	ENST00000262432.8	hg19	CCDS5803.2																																																																																			.	.		0.396	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396	
TRMT1L	81627	hgsc.bcm.edu	37	1	185089286	185089287	+	Frame_Shift_Ins	INS	-	-	A			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr1:185089286_185089287insA	ENST00000367506.5	-	15	2334_2335	c.2066_2067insT	c.(2065-2067)ttafs	p.L689fs	TRMT1L_ENST00000465827.1_5'UTR|TRMT1L_ENST00000367504.3_3'UTR	NM_001202423.1|NM_030934.4	NP_001189352.1|NP_112196.3	Q7Z2T5	TRM1L_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)-like	689					adult locomotory behavior (GO:0008344)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	21						TGCTGTACTTTAAAAGGATAGA	0.441																																					p.L689fs		Atlas-Indel,Pindel	.											.	TRMT1L	50	.	0			c.2067_2068insT						.																																			SO:0001589	frameshift_variant	81627	exon15			.	AF288399	CCDS1366.1	1q25.2	2012-06-29	2012-06-29	2011-01-24	ENSG00000121486	ENSG00000121486			16782	protein-coding gene	gene with protein product	"""TRM1-like"""	611673	"""chromosome 1 open reading frame 25"", ""TRM1 tRNA methyltransferase 1-like"""	C1orf25		11318611, 17198746	Standard	NM_030934		Approved		uc001grf.4	Q7Z2T5	OTTHUMG00000035389	ENST00000367506.5:c.2067dupT	chr1.hg19:g.185089290_185089290dupA	ENSP00000356476:p.Leu689fs	84.0	0.0		412.0	102.0	NM_030934	Q5TEN0|Q6ZMX0|Q8IWH5|Q8NC68|Q9BZQ1	Frame_Shift_Ins	INS	ENST00000367506.5	hg19	CCDS1366.1																																																																																			.	.		0.441	TRMT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085787.1	NM_030934	
CRELD2	79174	hgsc.bcm.edu	37	22	50315943	50315980	+	Intron	DEL	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	-	rs377640443|rs562885075|rs542695980|rs113299196|rs7410276|rs12160965|rs386822607|rs386822606|rs564615833|rs368043307|rs71805922|rs386822608|rs73891177	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr22:50315943_50315980delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG	ENST00000328268.4	+	6	666				CRELD2_ENST00000403427.3_Intron|CRELD2_ENST00000404488.3_Splice_Site_p.PQQSGPASPILTR198fs|CRELD2_ENST00000407217.3_Intron|CRELD2_ENST00000444954.1_Intron	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2							endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		GCCCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCGCCTTGCTGTCTGTCTCT	0.618																																					p.198_207del		Atlas-Indel,Pindel	.											.	CRELD2	57	.	0			c.593_620del						.																																			SO:0001627	intron_variant	79174	exon6			.	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.593-280CCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG>-	chr22.hg19:g.50315943_50315980delCCTCAGCAGTCAGGACCGGCCTCTCCGATTCTTACCCG		33.0	0.0		77.0	23.0	NM_001135101	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Frame_Shift_Del	DEL	ENST00000328268.4	hg19	CCDS14082.1																																																																																			.	.		0.618	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324	
SMURF1	57154	hgsc.bcm.edu	37	7	98655111	98655111	+	Frame_Shift_Del	DEL	T	T	-			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:98655111delT	ENST00000361125.1	-	4	586	c.267delA	c.(265-267)aaafs	p.K89fs	SMURF1_ENST00000480055.1_5'UTR|SMURF1_ENST00000361368.2_Frame_Shift_Del_p.K89fs	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	89	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			CAGCTCCCTGTTTCTTGTGAA	0.423																																					p.Q90fs		Atlas-Indel,Pindel	.											.	SMURF1	58	.	0			c.268delC						.						124.0	132.0	129.0					7																	98655111		2203	4300	6503	SO:0001589	frameshift_variant	57154	exon4			.	AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.267delA	chr7.hg19:g.98655111delT	ENSP00000354621:p.Lys89fs	93.0	0.0		247.0	89.0	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Frame_Shift_Del	DEL	ENST00000361125.1	hg19	CCDS34690.1																																																																																			.	.		0.423	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429	
BCAP29	55973	hgsc.bcm.edu	37	7	107254121	107254122	+	Intron	INS	-	-	A	rs576177767	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:107254121_107254122insA	ENST00000005259.4	+	7	1029				BCAP29_ENST00000379121.2_Intron|BCAP29_ENST00000379117.2_Intron|BCAP29_ENST00000465919.1_Intron|BCAP29_ENST00000445771.2_Frame_Shift_Ins_p.S239fs|BCAP29_ENST00000379119.2_Frame_Shift_Ins_p.S239fs|BCAP29_ENST00000494086.1_Intron	NM_018844.3	NP_061332.2	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein 29						apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	14						GGTGAATTTTTAAGCAAAAGAA	0.366																																					p.L238fs		Atlas-INDEL	.											.	BCAP29	46	.	0			c.713_714insA						.																																			SO:0001627	intron_variant	55973	exon7			.		CCDS34730.1, CCDS34731.1	7q22.3	2012-09-20			ENSG00000075790	ENSG00000075790			24131	protein-coding gene	gene with protein product						12477932	Standard	NM_018844		Approved	BAP29, DKFZp686M2086	uc011kma.1	Q9UHQ4	OTTHUMG00000154770	ENST00000005259.4:c.690+244->A	chr7.hg19:g.107254123_107254123dupA		72.0	0.0		199.0	15.0	NM_001008405	G5E9L4|O95003	Frame_Shift_Ins	INS	ENST00000005259.4	hg19	CCDS34731.1																																																																																			.	.		0.366	BCAP29-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337011.2	NM_018844	
APOB	338	hgsc.bcm.edu	37	2	21231993	21231994	+	Frame_Shift_Ins	INS	-	-	CTCTACC			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr2:21231993_21231994insCTCTACC	ENST00000233242.1	-	26	7873_7874	c.7746_7747insGGTAGAG	c.(7744-7749)gagcaafs	p.Q2583fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2583					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTGAACCCTTGCTCTACCAATG	0.45																																					p.Q2583fs		Atlas-Indel,Pindel	.											.	APOB	761	.	0			c.7747_7748insGGTAGAG						.																																			SO:0001589	frameshift_variant	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.7740_7746dupGGTAGAG	chr2.hg19:g.21231994_21232000dupCTCTACC	ENSP00000233242:p.Gln2583fs	59.0	0.0		146.0	33.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.450	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
CATIP	375307	hgsc.bcm.edu	37	2	219222270	219222288	+	Frame_Shift_Del	DEL	ACAGATGCTGTTCTTCTCT	ACAGATGCTGTTCTTCTCT	-			TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	ACAGATGCTGTTCTTCTCT	ACAGATGCTGTTCTTCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr2:219222270_219222288delACAGATGCTGTTCTTCTCT	ENST00000289388.3	+	3	161_179	c.132_150delACAGATGCTGTTCTTCTCT	c.(130-150)ctacagatgctgttcttctctfs	p.LQMLFFS44fs	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		44					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L44L(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGAGGAGCTACAGATGCTGTTCTTCTCTGAGACGCTGG	0.584																																					p.44_50del		Pindel	.											.	C2orf62	28	.	1	Substitution - coding silent(1)	endometrium(1)	c.131_149del						.																																			SO:0001589	frameshift_variant	375307	exon3			.																												ENST00000289388.3:c.132_150delACAGATGCTGTTCTTCTCT	chr2.hg19:g.219222270_219222288delACAGATGCTGTTCTTCTCT	ENSP00000289388:p.Leu44fs	0.0	0.0		10.0	10.0	NM_198559		Frame_Shift_Del	DEL	ENST00000289388.3	hg19	CCDS2414.1																																																																																			.	.		0.584	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1		
METTL2B	55798	hgsc.bcm.edu	37	7	128140982	128140983	+	Frame_Shift_Del	DEL	TG	TG	-	rs10257897|rs139332186	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr7:128140982_128140983delTG	ENST00000262432.8	+	8	979_980	c.942_943delTG	c.(940-945)tatgtgfs	p.V315fs	METTL2B_ENST00000480046.1_Frame_Shift_Del_p.V250fs	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	315					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GAAATTTCTATGTGAGAGGTGA	0.396																																					p.314_314del		Pindel	.											.	METTL2B	34	.	0			c.941_942del						.																																			SO:0001589	frameshift_variant	55798	exon8			.	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"""methyltransferase like 2"""	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.942_943delTG	chr7.hg19:g.128140984_128140985delTG	ENSP00000262432:p.Val315fs	0.0	0.0		25.0	25.0	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Frame_Shift_Del	DEL	ENST00000262432.8	hg19	CCDS5803.2																																																																																			.	.		0.396	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396	
CDC27	996	hgsc.bcm.edu	37	17	45234594	45234729	+	Splice_Site	DEL	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	-	rs149474782|rs113608268|rs370849730|rs78395997|rs76624491|rs370261409|rs75353677|rs368304141|rs376818791|rs372212798|rs375653477|rs374472811|rs76359747|rs147617501|rs374614181|rs78108688|rs142987740|rs143453365|rs75990396|rs144985864|rs367644695|rs202182614|rs139751753|rs11570485|rs372926889|rs140171160|rs368750026|rs201098929|rs199899451|rs75175938|rs200340309|rs537990668	byFrequency	TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	CTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr17:45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT	ENST00000066544.3	-	6	590_724	c.497_631delAGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG	c.(496-633)cagttcttacggaaacaccccaggacacaattgtaagtgtcttatattctagtgttcaaaatattatgaaaactacaaagaatgatctgaactaaataatatattgtgaatgacttggtagaaattttctgtttcaga>cga	p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs	CDC27_ENST00000527547.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000446365.2_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF105fs|CDC27_ENST00000531206.1_Splice_Site_p.QFLRKHPRTQL*VSYILVFKIL*KLQRMI*TK*YIVNDLVEIFCF166fs|CDC27_ENST00000528748.1_5'UTR	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	166					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.T167T(7)|p.T171T(3)|p.V201I(2)|p.E199E(2)|p.T200T(2)|p.L173S(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACTGTCTCAGGCTGTCTGTGAGATAAACTATGATTAGGTACTTGTGTTGTGCAAGAGTTGGGCAGACAGTTGCTAAAGTTCTGTAAAGATGTGAATTTAAATGTTTGGTCAGGATC	0.342																																					p.201_211del		Pindel	.											.	CDC27	337	.	17	Substitution - coding silent(14)|Substitution - Missense(3)	large_intestine(6)|prostate(6)|kidney(4)|NS(1)	c.601_631del						.																																			SO:0001630	splice_region_variant	996	exon6			.	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.631-104AGTTCTTACGGAAACACCCCAGGACACAATTGTAAGTGTCTTATATTCTAGTGTTCAAAATATTATGAAAACTACAAAGAATGATCTGAACTAAATAATATATTGTGAATGACTTGGTAGAAATTTTCTGTTTCAG>-	chr17.hg19:g.45234594_45234729delCTGAAACAGAAAATTTCTACCAAGTCATTCACAATATATTATTTAGTTCAGATCATTCTTTGTAGTTTTCATAATATTTTGAACACTAGAATATAAGACACTTACAATTGTGTCCTGGGGTGTTTCCGTAAGAACT		0.0	0.0		19.0	19.0	NM_001114091	G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	hg19	CCDS11509.1																																																																																			.	.		0.342	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		Frame_Shift_Del
NCAM1	4684	hgsc.bcm.edu	37	11	112832332	112832363	+	5'UTR	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	rs6589347|rs11284059|rs559828324|rs201772924|rs563686839|rs7105734|rs112306738		TCGA-EP-A12J-01A-11D-A12Z-10	TCGA-EP-A12J-10A-01D-A12Z-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73c7f411-7d71-42ff-a525-9e6b3a2eff55	06c493d1-681d-483a-9c11-20d996f21545	g.chr11:112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC	ENST00000533760.1	+	0	243_274				NCAM1_ENST00000397957.4_3'UTR|RP11-629G13.1_ENST00000532002.1_RNA|RP11-629G13.1_ENST00000500537.2_RNA	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CAGCAGATTACAATGCTGCCAAACTAAGGATTTCATTTGGACTTTGTTTTTC	0.491																																					.		Pindel	.											.	NCAM1	372	.	0			.						.																																			SO:0001623	5_prime_UTR_variant	4684	wholegene			.		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.-326CATCCCTCCCAGCCAGCAGATTACAATGCTGC>-	chr11.hg19:g.112832332_112832363delCATCCCTCCCAGCCAGCAGATTACAATGCTGC		0.0	0.0		27.0	27.0	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Frame_Shift_Del	DEL	ENST00000533760.1	hg19																																																																																				.	.		0.491	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615	
